diff --git a/.codespell-ignore.txt b/.codespell-ignore.txt new file mode 100644 index 0000000..ef4f496 --- /dev/null +++ b/.codespell-ignore.txt @@ -0,0 +1,10 @@ +requestor +NAMD +preformed +identifying +intrisic +specificy +transferrin +trough +Rouge +identifiying diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 00087eb..5a4ecbc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -30,6 +30,14 @@ repos: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] + - repo: https://github.com/codespell-project/codespell + rev: v2.4.2 + hooks: + - id: codespell + additional_dependencies: + - tomli + exclude: ^src/kf_access_model/schema/upstream-models/.*\.yaml$ + - repo: https://github.com/crate-ci/typos rev: v1.31.1 hooks: diff --git a/COLLABORATORS.md b/COLLABORATORS.md index 2920815..fead2cb 100644 --- a/COLLABORATORS.md +++ b/COLLABORATORS.md @@ -6,19 +6,16 @@ properties, those models should adhere to use this model as a Git submodule. ## Key Integration Guidelines -All changes to this model should be made with the understanding that those -changes are completely valid for all or many of the downstream models. Those -changes should be made directly within this repository and not as changes to the -versions from the submodules themselves. - -Please see the following notes when integrating this model as a submodule within -one of the downtream modules: - -- Do Not Modify the Submodule from within this repository: All foundational - classes, slots, and enums live in the core submodule. Any program-specific - customizations must happen strictly in your downstream files. -- Leverage Imports: At this time, the current model imports the - common_access_model.yaml directly within the main model definition. +The classes and slots defined herein are shared across all downstream models. As +such, changes required to satisfy a downstream model's requirements should be +contained solely within the downstream model itself, or updated here with the +understanding that those changes will make their way to all of the other +downstream models in time. + +Downstream model development guidance: + +- Leverage Imports: At this time, the downstream model imports the + common_access_model-{version}.yaml directly within the main model definition. - Extend via Inheritance: Use the is_a or mixins keys to create program-specific subclasses that inherit core slots while allowing you to add local attributes. - Refine via Slot Usage: If you need to restrict or change the behavior of an @@ -27,64 +24,37 @@ one of the downtream modules: ## Getting Started -If you aren't already familiar with working with submodules, there are just a -couple of key takeaways to keep in mind: - -- The submodule has been pinned to a specific git commit hash to avoid - unexpected changes the CAM creeping into downstream model interfering with - local builds, CI/CD scripts, etc. -- The submodule itself should only be updated by deliberate action with the - expectation that downstream model changes may be required to reflect incoming - updates. +When you initialized your working environment using 'just install', a pre-commit +hook should have been installed for you that will apply various style fixes +before each commit. In general, only the files being committed are tested. -### Initializing the submodule - -Before you can actually compile the model on a new machine, you'll need to pull -the submodule's content down. A convenient just recipe has been created for -exactly that: +For those whose local copies of the model predate this change, you may simply +run the following just recipe to hook the pre-commit runs into your local clone. +Please note that this must be run again if you ever pull the code down into a +new directory. ```bash -just init-submodule +just precommit ``` -or, if you prefer to do it directly yourself: - -```bash -git submodule update --init --recursive -# make sure nothing is broken -just lint && just test -``` - -Subsequent calls can drop the init if you know for a fact that no other -submodules have been added. The just recipe does call the linter and runs the -linkml test as a subsequent dependency, in case there are upstream changes that -invalidate the downstream model. - -### Updating the pinned hash +### Updating (and initializing) the Common Access Model -Once it has been decided that it is time to update the CAM to use the latest -version, the maintainer should run the following commands to fetch, test and -lock the new version into the downstream model's main. +To incorporate the Common Access Model into a downstream model, either for the +first time or to update to a newer version, a just recipe has been provided: ```bash -# Navigate into the submodule directory -cd src/kf_access_model/schema/common_access_model - -# Fetch and check out the desired remote target (e.g., main branch) -git fetch origin -git checkout origin/main - -# Move back to the repository root -cd - - -# Run linter and tests -just lint && just test +just update-cam +``` +This will download the latest version of the common access model to +src/{model_name}/upstream-models/. The resulting file will be a complete +monolithic copy of the common access model with the version as part of the name. +It is up to the user to update the downstream model to include the updated CAM +model file. -# Commit the new submodule hash pointer to this repository -git add src/kf_access_model/schema/common_access_model -git commit -m "chore: update common_access_model submodule to latest hash" -``` +This file is tracked in github, so once the newest version is correctly checked +in, other contributors will pick up the correct version directly from their git +pulls. ## Release Artifacts @@ -154,18 +124,23 @@ any manual intervention: uv run pre-commit run --all-files ``` - ## Commands to Expand Enum Files + ### To write the expanded output: + `just expand` -This has also been added as a dependency to the recipes _test-schema and lint, and will automatically be run with `just test` and `just lint`. +This has also been added as a dependency to the recipes _test-schema and lint, +and will automatically be run with `just test` and `just lint`. #### Regenerate expanded output -Enums that already have a `permissible_values` will not be expanded. -To rerun the expansion script on a file, delete the current `permissible_values` from the YAML file, then run `just expand`, `just _test`, or `just lint`. -The `permissible_values` for any given enum can be deleted manually or by running the following command for each file: +Enums that already have a `permissible_values` will not be expanded. To rerun +the expansion script on a file, delete the current `permissible_values` from the +YAML file, then run `just expand`, `just _test`, or `just lint`. + +The `permissible_values` for any given enum can be deleted manually or by +running the following command for each file: `just clear {file_name}` diff --git a/_typos.toml b/_typos.toml new file mode 100644 index 0000000..ee0492e --- /dev/null +++ b/_typos.toml @@ -0,0 +1,9 @@ +# These were caught as typos +[default.extend-words] +NAMD = "NAMD" +BA = "BA" + +# Real typos that are encountered from other sources +# (currently one from OBI, specify) and an unrecognized acronym, NAMD +[default.extend-identifiers] +specificy = "specificy" diff --git a/justfile b/justfile index 07d12ff..d91ee4c 100644 --- a/justfile +++ b/justfile @@ -61,7 +61,7 @@ _setup_part2: gen-project gen-doc # Install project dependencies [group('project management')] -install: +install: precommit uv sync --group dev # Updates project template and LinkML package diff --git a/project.justfile b/project.justfile index 216be23..085e984 100644 --- a/project.justfile +++ b/project.justfile @@ -33,3 +33,7 @@ gen-dbtmodel: [group('model development')] gen-monolith: uv run gen-monolith + +[group('project management')] +precommit: + pre-commit install diff --git a/pyproject.toml b/pyproject.toml index c476fa8..31512fe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -80,6 +80,7 @@ skip = [ "src/common_access_model/datamodel/common_access_model_pydantic.py", "src/common_access_model/datamodel/common_access_model.py", ] +ignore-words = ".codespell-ignore.txt" # Reminder: words have to be lowercased for the ignore-words-list ignore-words-list = "linke" diff --git a/src/common_access_model/schema/enums/EnumAssayType.yaml b/src/common_access_model/schema/enums/EnumAssayType.yaml index ebe9dd8..03f205e 100644 --- a/src/common_access_model/schema/enums/EnumAssayType.yaml +++ b/src/common_access_model/schema/enums/EnumAssayType.yaml @@ -19,36 +19,42 @@ enums: meaning: OBI:0000070 CHMO:0000087: title: fluorescence microscopy assay - description: Any type of light microscopy assay where the specimen can be + description: + Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. meaning: CHMO:0000087 CHMO:0000089: title: confocal fluorescence microscopy assay - description: Microscopy where the specimen can be made to fluoresce (emit + description: + Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. meaning: CHMO:0000089 CHMO:0000102: title: light microscopy assay - description: Microscopy where the specimen is illuminated with visible light + description: + Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. meaning: CHMO:0000102 CHMO:0000701: title: liquid chromatography-tandem mass spectrometry - description: A method where a sample mixture is first separated by liquid + description: + A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. meaning: CHMO:0000701 OBI:0000117: title: Bernoulli trial - description: An assay where the output data is a datum with one of two values + description: + An assay where the output data is a datum with one of two values denoting success and failure. meaning: OBI:0000117 OBI:0000182: title: NMR 3D molecular structure determination assay - description: A 3D molecular structure determination assay that uses magnetic + description: + A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. meaning: OBI:0000182 @@ -58,53 +64,63 @@ enums: meaning: OBI:0000185 OBI:0000201: title: radioactivity detection - description: An assay that measures the amount of radiation in the radioactive + description: + An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. meaning: OBI:0000201 OBI:0000288: title: protein-protein interaction detection assay - description: An assay that determines interactions between proteins, such + description: + An assay that determines interactions between proteins, such as protein-protein binding. meaning: OBI:0000288 OBI:0000291: title: transcription factor binding site assay - description: An assay tthat determines DNA regions specifically recognized + description: + An assay that determines DNA regions specifically recognized by proteins that function as transcription factors meaning: OBI:0000291 OBI:0000366: title: metabolite profiling assay - description: An assay that detects and identifies chemical entities resulting + description: + An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism meaning: OBI:0000366 OBI:0000418: title: measuring glucose concentration in blood serum assay - description: An assay that determines the concentration of glucose molecules + description: + An assay that determines the concentration of glucose molecules in a blood serum sample meaning: OBI:0000418 OBI:0000424: title: transcription profiling assay - description: An assay that determines gene expression and transcription activity + description: + An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. meaning: OBI:0000424 OBI:0000433: title: DNA sequence feature detection assay - description: An assay with the objective to determine a sequence feature of + description: + An assay with the objective to determine a sequence feature of DNA meaning: OBI:0000433 OBI:0000435: title: genotyping assay - description: An assay which generates data about a genotype from a specimen + description: + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. meaning: OBI:0000435 OBI:0000438: title: DNA sequence variation detection assay - description: An assay that measures changes (expansion, amplification, deletion, + description: + An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. meaning: OBI:0000438 OBI:0000443: title: analyte assay - description: An assay with the objective to capture information about the + description: + An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. meaning: OBI:0000443 OBI:0000445: @@ -113,41 +129,48 @@ enums: meaning: OBI:0000445 OBI:0000447: title: intracellular electrophysiology recording assay - description: An electrophysiology assay where the recording location of the + description: + An electrophysiology assay where the recording location of the electrode is intracellular. meaning: OBI:0000447 OBI:0000454: title: extracellular electrophysiology recording assay - description: An electrophysiology assay where the recording location of the + description: + An electrophysiology assay where the recording location of the electrode is extracellular. meaning: OBI:0000454 OBI:0000470: title: mass spectrometry assay - description: An assay that identifies the amount and type of material entities + description: + An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. meaning: OBI:0000470 OBI:0000520: title: clinical chemistry assay - description: An analyte assay which uses analytical methods to produce measurements + description: + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a specimen collected from an organism in order to determine a phenotype of that organism. meaning: OBI:0000520 OBI:0000537: title: copy number variation profiling assay - description: An assay that determines lost or amplified genomic regions of + description: + An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping meaning: OBI:0000537 OBI:0000615: title: protein expression profiling assay - description: An assay that determines protein expression and translation activity + description: + An assay that determines protein expression and translation activity using protein extracts collected from a material entity. meaning: OBI:0000615 OBI:0000623: title: NMR spectroscopy assay - description: An assay that exploits the magnetic properties of certain nuclei + description: + An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex @@ -155,24 +178,28 @@ enums: meaning: OBI:0000623 OBI:0000626: title: DNA sequencing assay - description: A sequencing assay which determines information on the sequence + description: + A sequencing assay which determines information on the sequence of a DNA molecule. meaning: OBI:0000626 OBI:0000630: title: hematology assay - description: An assay that studies phenotypes of an organism involving its + description: + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments meaning: OBI:0000630 OBI:0000634: title: DNA methylation profiling assay - description: An assay that measures the state of methylation of DNA molecules + description: + An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. meaning: OBI:0000634 OBI:0000661: title: enzyme-linked immunosorbent assay - description: An analyte assay where binding of an enzyme linked antibody to + description: + An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody @@ -180,14 +207,16 @@ enums: meaning: OBI:0000661 OBI:0000664: title: BrdU incorporation assay - description: A cell proliferation assay in which cells are cultured in the + description: + A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. meaning: OBI:0000664 OBI:0000669: title: tritiated thymidine incorporation assay - description: A cell proliferation assay in which cells are cultured in the + description: + A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively @@ -195,7 +224,8 @@ enums: meaning: OBI:0000669 OBI:0000693: title: MeDIP-seq assay - description: A DNA methylation profiling assay that identifies methylated + description: + A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end @@ -203,7 +233,8 @@ enums: meaning: OBI:0000693 OBI:0000695: title: chain termination sequencing assay - description: A DNA sequencing assay which rely on the use of dideoxynucleotides + description: + A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated @@ -213,7 +244,8 @@ enums: meaning: OBI:0000695 OBI:0000697: title: Helicos sequencing assay - description: A DNA sequencing by synthesis assay that identifiies the sequnece + description: + A DNA sequencing by synthesis assay that identifiies the sequence of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to @@ -221,19 +253,22 @@ enums: meaning: OBI:0000697 OBI:0000699: title: survival assessment assay - description: An assay that measures the occurrence of death events in one + description: + An assay that measures the occurrence of death events in one or more organisms over time meaning: OBI:0000699 OBI:0000705: title: Edman degradation - description: A sequencing assay in which the amino acid sequence of input + description: + A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. meaning: OBI:0000705 OBI:0000706: title: SOLiD sequencing assay - description: A DNA sequencing by ligation assay that identifies sequence information + description: + A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage @@ -243,25 +278,29 @@ enums: meaning: OBI:0000706 OBI:0000716: title: ChIP-seq assay - description: An assay in which chromatin is immunoprecipitated and subsequently + description: + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin meaning: OBI:0000716 OBI:0000721: title: glucose tolerance test - description: An assay that measures glucose clearance from blood over time + description: + An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. meaning: OBI:0000721 OBI:0000723: title: DNA sequencing by ligation assay - description: A DNA sequencing assay that performs chain extension during the + description: + A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase meaning: OBI:0000723 OBI:0000724: title: Solexa sequencing assay - description: A DNA sequencing by synthesis assay that identifies sequence + description: + A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles @@ -271,7 +310,8 @@ enums: meaning: OBI:0000724 OBI:0000730: title: pyrosequencing assay - description: A DNA sequencing by synthesis assay which sequences a single + description: + A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides @@ -285,7 +325,8 @@ enums: meaning: OBI:0000730 OBI:0000734: title: DNA sequencing by synthesis assay - description: A DNA sequencing assay that relies on DNA polymerase activity + description: + A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. meaning: OBI:0000734 OBI:0000743: @@ -294,7 +335,8 @@ enums: meaning: OBI:0000743 OBI:0000748: title: bisulfite sequencing assay - description: A DNA methylation profiling assay which determines the methylation + description: + A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. meaning: OBI:0000748 @@ -304,7 +346,8 @@ enums: meaning: OBI:0000787 OBI:0000802: title: prothrombin time assay - description: An assay that measures the prothrombin ratio, which is the prothrombin + description: + An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of @@ -315,7 +358,8 @@ enums: meaning: OBI:0000802 OBI:0000805: title: antithrombin-III berichrome assay - description: An antithrombin-III (AT-III) assay in which exogenous bovine + description: + An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity @@ -325,7 +369,8 @@ enums: meaning: OBI:0000805 OBI:0000808: title: spectrolyse heparin antifactor-Xa assay - description: An assay that quantitatively measures heparin in human plasma + description: + An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic @@ -337,7 +382,8 @@ enums: meaning: OBI:0000812 OBI:0000820: title: activated partial thromboplastin time assay - description: An assay that evaluates blood coagulation by measuring the time + description: + An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, @@ -347,35 +393,40 @@ enums: meaning: OBI:0000820 OBI:0000823: title: thrombin time assay - description: An assay that measures the time between the addition of the thrombin + description: + An assay that measures the time between the addition of the thrombin and the clot formation in plasma. meaning: OBI:0000823 OBI:0000854: title: western blot assay - description: An analyte assay that detects specific peptides in an input material - by separating it using gel electrophoresis, transfering the separated molecules + description: + An analyte assay that detects specific peptides in an input material + by separating it using gel electrophoresis, transferring the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. meaning: OBI:0000854 OBI:0000860: title: northern blot assay - description: An assay that determines the presence of gene transcripts by + description: + An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from - tissue or cell cultures, resolved on denaturing gel, transfered by a blotting + tissue or cell cultures, resolved on denaturing gel, transferred by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. meaning: OBI:0000860 OBI:0000865: title: 96-well neutralization assay - description: A serum neutralization of viral infectivity assay which is performed + description: + A serum neutralization of viral infectivity assay which is performed in a 96-well plate. meaning: OBI:0000865 OBI:0000870: title: single-nucleotide-resolution nucleic acid structure mapping assay - description: An assay that provides information about the secondary structure + description: + An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent - of base-pairing or solvent accessiblity. + of base-pairing or solvent accessibility. meaning: OBI:0000870 OBI:0000871: title: viral hemagglutination assay @@ -383,7 +434,8 @@ enums: meaning: OBI:0000871 OBI:0000872: title: serum neutralization of viral infectivity assay - description: An analyte assay that measures virus-neutralizing abilities of + description: + An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The @@ -392,13 +444,15 @@ enums: meaning: OBI:0000872 OBI:0000874: title: detection of specific nucleic acid polymers with complementary probes - description: An analyte assay in which a specified input material (the evaluant) + description: + An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. meaning: OBI:0000874 OBI:0000875: title: viral hemagglutination inhibition assay - description: An assay that measures the ability of an evaluant to inhibit + description: + An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of @@ -406,22 +460,26 @@ enums: meaning: OBI:0000875 OBI:0000882: title: cell-cell killing assay - description: A cytometry assay that monitors a cell population to track how + description: + A cytometry assay that monitors a cell population to track how many are killed by other cells. meaning: OBI:0000882 OBI:0000883: title: in vivo cell killing assay - description: A cell killing assay that measures if and how many target cells + description: + A cell killing assay that measures if and how many target cells are killed within an organism. meaning: OBI:0000883 OBI:0000891: title: cell proliferation assay - description: A cytometry assay which measures the degreee to which input cells + description: + A cytometry assay which measures the degree to which input cells are replicating. meaning: OBI:0000891 OBI:0000892: title: Southern blot assay - description: An analyte assay that detects the presence of a specific sequence + description: + An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence @@ -429,7 +487,8 @@ enums: meaning: OBI:0000892 OBI:0000893: title: real time polymerase chain reaction assay - description: An assay, based on the PCR, that amplifies and simultaneously + description: + An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing @@ -437,101 +496,118 @@ enums: meaning: OBI:0000893 OBI:0000897: title: DEPC structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe meaning: OBI:0000897 OBI:0000903: title: in vitro cell killing assay - description: A cell killing assay that measures if and how many target cells + description: + A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. meaning: OBI:0000903 OBI:0000904: title: reporter cell line analyte detection bioassay - description: An analyte assay in which a cell line whose growth is known to + description: + An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. meaning: OBI:0000904 OBI:0000910: title: radio immuno assay - description: An assay in which a radioactive labeled antigen or antibody is + description: + An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. meaning: OBI:0000910 OBI:0000911: title: real time reverse-transcription polymerase chain reaction assay - description: An assay that uses a reverse transcription step (an RNA strand + description: + An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. meaning: OBI:0000911 OBI:0000912: title: X-ray crystallography 3D molecular structure determination assay - description: A 3D molecular structure determination assay in which the diffraction + description: + A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. meaning: OBI:0000912 OBI:0000913: title: promoter activity detection by reporter gene assay - description: An assay in which the activity of a promoter in a cell is monitored + description: + An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. meaning: OBI:0000913 OBI:0000916: title: flow cytometry assay - description: A cytometry assay in which an input cell population is put in + description: + A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. meaning: OBI:0000916 OBI:0000920: title: cytometric bead array assay - description: An analyte assay in which a series of beads coated with antibodies, + description: + An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. meaning: OBI:0000920 OBI:0000923: title: surface plasmon resonance binding assay - description: A binding assay that uses the detection of electromagnetic waves + description: + A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. meaning: OBI:0000923 OBI:0000944: title: handedness assay - description: An assay that measures the unequal distribution of fine motor + description: + An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. meaning: OBI:0000944 OBI:0000957: title: self reported handedness assessment - description: An assay where a person makes a statement that indicates what + description: + An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. meaning: OBI:0000957 OBI:0000964: title: in live cell assay - description: An assay in which a measurement is made by observing entities + description: + An assay in which a measurement is made by observing entities located in a live cell. meaning: OBI:0000964 OBI:0000966: title: in live organism assay - description: An assay in which a measurement is made by observing entities + description: + An assay in which a measurement is made by observing entities located in an organism. meaning: OBI:0000966 OBI:0000975: title: cell-cell binding detection by flow cytometry assay - description: A binding assay which uses a flow cytometer to detect pairs of + description: + A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. meaning: OBI:0000975 OBI:0000978: title: in container assay - description: An assay in which a measurement is made by observing entities + description: + An assay in which a measurement is made by observing entities located in a container. meaning: OBI:0000978 OBI:0001001: title: Edinburgh handedness assay - description: An assay that uses a set of questions (the Edinburgh Handedness + description: + An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting @@ -540,106 +616,125 @@ enums: meaning: OBI:0001001 OBI:0001005: title: RNASE CL3 structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. meaning: OBI:0001005 OBI:0001006: title: CMCT structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure meaning: OBI:0001006 OBI:0001008: title: MPE-Fe(II) structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. meaning: OBI:0001008 OBI:0001011: title: ENU structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe meaning: OBI:0001011 OBI:0001012: title: RNASE V1 structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe meaning: OBI:0001012 OBI:0001013: title: kethoxal structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe meaning: OBI:0001013 OBI:0001014: - title: single-nucleotide-resolution nucleic acid structure mapping assay using + title: + single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. meaning: OBI:0001014 OBI:0001015: title: DMS structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping - assay which determins nucleic acid secondary structure at a nucleotide resolution + description: + A single-nucleotide-resolution nucleic acid structure mapping + assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe meaning: OBI:0001015 OBI:0001016: title: DNASE 1 structure mapping assay - description: A single-nucleotide-resolution deoxyribonucleic acid structure + description: + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure meaning: OBI:0001016 OBI:0001017: - title: single-nucleotide-resolution nucleic acid structure mapping assay using + title: + single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. meaning: OBI:0001017 OBI:0001018: title: Rhodium DNA structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. meaning: OBI:0001018 OBI:0001019: title: RNA ADA I RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. meaning: OBI:0001019 OBI:0001020: title: Lead structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe meaning: OBI:0001020 OBI:0001021: title: RNASE T2 structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe meaning: OBI:0001021 OBI:0001022: title: gene dosage assay - description: An assay that measures changes in phenotype due to increased + description: + An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. meaning: OBI:0001022 OBI:0001023: title: Fe-BABE RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. meaning: OBI:0001023 OBI:0001024: title: RNASE U2 structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe meaning: OBI:0001024 @@ -649,66 +744,77 @@ enums: meaning: OBI:0001025 OBI:0001026: title: NMIA RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe meaning: OBI:0001026 OBI:0001027: title: Terbium RNA structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe meaning: OBI:0001027 OBI:0001029: title: OH-radical structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe meaning: OBI:0001029 OBI:0001030: title: RNASE T1 structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. meaning: OBI:0001030 OBI:0001035: title: Nuclease S1 structure mapping assay - description: A single-nucleotide-resolution deoxyribonucleic acid structure + description: + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. meaning: OBI:0001035 OBI:0001038: title: Ruthenium structure mapping assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe meaning: OBI:0001038 OBI:0001039: title: inline probing RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity meaning: OBI:0001039 OBI:0001145: title: 3D structure determination of bound molecular complex assay - description: A 3D molecular structure determination assay in which a complex - of 2 or more molecular enties is characterized which provides information + description: + A 3D molecular structure determination assay in which a complex + of 2 or more molecular entries is characterized which provides information on their binding configuration. meaning: OBI:0001145 OBI:0001146: title: binding assay - description: An assay with the objective to characterize the disposition of + description: + An assay with the objective to characterize the disposition of two or more material entities to form a complex. meaning: OBI:0001146 OBI:0001158: title: age determination assay - description: An assay that determines the duration of part of the life of + description: + An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). meaning: OBI:0001158 OBI:0001170: title: reverse transcription polymerase chain reaction assay - description: An assay that determines the concentration of RNA in a sample + description: + An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. @@ -719,331 +825,417 @@ enums: meaning: OBI:0001177 OBI:0001178: title: efficacy of epitope intervention experiment - description: An assay that tests if inducing an epitope specific immune response + description: + An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. meaning: OBI:0001178 OBI:0001179: title: epitope protection from infectious challenge experiment - description: An epitope protection experiment in which the ability of the + description: + An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. meaning: OBI:0001179 OBI:0001183: title: epitope protection from tumor challenge experiment - description: An epitope protection experiment in which the ability of the + description: + An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. meaning: OBI:0001183 OBI:0001184: title: epitope protection experiment - description: An efficacy of epitope intervention experiment that tests the + description: + An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. meaning: OBI:0001184 OBI:0001186: - title: epitope protection from infectious challenge experiment based on pathogen + title: + epitope protection from infectious challenge experiment based on pathogen burden - description: An epitope protection from infectious challenge experiment in + description: + An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. meaning: OBI:0001186 OBI:0001187: title: infectious agent detection assay - description: An assay that measures the presence or amount of an infectious + description: + An assay that measures the presence or amount of an infectious agent in an evaluant meaning: OBI:0001187 OBI:0001188: title: epitope disease exacerbation experiment - description: An efficacy of epitope intervention experiment that tests the + description: + An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. meaning: OBI:0001188 OBI:0001189: title: epitope protection experiment based on survival - description: An epitope protection experiment that determines the success + description: + An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. meaning: OBI:0001189 OBI:0001190: title: epitope treatment experiment - description: An epitope intervention experiment that tests the ability of + description: + An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. meaning: OBI:0001190 OBI:0001194: - title: ELISPOT assay measuring epitope specific transforming growth factor-beta + title: + ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells - description: An enzyme-linked immunospot assay that detects transforming growth + description: + An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. meaning: OBI:0001194 OBI:0001196: - title: cytometric bead array assay measuring epitope specific IP-10 production + title: + cytometric bead array assay measuring epitope specific IP-10 production by T cells - description: A cytometric bead array assay that detects IP-10 production by + description: + A cytometric bead array assay that detects IP-10 production by T cells. meaning: OBI:0001196 OBI:0001198: title: assay measuring epitope specific interleukin-27 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. meaning: OBI:0001198 OBI:0001203: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. meaning: OBI:0001203 OBI:0001206: - title: ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating + title: + ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: An enzyme-linked immunospot assay that detects granulocyte macrophage + description: + An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001206 OBI:0001209: title: assay measuring epitope specific interleukin-10 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. meaning: OBI:0001209 OBI:0001210: - title: cytometric bead array assay measuring epitope specific transforming + title: + cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells - description: A cytometric bead array assay that detects transforming growth + description: + A cytometric bead array assay that detects transforming growth factor-beta production by T cells meaning: OBI:0001210 OBI:0001215: - title: intracellular material detection assay measuring epitope specific perforin + title: + intracellular material detection assay measuring epitope specific perforin release - description: A flow cytometry assay that detects epitope specific perforin + description: + A flow cytometry assay that detects epitope specific perforin release by T cells. meaning: OBI:0001215 OBI:0001216: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. meaning: OBI:0001216 OBI:0001217: title: assay measuring epitope specific interleukin-22 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. meaning: OBI:0001217 OBI:0001218: title: assay measuring epitope specific interleukin-8 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. meaning: OBI:0001218 OBI:0001220: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. meaning: OBI:0001220 OBI:0001221: title: ChIP-chip by SNP array assay - description: A ChIP-ChIP assay in which immunoprecipitated chromatin is run + description: + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin meaning: OBI:0001221 OBI:0001222: title: ELISA measuring epitope specific RANTES production by T cells - description: An enzyme-linked immunosorbent assay that detects RANTES production + description: + An enzyme-linked immunosorbent assay that detects RANTES production by T cells. meaning: OBI:0001222 OBI:0001223: - title: cytometric bead array assay measuring epitope specific interleukin-1 + title: + cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells - description: A cytometric bead array assay that detects interleukin-1 beta + description: + A cytometric bead array assay that detects interleukin-1 beta production by T cells. meaning: OBI:0001223 OBI:0001227: - title: ELISPOT assay measuring epitope specific interleukin-6 production by + title: + ELISPOT assay measuring epitope specific interleukin-6 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-6 + description: + An enzyme-linked immunospot assay that detects interleukin-6 production by T cells meaning: OBI:0001227 OBI:0001228: - title: in vivo assay measuring epitope specific helper T cell enhancement + title: + in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response - description: A T cell epitope specific helper activity assay that detects + description: + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. meaning: OBI:0001228 OBI:0001229: - title: plasmon resonance assay measuring the dissociation constant [KD] of + title: + plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - description: A surface plasmon resonance binding assay that measures the dissociation + description: + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. meaning: OBI:0001229 OBI:0001230: title: assay measuring epitope specific interleukin-5 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. meaning: OBI:0001230 OBI:0001231: - title: ELISA measuring epitope specific transforming growth factor-beta production + title: + ELISA measuring epitope specific transforming growth factor-beta production by T cells - description: An enzyme-linked immunosorbent assay that detects transforming + description: + An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. meaning: OBI:0001231 OBI:0001232: title: assay measuring epitope specific RANTES production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects RANTES production by T cells. meaning: OBI:0001232 OBI:0001233: - title: assay measuring epitope specific granulocyte macrophage colony stimulating + title: + assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001233 OBI:0001235: title: transcription profiling by tiling array assay - description: A transcription profiling by array assay that uses a tiling path + description: + A transcription profiling by array assay that uses a tiling path array. meaning: OBI:0001235 OBI:0001236: title: ELISA measuring epitope specific interleukin-22 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-22 + description: + An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. meaning: OBI:0001236 OBI:0001237: title: assay measuring epitope specific interleukin-21 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. meaning: OBI:0001237 OBI:0001238: title: ELISA measuring epitope specific interleukin-9 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-9 + description: + An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. meaning: OBI:0001238 OBI:0001240: - title: intracellular cytokine staining assay measuring epitope specific interleukin-6 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells - description: A flow cytometry assay that detects interleukin-6 production + description: + A flow cytometry assay that detects interleukin-6 production by T cells. meaning: OBI:0001240 OBI:0001241: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. meaning: OBI:0001241 OBI:0001242: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. meaning: OBI:0001242 OBI:0001243: - title: cytometric bead array assay measuring epitope specific monocyte chemotactic + title: + cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: A cytometric bead array assay that detects monocyte chemotactic + description: + A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001243 OBI:0001244: title: ELISA measuring epitope specific interleukin-23 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-23 + description: + An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. meaning: OBI:0001244 OBI:0001245: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release - description: A detection of specific nucleic acids with complementary probes + description: + A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. meaning: OBI:0001245 OBI:0001246: - title: ELISA measuring epitope specific tumor necrosis factor superfamily + title: + ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: An enzyme-linked immunosorbent assay that detects tumor necrosis + description: + An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001246 OBI:0001247: title: genotyping by high throughput sequencing assay - description: A genotyping assay that uses a high througput sequencer + description: A genotyping assay that uses a high throughput sequencer meaning: OBI:0001247 OBI:0001248: title: ChIP-chip assay - description: An assay in which chromatin is immunoprecipitated and subsequently + description: + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin meaning: OBI:0001248 OBI:0001251: title: assay measuring epitope specific interleukin-13 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. meaning: OBI:0001251 OBI:0001253: title: assay measuring interleukin-9 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. meaning: OBI:0001253 OBI:0001255: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. meaning: OBI:0001255 OBI:0001260: title: ELISA measuring epitope specific interleukin-3 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-3 + description: + An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. meaning: OBI:0001260 OBI:0001261: - title: ELISA measuring epitope specific interleukin-1 alpha production by + title: + ELISA measuring epitope specific interleukin-1 alpha production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-1 + description: + An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. meaning: OBI:0001261 OBI:0001263: - title: in vivo assay measuring epitope specific helper T cell enhancement + title: + in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response - description: A T cell epitope specific helper activity assay that detects + description: + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. meaning: OBI:0001263 OBI:0001264: - title: assay measuring epitope specific transforming growth factor-beta production + title: + assay measuring epitope specific transforming growth factor-beta production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. meaning: OBI:0001264 OBI:0001266: title: DNA methylation profiling by high throughput sequencing assay - description: A DNA methylation profiling assay in which the methylation state + description: + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology meaning: OBI:0001266 OBI:0001268: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. meaning: OBI:0001268 OBI:0001269: title: assay measuring epitope specific cytotoxic T cell degranulation - description: A T cell epitope dependent biological activity assay that detects + description: + A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. meaning: OBI:0001269 OBI:0001270: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. meaning: OBI:0001270 OBI:0001271: title: transcription profiling by RNA sequencing assay - description: A type of transcription profiling assay where transcripts are + description: + A type of transcription profiling assay where transcripts are extracted from a sample, usually (but not always) transformed into cDNA, and then sequenced. Sequence reads are generally mapped to a reference and quantified to establish levels of gene transcription. meaning: OBI:0001271 OBI:0001272: - title: ELISPOT assay measuring epitope specific tumor necrosis factor superfamily + title: + ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: An enzyme-linked immunospot assay that detects tumor necrosis + description: + An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001272 OBI:0001273: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. meaning: OBI:0001273 OBI:0001274: @@ -1051,36 +1243,45 @@ enums: description: A genotyping assay that uses an array meaning: OBI:0001274 OBI:0001276: - title: assay measuring epitope specific chemokine (C-C motif) ligand 1 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. meaning: OBI:0001276 OBI:0001277: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. meaning: OBI:0001277 OBI:0001279: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. meaning: OBI:0001279 OBI:0001280: title: assay measuring epitope specific interleukin-16 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. meaning: OBI:0001280 OBI:0001281: title: ELISA measuring epitope specific IP-10 production by T cells - description: An enzyme-linked immunosorbent assay that detects IP-10 production + description: + An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. meaning: OBI:0001281 OBI:0001282: title: translation profiling assay - description: An assay in which surface-bound, translationally competent ribosome + description: + An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a @@ -1096,93 +1297,120 @@ enums: meaning: OBI:0001282 OBI:0001283: title: ELISA measuring epitope specific interleukin-15 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-15 + description: + An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. meaning: OBI:0001283 OBI:0001284: - title: cytometric bead array assay measuring epitope specific interleukin-12 + title: + cytometric bead array assay measuring epitope specific interleukin-12 production by T cells - description: A cytometric bead array assay that detects interleukin-12 production + description: + A cytometric bead array assay that detects interleukin-12 production by T cells. meaning: OBI:0001284 OBI:0001288: title: ELISA measuring epitope specific lymphotoxin A production by T cells - description: An enzyme-linked immunosorbent assay that detects lymphotoxin + description: + An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. meaning: OBI:0001288 OBI:0001289: - title: cytometric bead array assay measuring epitope specific interleukin-5 + title: + cytometric bead array assay measuring epitope specific interleukin-5 production by T cells - description: A cytometric bead array assay that detects interleukin-5 production + description: + A cytometric bead array assay that detects interleukin-5 production by T cells. meaning: OBI:0001289 OBI:0001291: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. meaning: OBI:0001291 OBI:0001292: title: assay measuring epitope specific interleukin-15 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. meaning: OBI:0001292 OBI:0001295: title: assay measuring epitope specific interleukin-17 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. meaning: OBI:0001295 OBI:0001296: - title: cytometric bead array assay measuring epitope specific interleukin-17 + title: + cytometric bead array assay measuring epitope specific interleukin-17 production by T cells - description: A cytometric bead array assay that detects interleukin-17 production + description: + A cytometric bead array assay that detects interleukin-17 production by T cells. meaning: OBI:0001296 OBI:0001297: - title: cytometric bead array assay measuring epitope specific interleukin-10 + title: + cytometric bead array assay measuring epitope specific interleukin-10 production by T cells - description: A cytometric bead array assay that detects interleukin-10 production + description: + A cytometric bead array assay that detects interleukin-10 production by T cells. meaning: OBI:0001297 OBI:0001298: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. meaning: OBI:0001298 OBI:0001299: - title: intracellular cytokine staining assay measuring epitope specific interleukin-5 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells - description: A flow cytometry assay that detects interleukin-5 production + description: + A flow cytometry assay that detects interleukin-5 production by T cells. meaning: OBI:0001299 OBI:0001300: - title: cytometric bead array assay measuring epitope specific interleukin-2 + title: + cytometric bead array assay measuring epitope specific interleukin-2 production by T cells - description: A cytometric bead array assay that detects interleukin-2 production + description: + A cytometric bead array assay that detects interleukin-2 production by T cells. meaning: OBI:0001300 OBI:0001301: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. meaning: OBI:0001301 OBI:0001302: - title: ELISA measuring epitope specific macrophage inflammatory protein-1 + title: + ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: An enzyme-linked immunosorbent assay that detects macrophage + description: + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001302 OBI:0001303: - title: intracellular cytokine staining assay measuring epitope specific granulocyte + title: + intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: A flow cytometry assay that detects granulocyte macrophage colony + description: + A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001303 OBI:0001304: title: RNAi profiling by array assay - description: An assay in which double stranded RNA is synthesized with a sequence + description: + An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means @@ -1190,457 +1418,589 @@ enums: meaning: OBI:0001304 OBI:0001308: title: assay measuring epitope specific IP-10 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. meaning: OBI:0001308 OBI:0001309: - title: intracellular cytokine staining assay measuring epitope specific interleukin-13 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells - description: A flow cytometry assay that detects interleukin-13 production + description: + A flow cytometry assay that detects interleukin-13 production by T cells. meaning: OBI:0001309 OBI:0001311: - title: X-ray crystallography assay determining the 3D structure of a T cell + title: + X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex - description: A X-ray crystallography 3D molecular structure determination + description: + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. meaning: OBI:0001311 OBI:0001315: - title: ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production + title: + ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: An enzyme-linked immunosorbent assay that detects chemokine (C-C + description: + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. meaning: OBI:0001315 OBI:0001317: - title: flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR + title: + flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex - description: A flow cytometry assay that measures the cell-cell binding of + description: + A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. meaning: OBI:0001317 OBI:0001318: title: proteomic profiling by array assay - description: An assay that detects proteins in a sample (quantified or otherwise + description: + An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. meaning: OBI:0001318 OBI:0001319: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. meaning: OBI:0001319 OBI:0001322: title: ELISPOT assay measuring epitope specific granzyme B release by T cells - description: An enzyme-linked immunospot assay that detects epitope specific + description: + An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. meaning: OBI:0001322 OBI:0001324: title: in vivo assay measuring T cell epitope specific tolerance induction - description: An efficacy of T cell epitope intervention experiment that uses + description: + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. meaning: OBI:0001324 OBI:0001325: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. meaning: OBI:0001325 OBI:0001326: - title: cytometric bead array assay measuring epitope specific interleukin-4 + title: + cytometric bead array assay measuring epitope specific interleukin-4 production by T cells - description: A cytometric bead array assay that detects interleukin-4 production + description: + A cytometric bead array assay that detects interleukin-4 production by T cells meaning: OBI:0001326 OBI:0001327: title: assay measuring epitope specific lymphotoxin A production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. meaning: OBI:0001327 OBI:0001330: - title: ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production + title: + ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: An enzyme-linked immunosorbent assay that detects chemokine (C-X-C + description: + An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001330 OBI:0001332: title: DNA methylation profiling by array assay - description: A DNA methylation profiling assay in which the methylation state + description: + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology meaning: OBI:0001332 OBI:0001333: - title: assay measuring epitope specific macrophage inflammatory protein-1 + title: + assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001333 OBI:0001335: title: microRNA profiling by array assay - description: An assay that analyses the microRNA component of the transcriptome + description: + An assay that analyses the microRNA component of the transcriptome using a microRNA array. meaning: OBI:0001335 OBI:0001339: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. meaning: OBI:0001339 OBI:0001341: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001341 OBI:0001342: - title: intracellular cytokine staining assay measuring epitope specific interleukin-21 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells - description: A flow cytometry assay that detects interleukin-21 production + description: + A flow cytometry assay that detects interleukin-21 production by T cells. meaning: OBI:0001342 OBI:0001343: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001343 OBI:0001344: - title: ELISA measuring epitope specific monocyte chemotactic protein-1 production + title: + ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: An enzyme-linked immunosorbent assay that detects monocyte chemotactic + description: + An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001344 OBI:0001345: - title: assay measuring epitope specific chemokine (C-C motif) ligand 4 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001345 OBI:0001346: title: ELISA measuring epitope specific interleukin-21 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-21 + description: + An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. meaning: OBI:0001346 OBI:0001348: title: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity - description: An efficacy of T cell epitope intervention experiment that detects + description: + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. meaning: OBI:0001348 OBI:0001349: - title: cytometric bead array assay measuring epitope specific interleukin-13 + title: + cytometric bead array assay measuring epitope specific interleukin-13 production by T cells - description: A cytometric bead array assay that detects interleukin-13 production + description: + A cytometric bead array assay that detects interleukin-13 production by T cells. meaning: OBI:0001349 OBI:0001350: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. meaning: OBI:0001350 OBI:0001353: - title: cytometric bead array assay measuring epitope specific tumor necrosis + title: + cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells - description: A cytometric bead array assay that detects tumor necrosis factor + description: + A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. meaning: OBI:0001353 OBI:0001354: - title: ELISPOT assay measuring epitope specific interleukin-17 production + title: + ELISPOT assay measuring epitope specific interleukin-17 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-17 + description: + An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. meaning: OBI:0001354 OBI:0001356: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. meaning: OBI:0001356 OBI:0001357: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001357 OBI:0001359: title: ELISA measuring epitope specific interleukin-8 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-8 + description: + An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. meaning: OBI:0001359 OBI:0001360: - title: cytometric bead array assay measuring epitope specific interleukin-6 + title: + cytometric bead array assay measuring epitope specific interleukin-6 production by T cells - description: A cytometric bead array assay that detects interleukin-6 production + description: + A cytometric bead array assay that detects interleukin-6 production by T cells. meaning: OBI:0001360 OBI:0001361: title: transcription profiling by RT-PCR assay - description: A transcription profiling assay that uses reverse transcription + description: + A transcription profiling assay that uses reverse transcription PCR (RT-PCR). meaning: OBI:0001361 OBI:0001363: title: assay measuring epitope specific interleukin-23 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. meaning: OBI:0001363 OBI:0001367: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. meaning: OBI:0001367 OBI:0001368: - title: cytometric bead array assay measuring epitope specific tumor necrosis + title: + cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: A cytometric bead array assay that detects tumor necrosis factor + description: + A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001368 OBI:0001370: - title: intracellular cytokine staining assay measuring epitope specific chemokine + title: + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: A flow cytometry assay that detects chemokine (C-C motif) ligand + description: + A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001370 OBI:0001376: - title: intracellular cytokine staining assay measuring epitope specific interleukin-3 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells - description: A flow cytometry assay that detects interleukin-3 production + description: + A flow cytometry assay that detects interleukin-3 production by T cells. meaning: OBI:0001376 OBI:0001378: - title: ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production + title: + ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: An enzyme-linked immunosorbent assay that detects chemokine (C-C + description: + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001378 OBI:0001379: - title: cytometric bead array assay measuring epitope specific interferon-gamma + title: + cytometric bead array assay measuring epitope specific interferon-gamma production by T cells - description: A cytometric bead array assay that detects interferon-gamma production + description: + A cytometric bead array assay that detects interferon-gamma production by T cells. meaning: OBI:0001379 OBI:0001380: title: assay measuring epitope specific interleukin-18 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. meaning: OBI:0001380 OBI:0001382: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. meaning: OBI:0001382 OBI:0001383: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. meaning: OBI:0001383 OBI:0001384: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. meaning: OBI:0001384 OBI:0001385: - title: intracellular cytokine staining assay measuring epitope specific tumor + title: + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: A flow cytometry assay that detects tumor necrosis factor superfamily + description: + A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001385 OBI:0001388: - title: assay measuring epitope specific interleukin-1 alpha production by + title: + assay measuring epitope specific interleukin-1 alpha production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. meaning: OBI:0001388 OBI:0001389: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. meaning: OBI:0001389 OBI:0001390: title: assay measuring epitope specific interferon-beta production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. meaning: OBI:0001390 OBI:0001391: title: assay measuring epitope specific interleukin-12 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. meaning: OBI:0001391 OBI:0001392: title: in vivo assay measuring epitope specific T cell killing - description: An in vivo cell killing assay that measures the killing of antigen + description: + An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. meaning: OBI:0001392 OBI:0001393: title: comparative genomic hybridization by array assay - description: An assay that measures changes in DNA sequence copy number using + description: + An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. meaning: OBI:0001393 OBI:0001395: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. meaning: OBI:0001395 OBI:0001397: - title: cytometric bead array assay measuring epitope specific granulocyte + title: + cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells - description: A cytometric bead array assay that detects granulocyte colony + description: + A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001397 OBI:0001400: - title: assay measuring epitope specific tumor necrosis factor superfamily + title: + assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001400 OBI:0001402: - title: promoter activity detection by reporter gene assay measuring epitope + title: + promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells - description: A promoter activity detection by reporter gene assay that detects + description: + A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. meaning: OBI:0001402 OBI:0001405: - title: cytometric bead array assay measuring epitope specific macrophage inflammatory + title: + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: A cytometric bead array assay that detects macrophage inflammatory + description: + A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001405 OBI:0001406: title: assay measuring epitope specific interleukin-3 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. meaning: OBI:0001406 OBI:0001407: title: assay measuring epitope specific T cell activation - description: A T cell epitope dependent biological activity assay that detects + description: + A T cell epitope dependent biological activity assay that detects T cell activation. meaning: OBI:0001407 OBI:0001412: - title: cytometric bead array assay measuring epitope specific RANTES production + title: + cytometric bead array assay measuring epitope specific RANTES production by T cells - description: A cytometric bead array assay that detects RANTES production + description: + A cytometric bead array assay that detects RANTES production by T cells. meaning: OBI:0001412 OBI:0001413: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. meaning: OBI:0001413 OBI:0001414: title: assay measuring epitope specific interferon-gamma production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. meaning: OBI:0001414 OBI:0001416: - title: assay measuring epitope specific tumor necrosis factor alpha production + title: + assay measuring epitope specific tumor necrosis factor alpha production by T cells - description: An assay of epitope specific tumor necrosis factor alpha production + description: + An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. meaning: OBI:0001416 OBI:0001419: title: ChIP-chip by tiling array assay - description: A ChIP-ChIP assay in which immunoprecipitated chromatin is run + description: + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin meaning: OBI:0001419 OBI:0001423: - title: intracellular material detection measuring epitope specific granzyme + title: + intracellular material detection measuring epitope specific granzyme B release by T cells - description: A flow cytometry assay that detects epitope specific granzyme + description: + A flow cytometry assay that detects epitope specific granzyme B release by T cells meaning: OBI:0001423 OBI:0001433: - title: radio immuno assay measuring epitope specific interferon-gamma production + title: + radio immuno assay measuring epitope specific interferon-gamma production by T cells - description: A radio immuno assay that detects interferon-gamma production + description: + A radio immuno assay that detects interferon-gamma production by T cells. meaning: OBI:0001433 OBI:0001436: title: assay measuring epitope specific granzyme B release by T cells - description: A T cell epitope specific cytotoxic T cell degranulation assay + description: + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. meaning: OBI:0001436 OBI:0001437: - title: intracellular cytokine staining assay measuring epitope specific chemokine + title: + intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: A flow cytometry assay that detects chemokine (C-X-C motif) ligand + description: + A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001437 OBI:0001438: - title: ELISA measuring epitope specific macrophage inflammatory protein-1 + title: + ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: An enzyme-linked immunosorbent assay that detects macrophage + description: + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. meaning: OBI:0001438 OBI:0001445: title: assay measuring epitope specific interleukin-2 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. meaning: OBI:0001445 OBI:0001449: - title: assay measuring epitope specific interleukin-1 beta production by T + title: + assay measuring epitope specific interleukin-1 beta production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. meaning: OBI:0001449 OBI:0001450: title: assay measuring epitope specific interleukin-4 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. meaning: OBI:0001450 OBI:0001451: title: assay measuring epitope specific interleukin-6 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. meaning: OBI:0001451 OBI:0001452: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. meaning: OBI:0001452 OBI:0001453: - title: intracellular cytokine staining assay measuring epitope specific lymphotoxin + title: + intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells - description: A flow cytometry assay that detects lymphotoxin A production + description: + A flow cytometry assay that detects lymphotoxin A production by T cells. meaning: OBI:0001453 OBI:0001455: - title: ELISPOT assay measuring epitope specific interleukin-5 production by + title: + ELISPOT assay measuring epitope specific interleukin-5 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-5 + description: + An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. meaning: OBI:0001455 OBI:0001456: - title: assay measuring epitope specific macrophage inflammatory protein-1 + title: + assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. meaning: OBI:0001456 OBI:0001457: - title: cytometric bead array assay measuring epitope specific interleukin-8 + title: + cytometric bead array assay measuring epitope specific interleukin-8 production by T cells - description: A cytometric bead array assay that detects interleukin-8 production + description: + A cytometric bead array assay that detects interleukin-8 production by T cells. meaning: OBI:0001457 OBI:0001459: - title: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production + title: + assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001459 OBI:0001461: title: ELISA measuring epitope specific granzyme B release by T cells - description: An enzyme-linked immunosorbent assay that detects epitope specific + description: + An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. meaning: OBI:0001461 OBI:0001463: @@ -1648,124 +2008,157 @@ enums: description: A transcription profiling assay that uses array technology. meaning: OBI:0001463 OBI:0001465: - title: assay measuring epitope specific monocyte chemotactic protein-1 production + title: + assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001465 OBI:0001466: - title: intracellular cytokine staining assay measuring epitope specific interleukin-12 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells - description: A flow cytometry assay that detects interleukin-12 production + description: + A flow cytometry assay that detects interleukin-12 production by T cells. meaning: OBI:0001466 OBI:0001467: title: in vivo assay measuring T cell epitope specific disease exacerbation - description: An efficacy of T cell epitope intervention experiment that uses + description: + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. meaning: OBI:0001467 OBI:0001469: - title: monospecific T cell recognition assay measuring MHC ligand processing + title: + monospecific T cell recognition assay measuring MHC ligand processing and presentation - description: A MHC ligand processing and presentation assay in which the presence + description: + A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. meaning: OBI:0001469 OBI:0001473: - title: in vivo assay measuring T cell epitope specific protection after tumor + title: + in vivo assay measuring T cell epitope specific protection after tumor burden challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. meaning: OBI:0001473 OBI:0001475: - title: in vivo assay measuring T cell epitope specific protection from infectious + title: + in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. meaning: OBI:0001475 OBI:0001476: title: phage display binding assay - description: A binding assay in which a collection of phages expressing a + description: + A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. meaning: OBI:0001476 OBI:0001478: title: mass spectrometry assay measuring MHC ligand processing and presentation - description: A MHC ligand processing and presentation assay that uses a mass + description: + A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands meaning: OBI:0001478 OBI:0001482: - title: intracellular cytokine staining assay measuring epitope specific transforming + title: + intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells - description: A flow cytometry assay that detects transforming growth factor-beta + description: + A flow cytometry assay that detects transforming growth factor-beta production by T cells. meaning: OBI:0001482 OBI:0001484: title: assay measuring T cell epitope specific in vivo activity - description: A T cell epitope dependent biological activity determination + description: + A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. meaning: OBI:0001484 OBI:0001488: title: epitope tolerance induction experiment - description: An efficacy of epitope intervention experiment that tests the + description: + An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response meaning: OBI:0001488 OBI:0001489: - title: mass spectrometry assay measuring MHC ligand processing and presentation + title: + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC - description: A mass spectrometry of MHC ligands assay that identifies eluted + description: + A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. meaning: OBI:0001489 OBI:0001490: - title: cytometric bead array measuring epitope specific granulocyte macrophage + title: + cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: A cytometric bead array assay that detects granulocyte macrophage + description: + A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:0001490 OBI:0001491: title: binding assay using radioactivity detection - description: A binding assay that uses radioactivity detection as an indicator + description: + A binding assay that uses radioactivity detection as an indicator of binding. meaning: OBI:0001491 OBI:0001492: - title: in vivo assay measuring T cell epitope specific protection based on + title: + in vivo assay measuring T cell epitope specific protection based on survival - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from other challenge using survival. meaning: OBI:0001492 OBI:0001493: - title: cell bound MHC competitive binding assay of a MHC:ligand complex using + title: + cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition - description: A cell bound MHC binding assay that uses a T cell epitope recognition + description: + A cell bound MHC binding assay that uses a T cell epitope recognition assay. meaning: OBI:0001493 OBI:0001495: title: in vivo assay measuring epitope specific T cell helper activity - description: A T cell epitope dependent biological activity assay that detects + description: + A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. meaning: OBI:0001495 OBI:0001496: - title: intracellular cytokine staining assay measuring epitope specific interleukin-22 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells - description: A flow cytometry assay that detects interleukin-22 production + description: + A flow cytometry assay that detects interleukin-22 production by T cells. meaning: OBI:0001496 OBI:0001497: title: assay measuring epitope specific perforin release by T cells - description: A T cell epitope specific cytotoxic T cell degranulation assay + description: + A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. meaning: OBI:0001497 OBI:0001499: title: binding assay using fluorescence detection - description: A binding assay that uses fluorescence detection as an indicator + description: + A binding assay that uses fluorescence detection as an indicator of binding. meaning: OBI:0001499 OBI:0001500: - title: coelution assay measuring MHC ligand processing and presentation using + title: + coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand - description: A MHC ligand processing and presentation assay in which an HPL + description: + A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to @@ -1778,162 +2171,209 @@ enums: meaning: OBI:0001501 OBI:0001507: title: in vivo assay measuring T cell epitope specific treatment of disease - description: An efficacy of T cell epitope intervention experiment that detects + description: + An efficacy of T cell epitope intervention experiment that detects a decrease in disease. meaning: OBI:0001507 OBI:0001509: title: Edman degradation assay measuring MHC ligand processing and presentation - description: A MHC ligand processing and presentation assay that uses Edman + description: + A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands meaning: OBI:0001509 OBI:0001510: - title: mass spectrometry assay measuring MHC ligand processing and presentation + title: + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC - description: A mass spectrometry of MHC ligands that identifies eluted ligands + description: + A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. meaning: OBI:0001510 OBI:0001512: - title: cytometric bead array assay measuring epitope specific interleukin-17A + title: + cytometric bead array assay measuring epitope specific interleukin-17A production by T cells - description: A cytometric bead array assay that detects interleukin-17A production + description: + A cytometric bead array assay that detects interleukin-17A production by T cells. meaning: OBI:0001512 OBI:0001513: - title: radioactivity detection assay measuring competitive binding of a purified-MHC:ligand + title: + radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex - description: A radioactivity detection assay that detects loss of binding + description: + A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001513 OBI:0001516: - title: radioactivity detection assay measuring half maximal effective concentration + title: + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex - description: A radioactivity detection assay that measures half maximal effective + description: + A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001516 OBI:0001517: - title: radioactivity detection assay measuring half maximal inhibitory concentration + title: + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex - description: A radioactivity detection assay that measures half maximal inhibitory + description: + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001517 OBI:0001519: - title: fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand + title: + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - description: A fluorescence detection assay that detects direct binding of + description: + A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001519 OBI:0001520: - title: fluorescence detection assay measuring half maximal inhibitory concentration + title: + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures half maximal inhibitory + description: + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001520 OBI:0001521: - title: ELISA measuring epitope specific granulocyte colony stimulating factor + title: + ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells - description: An enzyme-linked immunosorbent assay that detects granulocyte + description: + An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001521 OBI:0001523: - title: cytometric bead array assay measuring epitope specific interleukin-17F + title: + cytometric bead array assay measuring epitope specific interleukin-17F production by T cells - description: A cytometric bead array assay that detects interleukin-17F production + description: + A cytometric bead array assay that detects interleukin-17F production by T cells. meaning: OBI:0001523 OBI:0001524: - title: fluorescence detection assay measuring equilibrium association constant + title: + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures equilibrium association + description: + A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001524 OBI:0001531: - title: fluorescence detection assay measuring half life to determine direct + title: + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures half life to detect + description: + A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001531 OBI:0001532: - title: cytometric bead array assay measuring epitope specific interleukin-9 + title: + cytometric bead array assay measuring epitope specific interleukin-9 production by T cells - description: A cytometric bead array assay that detects interleukin-9 production + description: + A cytometric bead array assay that detects interleukin-9 production by T cells. meaning: OBI:0001532 OBI:0001534: - title: fluorescence detection assay measuring competitive binding of a purified-MHC:ligand + title: + fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that detects loss of binding of + description: + A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001534 OBI:0001537: - title: fluorescence detection assay measuring equilibrium dissociation constant + title: + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures equilibrium dissociation + description: + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001537 OBI:0001539: - title: fluorescence detection assay measuring equilibrium dissociation constant + title: + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures equilibrium dissociation + description: + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001539 OBI:0001541: - title: fluorescence detection assay measuring binding on rate [kon] to determine + title: + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex - description: A fluorescence detection assay measuring binding on rate (kon) + description: + A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. meaning: OBI:0001541 OBI:0001542: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. meaning: OBI:0001542 OBI:0001543: - title: fluorescence detection assay measuring equilibrium dissociation constant + title: + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 - description: A fluorescence detection assay that measures equilibrium dissociation + description: + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. meaning: OBI:0001543 OBI:0001544: - title: radioactivity detection assay measuring equilibrium dissociation constant + title: + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex - description: A radioactivity detection assay that measures equilibrium dissociation + description: + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation. meaning: OBI:0001544 OBI:0001545: - title: intracellular cytokine staining assay measuring epitope specific macrophage + title: + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: A flow cytometry assay that detects macrophage inflammatory protein-1 + description: + A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001545 OBI:0001549: - title: radioactivity detection assay measuring equilibrium dissociation constant + title: + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - description: A radioactivity detection assay that measures equilibrium dissociation + description: + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001549 OBI:0001550: title: assay measuring binding of a cell-bound-MHC:ligand complex - description: A qualitative binding assay that detects the binding of a cell-bound-MHC + description: + A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001550 OBI:0001552: - title: intracellular cytokine staining assay measuring epitope specific tumor + title: + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - description: A flow cytometry assay that detects tumor necrosis factor (ligand) + description: + A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. meaning: OBI:0001552 OBI:0001553: @@ -1942,274 +2382,351 @@ enums: meaning: OBI:0001553 OBI:0001555: title: assay measuring binding of a purified-MHC:ligand complex - description: A qualitative binding assay that detects the binding of a purified-MHC + description: + A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. meaning: OBI:0001555 OBI:0001556: - title: radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand + title: + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - description: A radioactivity detection assay that detects direct binding of + description: + A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001556 OBI:0001558: - title: radioactivity detection assay measuring half life to determine direct + title: + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - description: A radioactivity detection assay that measures half life to detect + description: + A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001558 OBI:0001559: - title: fluorescence detection assay measuring half life to determine direct + title: + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures half life to detect + description: + A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001559 OBI:0001561: - title: fluorescence detection assay measuring half maximal effective concentration + title: + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures half maximal effective + description: + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001561 OBI:0001562: - title: intracellular cytokine staining assay measuring epitope specific interleukin-17F + title: + intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells - description: A flow cytometry assay that detects interleukin-17F production + description: + A flow cytometry assay that detects interleukin-17F production by T cells. meaning: OBI:0001562 OBI:0001564: - title: radioactivity detection assay measuring equilibrium dissociation constant + title: + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - description: A radioactivity detection assay that measures equilibrium dissociation + description: + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. meaning: OBI:0001564 OBI:0001565: - title: radioactivity detection assay measuring half life to determine direct + title: + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex - description: A radioactivity detection assay that measures half life to detect + description: + A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001565 OBI:0001567: - title: radioactivity detection assay measuring binding off rate [koff] to + title: + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex - description: A radioactivity detection assay that measures binding off rate + description: + A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001567 OBI:0001568: - title: radioactivity detection assay measuring half maximal inhibitory concentration + title: + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - description: A radioactivity detection assay that measures half maximal inhibitory + description: + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001568 OBI:0001569: - title: fluorescence detection assay measuring binding off rate [koff] to determine + title: + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures binding off rate + description: + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001569 OBI:0001570: - title: assay measuring epitope specific vascular endothelial growth factor + title: + assay measuring epitope specific vascular endothelial growth factor production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001570 OBI:0001577: - title: cytometric bead array assay measuring epitope specific intracellular + title: + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells - description: A cytometric bead array assay that detects interleukin-22 production + description: + A cytometric bead array assay that detects interleukin-22 production by T cells. meaning: OBI:0001577 OBI:0001578: - title: ELISA measuring epitope specific vascular endothelial growth factor + title: + ELISA measuring epitope specific vascular endothelial growth factor production by T cells - description: An enzyme-linked immunosorbent assay that detects vascular endothelial + description: + An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001578 OBI:0001579: title: assay measuring binding of a cell-lysate-MHC:ligand complex - description: A qualitative binding assay that detects the binding of a cell-lysate-MHC + description: + A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. meaning: OBI:0001579 OBI:0001584: - title: phage display binding assay measuring binding of a purified-MHC:ligand + title: + phage display binding assay measuring binding of a purified-MHC:ligand complex - description: A phage display binding assay that detects direct binding of + description: + A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001584 OBI:0001585: - title: cytometric bead array assay measuring epitope specific interleukin-7 + title: + cytometric bead array assay measuring epitope specific interleukin-7 production by T cells - description: A cytometric bead array assay that detects interleukin-7 production + description: + A cytometric bead array assay that detects interleukin-7 production by T cells. meaning: OBI:0001585 OBI:0001586: - title: radioactivity detection assay measuring half life to determine direct + title: + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - description: A radioactivity detection assay that measures half life to detect + description: + A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001586 OBI:0001587: title: assay measuring epitope specific interleukin-7 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. meaning: OBI:0001587 OBI:0001589: - title: intracellular cytokine staining assay measuring epitope specific interleukin-17A + title: + intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells - description: A flow cytometry assay that detects interleukin-17A production + description: + A flow cytometry assay that detects interleukin-17A production by T cells. meaning: OBI:0001589 OBI:0001590: - title: fluorescence detection assay measuring direct binding of a purified-MHC:ligand + title: + fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that detects direct binding of + description: + A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001590 OBI:0001591: title: direct binding assay - description: A binding assay that measures the formation or disassociation - of a complex of 2 material entities directly without use of a competitve + description: + A binding assay that measures the formation or disassociation + of a complex of 2 material entities directly without use of a competitive ligand. meaning: OBI:0001591 OBI:0001592: - title: fluorescence detection assay measuring half maximal effective concentration + title: + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures half maximal effective + description: + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001592 OBI:0001593: title: competitive inhibition of binding assay - description: A binding assay that detects the inhibition of binding between + description: + A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. meaning: OBI:0001593 OBI:0001594: - title: fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand + title: + fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that detects loss of binding of + description: + A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001594 OBI:0001595: - title: X-ray crystallography assay determining the 3D structure of a MHC:ligand + title: + X-ray crystallography assay determining the 3D structure of a MHC:ligand complex - description: A X-ray crystallography 3D molecular structure determination + description: + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. meaning: OBI:0001595 OBI:0001597: - title: cell bound MHC competitive binding assay measuring half maximal inhibitory + title: + cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition - description: A cell bound MHC ligand binding half maximal inhibitory concentration + description: + A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. meaning: OBI:0001597 OBI:0001599: - title: radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand + title: + radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - description: A radioactivity detection assay that detects loss of binding + description: + A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. meaning: OBI:0001599 OBI:0001600: - title: assay measuring epitope specific granulocyte colony stimulating factor + title: + assay measuring epitope specific granulocyte colony stimulating factor production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001600 OBI:0001601: - title: cytometric bead array assay measuring epitope specific intracellular + title: + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells - description: A cytometric bead array assay that detects interleukin-21 production + description: + A cytometric bead array assay that detects interleukin-21 production by T cells. meaning: OBI:0001601 OBI:0001602: - title: radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand + title: + radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex - description: A radioactivity detection assay that detects direct binding of + description: + A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001602 OBI:0001604: - title: fluorescence detection assay measuring 50% dissociation of binding + title: + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures the 50% dissociation + description: + A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. meaning: OBI:0001604 OBI:0001606: - title: fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand + title: + fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that detects direct binding of + description: + A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001606 OBI:0001607: - title: assay measuring epitope specific tumor necrosis factor (ligand) superfamily + title: + assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - description: An assay of epitope specific tumor necrosis factor (ligand) superfamily + description: + An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. meaning: OBI:0001607 OBI:0001608: - title: radioactivity detection assay measuring direct binding of a purified-MHC:ligand + title: + radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex - description: A radioactivity detection assay that detects direct binding of + description: + A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. meaning: OBI:0001608 OBI:0001609: - title: intracellular cytokine staining assay measuring epitope specific interleukin-8 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells - description: A flow cytometry assay that detects interleukin-8 production + description: + A flow cytometry assay that detects interleukin-8 production by T cells. meaning: OBI:0001609 OBI:0001610: - title: cytometric bead array assay measuring epitope specific intracellular + title: + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells - description: A cytometric bead array assay that detects interleukin-23 production + description: + A cytometric bead array assay that detects interleukin-23 production by T cells. meaning: OBI:0001610 OBI:0001613: - title: fluorescence detection assay measuring half maximal inhibitory concentration + title: + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - description: A fluorescence detection assay that measures half maximal inhibitory + description: + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001613 OBI:0001624: title: organism species detection assay - description: An organism detection assay that identifies the organism species + description: + An organism detection assay that identifies the organism species in a specimen. meaning: OBI:0001624 OBI:0001630: title: analytical chromatography - description: An analyte assay that uses a biomaterial's preferential affinity + description: + An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. meaning: OBI:0001630 OBI:0001631: title: electron microscopy imaging assay - description: An imaging assay in which an electrons are used to probe the + description: + An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. meaning: OBI:0001631 OBI:0001632: title: immuno staining assay - description: A assay detecting a molecular label assay in which the label + description: + A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. meaning: OBI:0001632 OBI:0001634: title: calorimetric binding assay - description: A binding assay in which the heat generated or absorbed during + description: + A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. meaning: OBI:0001634 OBI:0001635: title: antibody binding detection by fluorescence quenching - description: A binding assay in which affinity is measured by detecting a + description: + A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the @@ -2218,175 +2735,222 @@ enums: on the ligand binding region (epitope). meaning: OBI:0001635 OBI:0001638: - title: antigen inhibition assay measuring the dissociation constant [KD] of + title: + antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 - description: A B cell epitope equilibrium dissociation constant (KD) assay + description: + A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. meaning: OBI:0001638 OBI:0001639: title: assay measuring epitope specific Ig-mediated histamine release - description: A B cell epitope specific activation of additional immune response + description: + A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. meaning: OBI:0001639 OBI:0001640: title: assay measuring epitope specific immunoglobulin-mediated antigen activation - description: A B cell epitope dependent biological activity determination + description: + A B cell epitope dependent biological activity determination assay that detects antigen activation. meaning: OBI:0001640 OBI:0001641: title: assay measuring epitope specific complement-dependent cytotoxicity - description: A B cell epitope specific activation of additional immune response + description: + A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . meaning: OBI:0001641 OBI:0001642: title: assay measuring epitope specific antibody-dependent cellular cytotoxicity - description: A B cell epitope specific activation of additional immune response + description: + A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. meaning: OBI:0001642 OBI:0001643: title: assay measuring epitope specific immunoglobulin-mediated neutralization - description: A B cell epitope dependent biological activity determination + description: + A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. meaning: OBI:0001643 OBI:0001644: title: assay measuring epitope specific opsonization - description: A B cell epitope specific activation of additional immune response + description: + A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . meaning: OBI:0001644 OBI:0001645: title: calorimetry assay measuring binding of a B cell epitope:antibody complex - description: A calorimetric binding assay that detects the binding of an antigen + description: + A calorimetric binding assay that detects the binding of an antigen with an antibody. meaning: OBI:0001645 OBI:0001646: - title: electron microscopy assay determining the 3D structure of a B cell + title: + electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex - description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody + description: + An electron-microscopy 3D molecular structure determination assay + that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex meaning: OBI:0001646 OBI:0001647: - title: NMR assay determining the 3D structure of a B cell epitope:antibody + title: + NMR assay determining the 3D structure of a B cell epitope:antibody complex - description: A nuclear magnetic resonance 3D molecular structure determination + description: + A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. meaning: OBI:0001647 OBI:0001648: - title: cross blocking assay measuring binding of a B cell epitope:antibody + title: + cross blocking assay measuring binding of a B cell epitope:antibody complex - description: A cross-blocking assay that detects the binding of an antigen + description: + A cross-blocking assay that detects the binding of an antigen with an antibody. meaning: OBI:0001648 OBI:0001649: title: RIA measuring binding of a B cell epitope:antibody complex - description: A radio immuno assay that detects the binding of an antigen with + description: + A radio immuno assay that detects the binding of an antigen with an antibody. meaning: OBI:0001649 OBI:0001650: title: immunoblot assay measuring binding of a B cell epitope:antibody complex - description: An immunoblot assay that detects the binding of an antigen with + description: + An immunoblot assay that detects the binding of an antigen with an antibody. meaning: OBI:0001650 OBI:0001651: - title: plasmon resonance assay measuring binding of a B cell epitope:antibody + title: + plasmon resonance assay measuring binding of a B cell epitope:antibody complex - description: A surface plasmon resonance binding assay that detects the binding + description: + A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. meaning: OBI:0001651 OBI:0001652: - title: immuno staining assay measuring binding of a B cell epitope:antibody + title: + immuno staining assay measuring binding of a B cell epitope:antibody complex - description: An immuno staining assay that detects the binding of an antigen + description: + An immuno staining assay that detects the binding of an antigen with an antibody. meaning: OBI:0001652 OBI:0001653: - title: immunoprecipitation assay measuring binding of a B cell epitope:antibody + title: + immunoprecipitation assay measuring binding of a B cell epitope:antibody complex - description: An immunoprecipitation assay that detects the binding of an antigen + description: + An immunoprecipitation assay that detects the binding of an antigen with an antibody. meaning: OBI:0001653 OBI:0001654: - title: mass spectrometry assay measuring binding of a B cell epitope:antibody + title: + mass spectrometry assay measuring binding of a B cell epitope:antibody complex - description: A mass spectrometry assay that detects the binding of an antigen + description: + A mass spectrometry assay that detects the binding of an antigen with an antibody. meaning: OBI:0001654 OBI:0001655: - title: phage display assay measuring binding of a B cell epitope:antibody + title: + phage display assay measuring binding of a B cell epitope:antibody complex - description: A phage display binding assay that detects the binding of an + description: + A phage display binding assay that detects the binding of an antigen with an antibody. meaning: OBI:0001655 OBI:0001656: - title: electron microscopy assay measuring binding of a B cell epitope:antibody + title: + electron microscopy assay measuring binding of a B cell epitope:antibody complex - description: An electron microscopy imaging assay that detects the binding + description: + An electron microscopy imaging assay that detects the binding of an antigen with an antibody. meaning: OBI:0001656 OBI:0001657: title: ELISA measuring binding of a B cell epitope:antibody complex - description: An enzyme-linked immunosorbent assay that detects the binding + description: + An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. meaning: OBI:0001657 OBI:0001658: title: ELISPOT assay measuring binding of a B cell epitope:antibody complex - description: An enzyme-linked immunospot assay that detects the binding of + description: + An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. meaning: OBI:0001658 OBI:0001659: - title: flow cytometry assay measuring binding of a B cell epitope:antibody + title: + flow cytometry assay measuring binding of a B cell epitope:antibody complex - description: A flow cytometry assay that detects the binding of an antigen + description: + A flow cytometry assay that detects the binding of an antigen with an antibody. meaning: OBI:0001659 OBI:0001660: - title: intracellular material detection assay measuring epitope specific granzyme + title: + intracellular material detection assay measuring epitope specific granzyme A release by T cells - description: A flow cytometry assay that detects epitope specific granzyme + description: + A flow cytometry assay that detects epitope specific granzyme A release by T cells. meaning: OBI:0001660 OBI:0001661: - title: chromatography assay measuring binding of a B cell epitope:antibody + title: + chromatography assay measuring binding of a B cell epitope:antibody complex - description: An analytical chromatography assay that detects the binding of + description: + An analytical chromatography assay that detects the binding of an antigen with an antibody. meaning: OBI:0001661 OBI:0001662: title: NMR assay measuring binding of a B cell epitope:antibody complex - description: A B cell epitope qualitative binding to antibody assay that uses + description: + A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. meaning: OBI:0001662 OBI:0001663: title: ELISA measuring epitope specific granulysin release by T cells - description: An enzyme-linked immunosorbent assay that detects epitope specific + description: + An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. meaning: OBI:0001663 OBI:0001664: - title: intracellular material detection assay measuring epitope specific granulysin + title: + intracellular material detection assay measuring epitope specific granulysin release by T cells - description: A flow cytometry assay that detects epitope specific granulysin + description: + A flow cytometry assay that detects epitope specific granulysin release by T cells. meaning: OBI:0001664 OBI:0001665: - title: fluorescence detection assay measuring binding off rate [koff] to determine + title: + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures binding off rate + description: + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001665 OBI:0001666: - title: fluorescence detection assay measuring binding on rate [kon] to determine + title: + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex - description: A fluorescence detection assay that measures binding on rate + description: + A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. meaning: OBI:0001666 OBI:0001667: - title: fluorescence detection assay measuring equilibrium dissociation constant + title: + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - description: A fluorescence detection assay that measures equilibrium dissociation + description: + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates @@ -2394,7 +2958,8 @@ enums: meaning: OBI:0001667 OBI:0001668: title: split-ubiquitin assay - description: A binding assay that screens membrane soluble proteins by fusion + description: + A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, @@ -2405,14 +2970,16 @@ enums: meaning: OBI:0001668 OBI:0001669: title: far-western blot assay - description: An assay that measures protein-protein interactions by separating - target proteins on an SDS-PAGE gel, transfering them to a solid substrate, + description: + An assay that measures protein-protein interactions by separating + target proteins on an SDS-PAGE gel, transferring them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. meaning: OBI:0001669 OBI:0001670: title: RNA protection assay - description: An assay that determines the presence and estimates abundance + description: + An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded @@ -2421,7 +2988,8 @@ enums: meaning: OBI:0001670 OBI:0001671: title: electrophoretic mobility shift assay - description: An assay that measures information about Protein-DNA or Protein-RNA + description: + An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + @@ -2429,18 +2997,21 @@ enums: meaning: OBI:0001671 OBI:0001672: title: gene knock-down assay - description: An assay which transiently disrupts gene transcripts by expressing + description: + An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. meaning: OBI:0001672 OBI:0001673: title: nano-cap analysis of gene expression assay - description: A transcription profiling by RNA sequencing assay that is performed + description: + A transcription profiling by RNA sequencing assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). meaning: OBI:0001673 OBI:0001674: title: cap analysis of gene expression assay - description: A transcription profiling by RNA sequencing assay which measures + description: + A transcription profiling by RNA sequencing assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the @@ -2448,18 +3019,22 @@ enums: meaning: OBI:0001674 OBI:0001675: title: ELISA measuring epitope specific interleukin-17A production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-17A + description: + An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. meaning: OBI:0001675 OBI:0001676: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. meaning: OBI:0001676 OBI:0001679: title: yeast 2-hybrid assay - description: An assay that detects protein protein interactions and protein + description: + An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) @@ -2472,7 +3047,8 @@ enums: meaning: OBI:0001679 OBI:0001680: title: Sos-recruitment assay - description: A binding assay that detects interacting proteins for a targeted + description: + A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using @@ -2480,13 +3056,15 @@ enums: meaning: OBI:0001680 OBI:0001681: title: yeast one-hybrid assay - description: An assay that determines protein DNA interactions using a single + description: + An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. meaning: OBI:0001681 OBI:0001682: title: bacterial one-hybrid assay - description: An assay that identifies the sequence-specific target site of + description: + An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target @@ -2500,80 +3078,95 @@ enums: meaning: OBI:0001682 OBI:0001683: title: chromosome organization assay by fluorescence in-situ hybridization - description: An in-situ hybridization assay that uses fluorescence to detect + description: + An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity meaning: OBI:0001683 OBI:0001684: title: methylation-specific polymerase chain reaction assay - description: An assay that uses initial modification of DNA by sodium bisulfite, + description: + An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. meaning: OBI:0001684 OBI:0001685: title: amplification of intermethylated sites assay - description: An assay that estimates genome-wide DNA methylation and measures + description: + An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. meaning: OBI:0001685 OBI:0001686: title: in-situ hybridization assay - description: An assay that localizes a specific DNA or RNA sequence within + description: + An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. meaning: OBI:0001686 OBI:0001689: title: cytochalasin-induced inhibition of actin polymerization assay - description: 'An assay which uses compound cytochalasin (CHEBI: 23528) to + description: + "An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin - filament polymerization (GO:0030041).' + filament polymerization (GO:0030041)." meaning: OBI:0001689 OBI:0001692: title: in vivo assay measuring B cell epitope specific protection from fertility - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. meaning: OBI:0001692 OBI:0001693: title: in vivo assay measuring B cell epitope specific tolerance induction - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. meaning: OBI:0001693 OBI:0001694: title: in vivo assay measuring B cell epitope specific induction of hypersensitivity - description: An efficacy of B cell epitope intervention experiment that detects + description: + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. meaning: OBI:0001694 OBI:0001695: title: assay measuring epitope specific immune complex formation - description: A B cell epitope specific activation of additional immune response + description: + A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. meaning: OBI:0001695 OBI:0001696: - title: in vivo assay measuring B cell epitope specific protection based on + title: + in vivo assay measuring B cell epitope specific protection based on survival - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from other challenge using survival. meaning: OBI:0001696 OBI:0001697: title: in vivo assay measuring B cell epitope specific treatment of disease - description: An efficacy of B cell epitope intervention experiment that detects + description: + An efficacy of B cell epitope intervention experiment that detects a decrease in disease. meaning: OBI:0001697 OBI:0001698: title: assay measuring B cell epitope specific in vivo activity - description: A B cell epitope dependent biological activity determination + description: + A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. meaning: OBI:0001698 OBI:0001699: title: antibody cross-blocking assay - description: A competitive inhibition of binding assay in which two antibodies + description: + A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. meaning: OBI:0001699 OBI:0001700: title: immunoprecipitation assay - description: An analyte assay in which an input material is mixed with antibodies + description: + An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well @@ -2581,893 +3174,1149 @@ enums: specific antibodies. meaning: OBI:0001700 OBI:0001701: - title: antigen inhibition assay measuring binding of a B cell epitope:antibody + title: + antigen inhibition assay measuring binding of a B cell epitope:antibody complex - description: A B cell epitope qualitative binding to antibody assay that measures + description: + A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. meaning: OBI:0001701 OBI:0001703: title: assay measuring qualitative binding of a B cell epitope:antibody complex - description: An assay that detects the binding of an antigen with an antibody, + description: + An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. meaning: OBI:0001703 OBI:0001704: - title: assay measuring epitope specific activation of additional immune response + title: + assay measuring epitope specific activation of additional immune response in vitro - description: A B cell epitope dependent biological activity determination + description: + A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. meaning: OBI:0001704 OBI:0001705: title: assay measuring epitope specific antigen inhibition of antibody activity - description: A B cell epitope dependent biological activity determination + description: + A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. meaning: OBI:0001705 OBI:0001706: - title: assay measuring biological activity resulting from B cell epitope:antibody + title: + assay measuring biological activity resulting from B cell epitope:antibody binding - description: A B cell epitope assay that measures the immune response process + description: + A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope. meaning: OBI:0001706 OBI:0001708: - title: assay measuring the dissociation constant [KD] of a B cell epitope:antibody + title: + assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A B cell epitope binding constant determination assay that measures + description: + A B cell epitope binding constant determination assay that measures the dissociation constant KD. meaning: OBI:0001708 OBI:0001709: title: assay measuring a binding constant of a B cell epitope:antibody complex - description: A B cell epitope recognition assay that quantitavely characterizes + description: + A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. meaning: OBI:0001709 OBI:0001710: title: in vivo assay measuring B cell epitope specific protection from challenge - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. meaning: OBI:0001710 OBI:0001711: title: in vivo assay measuring B cell epitope specific disease exacerbation - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. meaning: OBI:0001711 OBI:0001718: title: assay measuring the on rate [kon] of a B cell epitope:antibody complex - description: A B cell epitope binding constant determination assay that measures + description: + A B cell epitope binding constant determination assay that measures the on rate. meaning: OBI:0001718 OBI:0001719: - title: assay measuring the association constant [KA] of a B cell epitope:antibody + title: + assay measuring the association constant [KA] of a B cell epitope:antibody complex - description: A B cell epitope binding constant determination assay that measures + description: + A B cell epitope binding constant determination assay that measures the association constant KA. meaning: OBI:0001719 OBI:0001721: title: 3D molecular structure determination assay of an antigen:antibody complex - description: A 3D structure determination of bound molecular complex assay + description: + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex. meaning: OBI:0001721 OBI:0001723: title: assay measuring the off rate [koff] of a B cell epitope:antibody complex - description: A B cell epitope binding constant determination assay that measures + description: + A B cell epitope binding constant determination assay that measures the off rate. meaning: OBI:0001723 OBI:0001724: - title: viral hemagglutination inhibition assay measuring binding of a B cell + title: + viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex - description: A viral hemagglutination inhibition assay that detects the binding + description: + A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. meaning: OBI:0001724 OBI:0001726: title: quenching assay measuring binding of a B cell epitope:antibody complex - description: A fluorescence quenching assay that detects the binding of an + description: + A fluorescence quenching assay that detects the binding of an antigen with an antibody. meaning: OBI:0001726 OBI:0001727: - title: RIA measuring the dissociation constant [KD] of a B cell epitope:antibody + title: + RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A radio immuno assay that measures the dissociation constant + description: + A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001727 OBI:0001728: - title: ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody + title: + ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: An enzyme-linked immunosorbent assay that measures the dissociation + description: + An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001728 OBI:0001729: - title: quenching assay measuring the dissociation constant [KD] of a B cell + title: + quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A fluorescence quenching assay that measures the dissociation + description: + A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001729 OBI:0001730: - title: surface plasmon resonance assay measuring the association constant + title: + surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex - description: A surface plasmon resonance binding assay that measures the association + description: + A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001730 OBI:0001731: - title: surface plasmon resonance assay measuring the dissociation constant + title: + surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A surface plasmon resonance binding assay that measures the dissociation + description: + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001731 OBI:0001732: - title: quenching assay measuring the association constant [KA] of a B cell + title: + quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex - description: A fluorescence quenching assay that measures the association + description: + A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001732 OBI:0001733: - title: calorimetry assay measuring the association constant [KA] of a B cell + title: + calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex - description: A calorimetric binding assay that measures the association constant + description: + A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001733 OBI:0001734: - title: calorimetry assay measuring the dissociation constant [KD] of a B cell + title: + calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A calorimetric binding assay that measures the dissociation constant + description: + A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001734 OBI:0001735: - title: ELISA measuring the association constant [KA] of a B cell epitope:antibody + title: + ELISA measuring the association constant [KA] of a B cell epitope:antibody complex - description: An enzyme-linked immunosorbent assay that measures the association + description: + An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001735 OBI:0001736: - title: RIA measuring the association constant [KA] of a B cell epitope:antibody + title: + RIA measuring the association constant [KA] of a B cell epitope:antibody complex - description: A radio immuno assay that measures the association constant [KA] + description: + A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001736 OBI:0001738: - title: X-ray crystallography assay determining the 3D structure of a B cell + title: + X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex - description: A X-ray crystallography 3D molecular structure determination - assay that characterizes the 3-dimensional molecular structrue of a B cell + description: + A X-ray crystallography 3D molecular structure determination + assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex. meaning: OBI:0001738 OBI:0001739: - title: surface plasmon resonance assay measuring the off rate [koff] of a + title: + surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex - description: A surface plasmon resonance binding assay that measures the off + description: + A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. meaning: OBI:0001739 OBI:0001740: - title: quenching assay measuring the off rate [koff] of a B cell epitope:antibody + title: + quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex - description: A fluorescence quenching assay that measures the off rate [koff] + description: + A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. meaning: OBI:0001740 OBI:0001741: - title: surface plasmon resonance assay measuring the on rate [kon] of a B + title: + surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex - description: A surface plasmon resonance binding assay that measures the on + description: + A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. meaning: OBI:0001741 OBI:0001742: - title: quenching assay measuring the on rate [kon] of a B cell epitope:antibody + title: + quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex - description: A fluorescence quenching assay that measures the on rate [kon] + description: + A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. meaning: OBI:0001742 OBI:0001743: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. meaning: OBI:0001743 OBI:0001744: - title: intracellular cytokine staining assay measuring epitope specific interleukin-1 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells - description: A flow cytometry assay that detects interleukin-1 alpha production + description: + A flow cytometry assay that detects interleukin-1 alpha production by T cells. meaning: OBI:0001744 OBI:0001745: - title: ELISPOT assay measuring epitope specific interleukin-1 alpha production + title: + ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-1 + description: + An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. meaning: OBI:0001745 OBI:0001746: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. meaning: OBI:0001746 OBI:0001747: - title: cytometric bead array assay measuring epitope specific interleukin-1 + title: + cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells - description: A cytometric bead array assay that detects interleukin-1 alpha + description: + A cytometric bead array assay that detects interleukin-1 alpha production by T cells. meaning: OBI:0001747 OBI:0001748: - title: ELISPOT assay measuring epitope specific interferon-beta production + title: + ELISPOT assay measuring epitope specific interferon-beta production by T cells - description: An enzyme-linked immunospot assay that detects interferon-beta + description: + An enzyme-linked immunospot assay that detects interferon-beta production by T cells. meaning: OBI:0001748 OBI:0001749: - title: intracellular cytokine staining assay measuring epitope specific interferon-beta + title: + intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells - description: A flow cytometry assay that detects interferon-beta production + description: + A flow cytometry assay that detects interferon-beta production by T cells. meaning: OBI:0001749 OBI:0001750: - title: intracellular cytokine staining assay measuring epitope specific granulocyte + title: + intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells - description: A flow cytometry assay that detects granulocyte colony stimulating + description: + A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001750 OBI:0001751: title: ELISA measuring epitope specific interferon-beta production by T cells - description: An enzyme-linked immunosorbent assay that detects interferon-beta + description: + An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. meaning: OBI:0001751 OBI:0001752: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001752 OBI:0001753: - title: ELISPOT assay measuring epitope specific granulocyte colony stimulating + title: + ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells - description: An enzyme-linked immunospot assay that detects granulocyte colony + description: + An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. meaning: OBI:0001753 OBI:0001754: - title: cytometric bead array assay measuring epitope specific chemokine (C-X-C + title: + cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: A cytometric bead array assay that detects chemokine (C-X-C motif) + description: + A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001754 OBI:0001756: - title: ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand + title: + ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: An enzyme-linked immunospot assay that detects chemokine (C-X-C + description: + An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001756 OBI:0001757: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. meaning: OBI:0001757 OBI:0001758: - title: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand + title: + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: An enzyme-linked immunospot assay that detects chemokine (C-C + description: + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001758 OBI:0001759: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. meaning: OBI:0001759 OBI:0001760: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. meaning: OBI:0001760 OBI:0001761: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. meaning: OBI:0001761 OBI:0001762: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. meaning: OBI:0001762 OBI:0001763: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. meaning: OBI:0001763 OBI:0001764: - title: cytometric bead array assay measuring epitope specific chemokine (C-C + title: + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: A cytometric bead array assay that detects chemokine (C-C motif) + description: + A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001764 OBI:0001765: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. meaning: OBI:0001765 OBI:0001766: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001766 OBI:0001767: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. meaning: OBI:0001767 OBI:0001768: - title: intracellular cytokine staining assay measuring epitope specific chemokine + title: + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: A flow cytometry assay that detects chemokine (C-C motif) ligand + description: + A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. meaning: OBI:0001768 OBI:0001770: - title: intracellular cytokine staining assay measuring epitope specific vascular + title: + intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells - description: A flow cytometry assay that detects vascular endothelial growth + description: + A flow cytometry assay that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001770 OBI:0001771: - title: ELISPOT assay measuring epitope specific vascular endothelial growth + title: + ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells - description: An enzyme-linked immunospot assay that detects vascular endothelial + description: + An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001771 OBI:0001772: title: assay measuring epitope specific interleukin-17F production by T cells - description: An assay of epitope specific interleukin-17 production by T cells + description: + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. meaning: OBI:0001772 OBI:0001773: title: assay measuring epitope specific interleukin-17A production by T cells - description: An assay of epitope specific interleukin-17 production by T cells + description: + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. meaning: OBI:0001773 OBI:0001774: - title: assay measuring epitope specific chemokine (C-C motif) ligand 21 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. meaning: OBI:0001774 OBI:0001775: - title: assay measuring epitope specific chemokine (C-C motif) ligand 19 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. meaning: OBI:0001775 OBI:0001776: - title: assay measuring epitope specific chemokine (C-X-C motif) ligand 12 + title: + assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. meaning: OBI:0001776 OBI:0001777: - title: assay measuring epitope specific chemokine (C-C motif) ligand 22 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. meaning: OBI:0001777 OBI:0001778: - title: assay measuring epitope specific chemokine (C-X-C motif) ligand 16 + title: + assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. meaning: OBI:0001778 OBI:0001779: - title: assay measuring epitope specific chemokine (C-X-C motif) ligand 13 + title: + assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. meaning: OBI:0001779 OBI:0001780: - title: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 + title: + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: An enzyme-linked immunospot assay that detects macrophage inflammatory + description: + An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001780 OBI:0001781: - title: cytometric bead array assay measuring epitope specific macrophage inflammatory + title: + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: A cytometric bead array assay that detects macrophage inflammatory + description: + A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. meaning: OBI:0001781 OBI:0001782: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. meaning: OBI:0001782 OBI:0001783: - title: intracellular cytokine staining assay measuring epitope specific monocyte + title: + intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: A flow cytometry assay that detects monocyte chemotactic protein-1 + description: + A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001783 OBI:0001784: - title: ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 + title: + ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - description: An enzyme-linked immunospot assay that detects monocyte chemotactic + description: + An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. meaning: OBI:0001784 OBI:0001785: - title: intracellular cytokine staining assay measuring epitope specific macrophage + title: + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: A flow cytometry assay that detects macrophage inflammatory protein-1 + description: + A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. meaning: OBI:0001785 OBI:0001786: - title: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 + title: + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - description: An enzyme-linked immunospot assay that detects inflammatory protein-1 + description: + An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. meaning: OBI:0001786 OBI:0001787: - title: cytometric bead array assay measuring epitope specific vascular endothelial + title: + cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells - description: A cytometric bead array assay that detects vascular endothelial + description: + A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. meaning: OBI:0001787 OBI:0001788: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0001788 OBI:0001789: - title: intracellular cytokine staining assay measuring epitope specific RANTES + title: + intracellular cytokine staining assay measuring epitope specific RANTES production by T cells description: A flow cytometry assay that detects RANTES production by T cells. meaning: OBI:0001789 OBI:0001790: title: ELISPOT assay measuring epitope specific RANTES production by T cells - description: An enzyme-linked immunospot assay that detects RANTES production + description: + An enzyme-linked immunospot assay that detects RANTES production by T cells. meaning: OBI:0001790 OBI:0001791: - title: ELISPOT assay measuring epitope specific lymphotoxin A production by + title: + ELISPOT assay measuring epitope specific lymphotoxin A production by T cells - description: An enzyme-linked immunospot assay that detects lymphotoxin A + description: + An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. meaning: OBI:0001791 OBI:0001792: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. meaning: OBI:0001792 OBI:0001793: - title: cytometric bead array assay measuring epitope specific lymphotoxin + title: + cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells - description: A cytometric bead array assay that detects lymphotoxin A production + description: + A cytometric bead array assay that detects lymphotoxin A production by T cells. meaning: OBI:0001793 OBI:0001794: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. meaning: OBI:0001794 OBI:0001795: title: ELISPOT assay measuring epitope specific IP-10 production by T cells - description: An enzyme-linked immunospot assay that detects IP-10 production + description: + An enzyme-linked immunospot assay that detects IP-10 production by T cells. meaning: OBI:0001795 OBI:0001796: - title: intracellular cytokine staining assay measuring epitope specific IP-10 + title: + intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells description: A flow cytometry assay that detects IP-10 production by T cells. meaning: OBI:0001796 OBI:0001797: - title: ELISPOT assay measuring epitope specific interleukin-9 production by + title: + ELISPOT assay measuring epitope specific interleukin-9 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-9 + description: + An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. meaning: OBI:0001797 OBI:0001798: - title: intracellular cytokine staining assay measuring epitope specific interleukin-9 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells - description: A flow cytometry assay that detects interleukin-9 production + description: + A flow cytometry assay that detects interleukin-9 production by T cells. meaning: OBI:0001798 OBI:0001799: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. meaning: OBI:0001799 OBI:0001800: - title: ELISPOT assay measuring epitope specific interleukin-8 production by + title: + ELISPOT assay measuring epitope specific interleukin-8 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-8 + description: + An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. meaning: OBI:0001800 OBI:0001801: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. meaning: OBI:0001801 OBI:0001802: - title: ELISPOT assay measuring epitope specific interleukin-3 production by + title: + ELISPOT assay measuring epitope specific interleukin-3 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-3 + description: + An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. meaning: OBI:0001802 OBI:0001803: title: ELISA measuring epitope specific interleukin-7 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-7 + description: + An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. meaning: OBI:0001803 OBI:0001804: - title: ELISPOT assay measuring epitope specific interleukin-7 production by + title: + ELISPOT assay measuring epitope specific interleukin-7 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-7 + description: + An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. meaning: OBI:0001804 OBI:0001805: - title: intracellular cytokine staining assay measuring epitope specific interleukin-7 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells - description: A flow cytometry assay that detects interleukin-7 production + description: + A flow cytometry assay that detects interleukin-7 production by T cells. meaning: OBI:0001805 OBI:0001806: - title: intracellular cytokine staining assay measuring epitope specific interleukin-27 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells - description: A flow cytometry assay that detects interleukin-27 production + description: + A flow cytometry assay that detects interleukin-27 production by T cells. meaning: OBI:0001806 OBI:0001807: - title: cytometric bead array assay measuring epitope specific interleukin-3 + title: + cytometric bead array assay measuring epitope specific interleukin-3 production by T cells - description: A cytometric bead array assay that detects interleukin-3 production + description: + A cytometric bead array assay that detects interleukin-3 production by T cells. meaning: OBI:0001807 OBI:0001808: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. meaning: OBI:0001808 OBI:0001809: title: assay measuring epitope specific granzyme A release by T cells - description: A T cell epitope specific cytotoxic T cell degranulation assay + description: + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. meaning: OBI:0001809 OBI:0001810: title: assay measuring epitope specific granulysin release by T cells - description: A T cell epitope specific cytotoxic T cell degranulation assay + description: + A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. meaning: OBI:0001810 OBI:0001811: - title: cytometric bead array assay measuring epitope specific interleukin-27 + title: + cytometric bead array assay measuring epitope specific interleukin-27 production by T cells - description: A cytometric bead array assay that detects interleukin-27 production + description: + A cytometric bead array assay that detects interleukin-27 production by T cells. meaning: OBI:0001811 OBI:0001812: - title: intracellular cytokine staining assay measuring epitope specific interleukin-23 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells - description: A flow cytometry assay that detects interleukin-23 production + description: + A flow cytometry assay that detects interleukin-23 production by T cells. meaning: OBI:0001812 OBI:0001813: - title: ELISPOT assay measuring epitope specific interleukin-27 production + title: + ELISPOT assay measuring epitope specific interleukin-27 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-27 + description: + An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. meaning: OBI:0001813 OBI:0001814: title: ELISA measuring epitope specific interleukin-27 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-27 + description: + An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. meaning: OBI:0001814 OBI:0001815: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. meaning: OBI:0001815 OBI:0001817: - title: ELISPOT assay measuring epitope specific interleukin-18 production + title: + ELISPOT assay measuring epitope specific interleukin-18 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-18 + description: + An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. meaning: OBI:0001817 OBI:0001821: - title: ELISPOT assay measuring epitope specific interleukin-22 production + title: + ELISPOT assay measuring epitope specific interleukin-22 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-22 + description: + An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. meaning: OBI:0001821 OBI:0001822: - title: ELISPOT assay measuring epitope specific interleukin-23 production + title: + ELISPOT assay measuring epitope specific interleukin-23 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-23 + description: + An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. meaning: OBI:0001822 OBI:0001824: - title: intracellular cytokine staining assay measuring epitope specific interleukin-18 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells - description: A flow cytometry assay that detects interleukin-18 production + description: + A flow cytometry assay that detects interleukin-18 production by T cells. meaning: OBI:0001824 OBI:0001826: - title: ELISPOT assay measuring epitope specific interleukin-21 production + title: + ELISPOT assay measuring epitope specific interleukin-21 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-21 + description: + An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. meaning: OBI:0001826 OBI:0001827: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. meaning: OBI:0001827 OBI:0001828: - title: cytometric bead array assay measuring epitope specific chemokine (C-C + title: + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: A cytometric bead array assay that detects chemokine (C-C motif) + description: + A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. meaning: OBI:0001828 OBI:0001829: - title: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand + title: + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - description: An enzyme-linked immunospot assay that detects chemokine (C-C + description: + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. meaning: OBI:0001829 OBI:0001830: - title: ELISPOT assay measuring epitope specific interleukin-17F production + title: + ELISPOT assay measuring epitope specific interleukin-17F production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-17F + description: + An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. meaning: OBI:0001830 OBI:0001831: title: ELISA measuring epitope specific interleukin-17F production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-17F + description: + An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. meaning: OBI:0001831 OBI:0001832: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. meaning: OBI:0001832 OBI:0001833: - title: ELISPOT assay measuring epitope specific interleukin-17A production + title: + ELISPOT assay measuring epitope specific interleukin-17A production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-17A + description: + An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. meaning: OBI:0001833 OBI:0001835: - title: cytometric bead array assay measuring epitope specific interleukin-18 + title: + cytometric bead array assay measuring epitope specific interleukin-18 production by T cells - description: A cytometric bead array assay that detects interleukin-18 production + description: + A cytometric bead array assay that detects interleukin-18 production by T cells. meaning: OBI:0001835 OBI:0001836: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. meaning: OBI:0001836 OBI:0001837: title: ELISA measuring epitope specific interleukin-16 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-16 + description: + An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. meaning: OBI:0001837 OBI:0001838: - title: ELISPOT assay measuring epitope specific interleukin-16 production + title: + ELISPOT assay measuring epitope specific interleukin-16 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-16 + description: + An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. meaning: OBI:0001838 OBI:0001839: - title: intracellular cytokine staining assay measuring epitope specific interleukin-16 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells - description: A flow cytometry assay that detects interleukin-16 production + description: + A flow cytometry assay that detects interleukin-16 production by T cells. meaning: OBI:0001839 OBI:0001840: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. meaning: OBI:0001840 OBI:0001841: - title: intracellular cytokine staining assay measuring epitope specific interleukin-1 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells - description: A flow cytometry assay that detects interleukin-1 beta production + description: + A flow cytometry assay that detects interleukin-1 beta production by T cells. meaning: OBI:0001841 OBI:0001842: - title: ELISPOT assay measuring epitope specific interleukin-1 beta production + title: + ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-1 + description: + An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. meaning: OBI:0001842 OBI:0001843: - title: detection of specific nucleic acids with complementary probes measuring + title: + detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. meaning: OBI:0001843 OBI:0001844: - title: ELISPOT assay measuring epitope specific interleukin-12 production + title: + ELISPOT assay measuring epitope specific interleukin-12 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-12 + description: + An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. meaning: OBI:0001844 OBI:0001845: - title: intracellular cytokine staining assay measuring epitope specific interleukin-15 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells - description: A flow cytometry assay that detects interleukin-15 production + description: + A flow cytometry assay that detects interleukin-15 production by T cells. meaning: OBI:0001845 OBI:0001846: - title: ELISPOT assay measuring epitope specific interleukin-15 production + title: + ELISPOT assay measuring epitope specific interleukin-15 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-15 + description: + An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. meaning: OBI:0001846 OBI:0001848: title: chromatin interaction analysis by paired-end tag sequencing assay - description: An assay that incorporates chromatin immunoprecipitation (ChIP)-based + description: + An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. meaning: OBI:0001848 OBI:0001849: title: structural analysis by paired-end tag sequencing assay - description: An assay that incorporates Paired-End Tags and sequencing technology + description: + An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. meaning: OBI:0001849 OBI:0001850: title: transcript analysis by paired-end tag sequencing assay - description: A transcription profiling by RNA sequencing assay that employs + description: + A transcription profiling by RNA sequencing assay that employs paired-end sequencing of RNA transcripts to determine things such as gene expression, gene structure, and alternative transcript structure. meaning: OBI:0001850 OBI:0001853: title: DNase I hypersensitive sites sequencing assay - description: An assay that identifies the location of regulatory regions, + description: + An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. meaning: OBI:0001853 OBI:0001857: - title: RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing + title: + RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay - description: An analyte assay that combines immunoprecipitation of an RNA-binding + description: + An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). meaning: OBI:0001857 OBI:0001858: title: cross-linking immunoprecipitation high-throughput sequencing assay - description: An analyte assay that employs UV-crosslinking between RNA and + description: + An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. meaning: OBI:0001858 OBI:0001859: title: formaldehyde-assisted isolation of regulatory elements assay - description: An assay to determine the sequences of those DNA regions in the + description: + An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. meaning: OBI:0001859 OBI:0001861: title: methylation-sensitive restriction enzyme sequencing assay - description: An assay that identifies unmethylated CpGs using methylation + description: + An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. meaning: OBI:0001861 OBI:0001862: title: reduced representation bisulfite sequencing assay - description: A bisulfite sequencing assay that identifies genomic methylation + description: + A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. meaning: OBI:0001862 OBI:0001863: title: shotgun bisulfite-seq assay - description: A bisulfite sequencing assay that identifies methylated cytosines + description: + A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. meaning: OBI:0001863 OBI:0001864: - title: RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression + title: + RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay - description: A transcription profiling by RNA sequencing assay that identifies + description: + A transcription profiling by RNA sequencing assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. meaning: OBI:0001864 OBI:0001915: title: DNA replication timing by array assay - description: An assay which quantifies the timing of DNA replication as a + description: + An assay which quantifies the timing of DNA replication as a function of genome position using array technology. meaning: OBI:0001915 OBI:0001918: title: RNA-binding protein immunoprecipitation array profiling assay - description: An assay that combines immunoprecipitation of an RNA-binding + description: + An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). meaning: OBI:0001918 OBI:0001919: title: Carbon-copy chromosome conformation capture assay - description: An assay that measures the organization of chromosomes at the + description: + An assay that measures the organization of chromosomes at the genome-wide scale. meaning: OBI:0001919 OBI:0001920: title: DNA replication timing by sequencing assay - description: An assay in which timing of DNA replication is quantified as + description: + An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. meaning: OBI:0001920 OBI:0001921: title: RNA-binding protein immunoprecipitation tiling array profiling assay - description: An RNA-binding protein immunoprecipitation array profiling assay + description: + An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). meaning: OBI:0001921 OBI:0001922: title: microRNA profiling by high throughput sequencing assay - description: A microRNA profiling assay that analyzes the microRNA component + description: + A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. meaning: OBI:0001922 OBI:0001923: title: protein sequencing by tandem mass spectrometry assay - description: A sequencing assay that detremines amino acid sequences of proteins + description: + A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. meaning: OBI:0001923 OBI:0001924: - title: micrococcal nuclease digestion followed by high throughput sequencing + title: + micrococcal nuclease digestion followed by high throughput sequencing assay - description: An assay that identifies nucleosome positioning by genome wide + description: + An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease meaning: OBI:0001924 OBI:0001925: title: chromatin immunoprecipitation with exonuclease sequencing assay - description: A ChIP-seq assay which uses immunoprecipitation to isolate protein + description: + A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site meaning: OBI:0001925 OBI:0001926: title: microRNA profiling assay - description: A transcription profiling assay that quantifies the microRNA + description: + A transcription profiling assay that quantifies the microRNA species within a biological sample. meaning: OBI:0001926 OBI:0001954: title: ChIP assay - description: An assay in which portions of chromatin, the ordered and organized - complex of DNA and its interaction partners that make up a chormosome, is + description: + An assay in which portions of chromatin, the ordered and organized + complex of DNA and its interaction partners that make up a chromosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed meaning: OBI:0001954 OBI:0001956: title: assay using chromatin immunoprecipitation - description: An assay that produces data about protein-DNA interaction or + description: + An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation meaning: OBI:0001956 OBI:0001960: title: taxonomic diversity assessment by targeted gene survey - description: An assay that dteremines taxonomic and community diversity information + description: + An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. meaning: OBI:0001960 OBI:0001976: title: hydrogen/deuterium exchange footprinting assay - description: A footprinting assay that uses a chemical reaction whereby a + description: + A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. @@ -3478,166 +4327,205 @@ enums: meaning: OBI:0001977 OBI:0001978: title: immunoblot assay - description: An analyte assay that detects specific molecules in an input - material by separating it using gel electrophoresis, transfering the separated + description: + An analyte assay that detects specific molecules in an input + material by separating it using gel electrophoresis, transferring the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. meaning: OBI:0001978 OBI:0001979: title: fluorescence quenching binding assay - description: A binding assay in which the proximity of two entities is monitored + description: + A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. meaning: OBI:0001979 OBI:0001980: title: in vivo intervention experiment - description: An assay in which the effect of a targeted process (the intervention) + description: + An assay in which the effect of a targeted process (the intervention) on an organism is tested. meaning: OBI:0001980 OBI:0001981: title: disease exacerbation in vivo intervention experiment - description: An in vivo intervention experiment that tests the ability of + description: + An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. meaning: OBI:0001981 OBI:0001982: title: protection from challenge in vivo intervention experiment - description: An in vivo intervention experiment that tests the ability of + description: + An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. meaning: OBI:0001982 OBI:0001983: title: tolerance induction intervention experiment - description: An in vivo intervention experiment that tests the ability of + description: + An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. meaning: OBI:0001983 OBI:0001984: title: treatment intervention experiment - description: An in vivo intervention experiment in which the ability of the + description: + An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. meaning: OBI:0001984 OBI:0001985: title: microarray assay - description: An analyte assay where binding of the analyte to immobilized + description: + An analyte assay where binding of the analyte to immobilized matrix is measured. meaning: OBI:0001985 OBI:0001986: title: immunohistochemistry - description: An immunostaining assay to detect and potentially localize antigens + description: + An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. meaning: OBI:0001986 OBI:0001987: title: assay measuring the association constant [KA] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring equilibrium + description: + A MHC binding constant determination assay measuring equilibrium association constant (KA). meaning: OBI:0001987 OBI:0001988: title: assay measuring the dissociation constant [KD] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring equilibrium + description: + A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). meaning: OBI:0001988 OBI:0001989: - title: radioactivity detection assay measuring equilibrium dissociation constant + title: + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - description: A radioactivity detection assay that measures equilibrium dissociation + description: + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. meaning: OBI:0001989 OBI:0001990: title: assay measuring the half life of a MHC:ligand complex - description: A MHC binding constant determination assay measuring half life + description: + A MHC binding constant determination assay measuring half life of binding. meaning: OBI:0001990 OBI:0001991: - title: assay measuring the half maximal effective concentration [EC50] of + title: + assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring half maximal + description: + A MHC binding constant determination assay measuring half maximal effective concentration (EC50). meaning: OBI:0001991 OBI:0001992: - title: assay measuring the half maximal inhibitory concentration [IC50] of + title: + assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring half maximal + description: + A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). meaning: OBI:0001992 OBI:0001993: title: assay measuring the off rate measurement [koff] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring binding + description: + A MHC binding constant determination assay measuring binding off rate measurement data item (koff). meaning: OBI:0001993 OBI:0001994: - title: assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand + title: + assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex - description: A MHC binding constant determination assay measuring binding + description: + A MHC binding constant determination assay measuring binding on rate (kon). meaning: OBI:0001994 OBI:0001995: - title: chromatography assay measuring the association constant [KA] of a B + title: + chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex - description: An analytical chromatography assay that measures the association + description: + An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. meaning: OBI:0001995 OBI:0001996: - title: chromatography assay measuring the dissociation constant [KD] of a + title: + chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: An analytical chromatography assay that measures the dissociation + description: + An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0001996 OBI:0001997: - title: hydrogen/deuterium exchange footprinting assay measuring binding of + title: + hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex - description: A hydrogen/deuterium exchange footprinting assay that detects + description: + A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. meaning: OBI:0001997 OBI:0001998: - title: immunohistochemistry assay measuring binding of a B cell epitope:antibody + title: + immunohistochemistry assay measuring binding of a B cell epitope:antibody complex - description: A immunohistochemistry assay that detects the binding of an antigen + description: + A immunohistochemistry assay that detects the binding of an antigen with an antibody. meaning: OBI:0001998 OBI:0001999: - title: 3D molecular structure determination assay of a T cell epitope:MHC:TCR + title: + 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex - description: A 3D structure determination of bound molecular complex assay + description: + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex. meaning: OBI:0001999 OBI:0002014: title: DNA methylation profiling by ChIP-chip assay - description: An epigenetic modification assay that identifies sites of DNA + description: + An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. meaning: OBI:0002014 OBI:0002015: title: transcription profiling by MPSS assay - description: A transcription profiling assay that uses Massive Parallel Signature + description: + A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). meaning: OBI:0002015 OBI:0002016: title: histone modification identification by ChIP-chip assay - description: An epigenetic modification assay that identifies regions containing + description: + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. meaning: OBI:0002016 OBI:0002017: title: histone modification identification by ChIP-Seq assay - description: An epigenetic modification assay that identifies regions containing + description: + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. meaning: OBI:0002017 OBI:0002018: title: transcription factor binding site identification by ChIP-chip assay - description: A transcription factor binding site assay that utilizes ChIP-chip + description: + A transcription factor binding site assay that utilizes ChIP-chip technology. meaning: OBI:0002018 OBI:0002019: title: transcription factor binding site identification by ChIP-Seq assay - description: A transcription factor binding site assay that utilizes ChIP-seq + description: + A transcription factor binding site assay that utilizes ChIP-seq technology. meaning: OBI:0002019 OBI:0002020: title: epigenetic modification assay - description: An assay that identifies epigenetic modifications including histone + description: + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. meaning: OBI:0002020 OBI:0002029: title: serial analysis of gene expression assay - description: A transcription profiling by RNA sequencing assay that quantifies + description: + A transcription profiling by RNA sequencing assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule that is then sequenced. meaning: OBI:0002029 @@ -3651,7 +4539,8 @@ enums: meaning: OBI:0002031 OBI:0002032: title: parallel analysis of RNA structure assay - description: A single-nucleotide-resolution nucleic acid structure mapping + description: + A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with @@ -3659,7 +4548,8 @@ enums: meaning: OBI:0002032 OBI:0002033: title: translation-associated transcript leader sequencing assay - description: A translation profiling assay that combines transcript leader + description: + A translation profiling assay that combines transcript leader sequencing with polysome fractionation. TATL-seq works by applying TL-seq across fractions of a polysome gradient, generating TL-specific translational measurements to identify how different transcript leader sequences effect @@ -3667,246 +4557,305 @@ enums: meaning: OBI:0002033 OBI:0002034: title: transcript leader sequencing assay - description: A transcription profiling by RNA sequencing assay that combines + description: + A transcription profiling by RNA sequencing assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. meaning: OBI:0002034 OBI:0002035: title: peptide mass fingerprinting assay - description: A mass spectrometry assay that measures the absolute mass of + description: + A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. meaning: OBI:0002035 OBI:0002036: title: array based nucleic acid structure mapping assay - description: An assay which aims to provide information about the in vivo + description: + An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. meaning: OBI:0002036 OBI:0002037: title: micrococcal nuclease digestion followed by tiling array assay - description: An array based nucleic acid structure mapping assay that identifies + description: + An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays meaning: OBI:0002037 OBI:0002038: title: ribosomal profiling by sequencing assay - description: A translation profiling assay that sequences only mRNA protected + description: + A translation profiling assay that sequences only mRNA protected by the ribosome during translation and thus provides information on which transcipts are undergoing active translation. meaning: OBI:0002038 OBI:0002039: title: assay for transposase-accessible chromatin using sequencing - description: An assay to capture the location of open chromatin, DNA-binding + description: + An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. meaning: OBI:0002039 OBI:0002040: title: chromatin isolation by RNA purification sequencing assay - description: A detection of specific nucleic acids with complementary probes + description: + A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. meaning: OBI:0002040 OBI:0002041: title: self-transcribing active regulatory region sequencing assay - description: An assay that identifies the sequences that act as transcriptional + description: + An assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. meaning: OBI:0002041 OBI:0002042: - title: carbon-copy chromosome conformation capture assay followed by sequencing + title: + carbon-copy chromosome conformation capture assay followed by sequencing assay - description: A carbon-copy chromosome conformation capture assay to analyze + description: + A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. meaning: OBI:0002042 OBI:0002043: - title: individual-nucleotide resolution cross-linking and immunoprecipitation + title: + individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay - description: A cross-linking immunoprecipitation high-throughput sequencing + description: + A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. meaning: OBI:0002043 OBI:0002044: title: RNA Bind-n-Seq assay - description: An assay that comprehensively characterizes sequence and structural + description: + An assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). meaning: OBI:0002044 OBI:0002045: title: polyA-site sequencing assay - description: A transcription profiling by RNA sequencing assay that quantitatively + description: + A transcription profiling by RNA sequencing assay that quantitatively profiles RNA polyadenylation at the transcriptome level. meaning: OBI:0002045 OBI:0002050: title: 3D molecular structure determination assay of a MHC:ligand complex - description: A 3D structure determination of bound molecular complex assay + description: + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex. meaning: OBI:0002050 OBI:0002051: - title: in vivo assay measuring B cell epitope specific protection from infectious + title: + in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. meaning: OBI:0002051 OBI:0002052: - title: in vivo assay measuring B cell epitope specific protection after tumor + title: + in vivo assay measuring B cell epitope specific protection after tumor burden challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. meaning: OBI:0002052 OBI:0002053: title: microarray assay measuring binding of a B cell epitope:antibody complex - description: A microarray assay that detects the binding of an antigen with + description: + A microarray assay that detects the binding of an antigen with an antibody. meaning: OBI:0002053 OBI:0002054: - title: NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody + title: + NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A B cell epitope equilibrium dissociation constant (KD) determination + description: + A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. meaning: OBI:0002054 OBI:0002055: - title: assay measuring biological activity resulting from T cell epitope:MHC:TCR + title: + assay measuring biological activity resulting from T cell epitope:MHC:TCR binding - description: A T cell epitope recognition assay that measures the immune response + description: + A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the - recongition of the epitope. + recognition of the epitope. meaning: OBI:0002055 OBI:0002056: - title: assay measuring epitope specific chemokine (C-C motif) ligand 17 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. meaning: OBI:0002056 OBI:0002057: - title: assay measuring epitope specific macrophage migration inhibitory factor + title: + assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. meaning: OBI:0002057 OBI:0002058: title: assay measuring epitope specific oncostatin M production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. meaning: OBI:0002058 OBI:0002059: title: assay measuring a binding constant of a T cell epitope:MHC:TCR complex - description: A T cell epitope recognition assay that quantitavely characterizes + description: + A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. meaning: OBI:0002059 OBI:0002060: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. meaning: OBI:0002060 OBI:0002061: - title: cytometric bead array assay measuring epitope specific chemokine (C-C + title: + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - description: A cytometric bead array assay that detects chemokine (C-C motif) + description: + A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. meaning: OBI:0002061 OBI:0002062: title: in vitro assay measuring epitope specific T cell killing - description: An in vitro cell killing assay that measures the killing of antigen + description: + An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. meaning: OBI:0002062 OBI:0002063: - title: cytometric bead array assay measuring epitope specific granzyme A release + title: + cytometric bead array assay measuring epitope specific granzyme A release by T cells - description: A cytometric bead array assay that detects epitope specific granzyme + description: + A cytometric bead array assay that detects epitope specific granzyme A release by T cells. meaning: OBI:0002063 OBI:0002064: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells - description: A detection of specific nucleic acids with complementary probes + description: + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. meaning: OBI:0002064 OBI:0002065: - title: cytometric bead array assay measuring epitope specific granzyme B release + title: + cytometric bead array assay measuring epitope specific granzyme B release by T cells - description: A cytometric bead array assay that detects epitope specific granzyme + description: + A cytometric bead array assay that detects epitope specific granzyme B release by T cells. meaning: OBI:0002065 OBI:0002066: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells - description: A detection of specific nucleic acids with complementary probes + description: + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells meaning: OBI:0002066 OBI:0002067: - title: cytometric bead array assay measuring epitope specific macrophage migration + title: + cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - description: A cytometric bead array assay that detects macrophage migration + description: + A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. meaning: OBI:0002067 OBI:0002068: - title: cytometric bead array assay measuring epitope specific oncostatin M + title: + cytometric bead array assay measuring epitope specific oncostatin M production by T cells - description: A cytometric bead array assay that detects oncostatin M production + description: + A cytometric bead array assay that detects oncostatin M production by T cells. meaning: OBI:0002068 OBI:0002069: title: ELISPOT assay measuring epitope specific perforin release by T cells - description: An enzyme-linked immunospot assay that detects epitope specific + description: + An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. meaning: OBI:0002069 OBI:0002070: title: in vivo assay measuring epitope specific proliferation of T cells - description: A T cell epitope specific proliferation assay that is performed + description: + A T cell epitope specific proliferation assay that is performed in vivo. meaning: OBI:0002070 OBI:0002071: title: in vitro assay measuring epitope specific proliferation of T cells - description: A T cell epitope specific proliferation assay that is performed + description: + A T cell epitope specific proliferation assay that is performed on cells in vitro. meaning: OBI:0002071 OBI:0002072: title: assay measuring qualitative binding of a MHC:ligand complex - description: An assay that detects the binding of a MHC molecule with a ligand, + description: + An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. meaning: OBI:0002072 OBI:0002073: title: in vivo assay measuring T cell epitope specific protection from challenge - description: An efficacy of T cell epitope intervention experiment that uses + description: + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. meaning: OBI:0002073 OBI:0002074: title: assay measuring T cell epitope specific suppression in vitro - description: T cell epitope dependent biological activity assay that detects + description: + T cell epitope dependent biological activity assay that detects suppression of an in vitro response. meaning: OBI:0002074 OBI:0002075: title: MHC ligand assay - description: An immune epitope assay that characterizes the structrue of a + description: + An immune epitope assay that characterizes the structure of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule. meaning: OBI:0002075 OBI:0002082: title: reporter gene assay - description: An assay that detects expression of a reporter gene that was + description: + An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. meaning: OBI:0002082 OBI:0002083: title: enhancer activity detection by reporter gene assay - description: A reporter gene assay that detects expression of a reporter gene + description: + A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. meaning: OBI:0002083 OBI:0002084: title: transcription cofactor activity region identification by ChIP-Seq assay - description: A ChIP-seq assay that identifies regions of chromatin bound to + description: + A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. meaning: OBI:0002084 OBI:0002085: - title: transcript expression location detection by hybridization chain reaction + title: + transcript expression location detection by hybridization chain reaction assay - description: An in situ hybridization assay in which the location (e.g. anatomical/tissue) + description: + An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which @@ -3915,7 +4864,8 @@ enums: meaning: OBI:0002085 OBI:0002086: title: Tet-assisted bisulfite sequencing assay - description: A bisulfite sequencing assay that identifies genomic methylation + description: + A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) @@ -3923,68 +4873,87 @@ enums: meaning: OBI:0002086 OBI:0002094: title: MethylC-Capture sequencing assay - description: A bisulfite sequencing assay in which a whole-genome sequencing + description: + A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. meaning: OBI:0002094 OBI:0002096: - title: carboxyfluorescein succinimidyl ester staining assay measuring epitope + title: + carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells - description: A CFSE assay that detects T cell epitope specific proliferation + description: + A CFSE assay that detects T cell epitope specific proliferation in vitro. meaning: OBI:0002096 OBI:0002097: - title: assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR + title: + assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - description: A T cell epitope binding constant determination assay that measures + description: + A T cell epitope binding constant determination assay that measures the dissociation constant KD. meaning: OBI:0002097 OBI:0002098: title: assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex - description: A T cell epitope binding constant determination assay that measures + description: + A T cell epitope binding constant determination assay that measures the on rate. meaning: OBI:0002098 OBI:0002099: title: assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex - description: A T cell epitope binding constant determination assay that measures + description: + A T cell epitope binding constant determination assay that measures the off rate. meaning: OBI:0002099 OBI:0002100: - title: assay measuring the association constant [KA] of a T cell epitope:MHC:TCR + title: + assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex - description: A T cell epitope binding constant determination assay that measures + description: + A T cell epitope binding constant determination assay that measures the association constant KA. meaning: OBI:0002100 OBI:0002101: - title: small-angle scattering assay determining the 3D structure of a B cell + title: + small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex - description: A small-angle scattering 3D molecular structure determination + description: + A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex meaning: OBI:0002101 OBI:0002102: - title: bio-layer interferometry assay measuring the on rate [kon] of a B cell + title: + bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex - description: A bio-layer interferometry assay that measures the on rate of + description: + A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. meaning: OBI:0002102 OBI:0002103: - title: bio-layer interferometry assay measuring the off rate [koff] of a B + title: + bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex - description: A bio-layer interferometry assay that measures the off rate of + description: + A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. meaning: OBI:0002103 OBI:0002104: - title: bio-layer interferometry assay measuring binding of a B cell epitope:antibody + title: + bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex - description: A bio-layer interferometry assay that detects the binding of + description: + A bio-layer interferometry assay that detects the binding of an antigen with an antibody. meaning: OBI:0002104 OBI:0002105: - title: bio-layer interferometry assay measuring the dissociation constant + title: + bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A bio-layer interferometry assay that measures the dissociation + description: + A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. meaning: OBI:0002105 OBI:0002106: @@ -3993,72 +4962,85 @@ enums: meaning: OBI:0002106 OBI:0002107: title: bio-layer interferometry assay - description: A binding assay that detects a shift in the interference pattern + description: + A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. meaning: OBI:0002107 OBI:0002108: title: small-angle scattering 3D molecular structure determination assay - description: A 3D molecular structure determination assay in which the scattering + description: + A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. meaning: OBI:0002108 OBI:0002111: - title: enhanced cross-linking immunoprecipitation high-throughput sequencing + title: + enhanced cross-linking immunoprecipitation high-throughput sequencing assay - description: An iCLIP assay that is enhanced to robustly identify protein-RNA + description: + An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. meaning: OBI:0002111 OBI:0002112: title: small RNA sequencing assay - description: A transcription profiling by RNA sequencing assay which is targeting + description: + A transcription profiling by RNA sequencing assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. meaning: OBI:0002112 OBI:0002113: title: bromouridine labeling and sequencing assay - description: A transcription profiling by RNA sequencing assay used to identify + description: + A transcription profiling by RNA sequencing assay used to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. meaning: OBI:0002113 OBI:0002114: title: bromouridine pulse-chase and sequencing assay - description: A transcription profiling by RNA sequencing assay used to identify + description: + A transcription profiling by RNA sequencing assay used to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. meaning: OBI:0002114 OBI:0002115: title: cytometry time of flight assay - description: A cytometry assay in which the presence of molecules of interest + description: + A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. meaning: OBI:0002115 OBI:0002116: title: high performance liquid chromatography assay - description: An analytical chromatography assay that utilizes a high performance + description: + An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. meaning: OBI:0002116 OBI:0002117: title: whole genome sequencing assay - description: A DNA sequencing assay that intends to provide information about + description: + A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. meaning: OBI:0002117 OBI:0002118: title: exome sequencing assay - description: A DNA sequencing assay that intends to provide information about + description: + A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). meaning: OBI:0002118 OBI:0002119: title: microscopy assay - description: An imaging assay that utilizes a microscope to magnify features + description: + An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. meaning: OBI:0002119 OBI:0002120: title: mixed lymphocyte reaction assay - description: A cytometry assay where lymphocytes from two individuals are + description: + A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition @@ -4066,17 +5048,20 @@ enums: meaning: OBI:0002120 OBI:0002121: title: killer cell immunoglobulin-like receptor typing assay - description: A genotyping assay in which the alleles of genes encoding for + description: + A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. meaning: OBI:0002121 OBI:0002122: title: major histocompatibility typing assay - description: A genotyping assay in which the alleles of genes encoding for + description: + A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. meaning: OBI:0002122 OBI:0002132: title: pulse stable isotope labeling by amino acids in cell culture - description: An assay that detects differences in protein abundance using + description: + An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based @@ -4084,15 +5069,19 @@ enums: stability. meaning: OBI:0002132 OBI:0002133: - title: cytometric bead array assay measuring epitope specific chemokine (C-C + title: + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells - description: A cytometric bead array assay that detects chemokine (C-C motif) + description: + A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. meaning: OBI:0002133 OBI:0002134: - title: assay measuring epitope specific chemokine (C-C motif) ligand 20 production + title: + assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. meaning: OBI:0002134 OBI:0002140: @@ -4105,19 +5094,22 @@ enums: meaning: OBI:0002141 OBI:0002142: title: Nanostring nCounter miRNA expression assay - description: A microRNA profiling assay using digital molecular barcoding + description: + A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. meaning: OBI:0002142 OBI:0002143: title: bromouride labeling and sequencing after UV exposure - description: A transcription profiling by RNA sequencing assay used to identify + description: + A transcription profiling by RNA sequencing assay used to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. meaning: OBI:0002143 OBI:0002144: title: extrachromosomal circular DNA sequencing assay - description: An assay which aims at identifying the endogenous population + description: + An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library @@ -4126,186 +5118,219 @@ enums: meaning: OBI:0002144 OBI:0002145: title: antigen specific antibodies assay - description: An analyte assay that measures the presence or amount of antibodies + description: + An analyte assay that measures the presence or amount of antibodies to a specified antigen. meaning: OBI:0002145 OBI:0002146: title: HIV antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. meaning: OBI:0002146 OBI:0002147: title: HIV group O antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. meaning: OBI:0002147 OBI:0002148: title: surface HBV antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. meaning: OBI:0002148 OBI:0002149: title: core HBV antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. meaning: OBI:0002149 OBI:0002150: title: core HBV IgM antibody assay - description: An antigen specific antibodies assay that is meant to detectimmunoglobulin + description: + An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. meaning: OBI:0002150 OBI:0002151: title: HCV antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. meaning: OBI:0002151 OBI:0002152: title: EBV IgG antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. meaning: OBI:0002152 OBI:0002153: title: EBV IgM antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. meaning: OBI:0002153 OBI:0002154: title: CMV antibody assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. meaning: OBI:0002154 OBI:0002155: title: venereal disease research laboratory test - description: An analyte assay that is meant to detect general antibodies that + description: + An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. meaning: OBI:0002155 OBI:0002156: title: rapid plasma reagin test - description: An analyte assay that is meant to detect with the aid of carbon + description: + An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. meaning: OBI:0002156 OBI:0002157: title: HBV surface antigen assay - description: An analyte assay that is meant to detect hepatitis B virus (HBV) + description: + An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. meaning: OBI:0002157 OBI:0002158: title: HIV-1 nucleic acid testing - description: An analyte assay that is meant to detect human immunodeficiency + description: + An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. meaning: OBI:0002158 OBI:0002159: title: HCV nucleic acid testing - description: An analyte assay that is meant to detect hepatitis C virus (HCV) + description: + An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. meaning: OBI:0002159 OBI:0002160: title: multiplexed indexed T7 ChIP-seq assay - description: A ChIP-seq assay which leverages T7 promoter amplification to + description: + A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. meaning: OBI:0002160 OBI:0002161: title: systematic evolution of ligands by exponential enrichment assay - description: A binding assay that identifies protein-binding sites on nucleic + description: + A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ meaning: OBI:0002161 OBI:0002162: title: footprinting assay - description: An assay that measures ligand binding and conformational changes + description: + An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. meaning: OBI:0002162 OBI:0002163: title: DNAse footprinting assay - description: An enzymatic footprinting assay that determines protein-binding + description: + An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis meaning: OBI:0002163 OBI:0002164: title: mammalian 2-hybrid assay - description: A binding assay that increases the expression of a reporter gene + description: + A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. meaning: OBI:0002164 OBI:0002165: title: protein localization assay - description: An assay that determines the specific location of a protein. + description: + An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. meaning: OBI:0002165 OBI:0002166: title: tissue-based protein localization assay - description: A protein localization assay that determines the specific location + description: + A protein localization assay that determines the specific location of a protein in a living tissue sample. meaning: OBI:0002166 OBI:0002167: title: subcellular protein localization assay - description: A protein localization assay that determines the specific subcellular + description: + A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. meaning: OBI:0002167 OBI:0002168: title: subcellular protein immunohistochemistry assay - description: An immunohistochemistry assay that uses antibodies to display + description: + An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. meaning: OBI:0002168 OBI:0002169: title: ChIP-qPCR assay - description: A ChIP assay that uses quantitative PCR to determine levels of + description: + A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. meaning: OBI:0002169 OBI:0002170: title: genomic SELEX - description: A systematic evolution of ligands by exponential enrichment assay + description: + A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. meaning: OBI:0002170 OBI:0002171: title: dot blot assay - description: An analyte assay that detects molecules in a mixture dotted on + description: + An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. meaning: OBI:0002171 OBI:0002172: title: Northwestern blot assay - description: A direct binding assay that detects interactions of labeled RNA + description: + A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. meaning: OBI:0002172 OBI:0002173: title: Southwestern blot assay - description: A direct binding assay that detects interactions of labeled DNA + description: + A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. meaning: OBI:0002173 OBI:0002174: title: immunocytochemistry - description: An immuno staining assay in which samples of intact cells are + description: + An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed meaning: OBI:0002174 OBI:0002175: title: ATP bioluminescence assay - description: An analyte assay that detects ATP concentration through light + description: + An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. meaning: OBI:0002175 OBI:0002176: title: electrophysiology assay - description: An assay that measures the electrical properties of biological + description: + An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage - changes or electric current (or other associated variables such as impedence + changes or electric current (or other associated variables such as impedance or capacitance). meaning: OBI:0002176 OBI:0002177: title: patch clamp assay - description: An intracellular electrophysiology assay where a glass micropipette + description: + An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette @@ -4314,7 +5339,8 @@ enums: meaning: OBI:0002177 OBI:0002178: title: whole-cell patch clamp assay - description: A patch-clamp assay where the electrode is left in place on the + description: + A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents @@ -4323,7 +5349,8 @@ enums: meaning: OBI:0002178 OBI:0002179: title: cell-attached patch clamp assay - description: A patch-clamp assay where the electrode is left in place on the + description: + A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording @@ -4332,7 +5359,8 @@ enums: meaning: OBI:0002179 OBI:0002180: title: inside-out patch clamp assay - description: A patch-clamp assay where a patch of the membrane is attached + description: + A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the @@ -4342,7 +5370,8 @@ enums: meaning: OBI:0002180 OBI:0002181: title: outside-out patch clamp assay - description: A patch-clamp assay where a patch of the membrane is attached + description: + A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in @@ -4356,14 +5385,16 @@ enums: meaning: OBI:0002181 OBI:0002182: title: voltage clamp assay - description: An cellular electrophysiology assay where the membrane potential + description: + An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. meaning: OBI:0002182 OBI:0002183: title: two electrode voltage clamp assay - description: The two electrode voltage clamp (TEVC) method utilizes two low-resistance + description: + The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as @@ -4376,7 +5407,8 @@ enums: meaning: OBI:0002183 OBI:0002184: title: cut open oocyte voltage clamp assay - description: The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique + description: + The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. @@ -4387,7 +5419,8 @@ enums: meaning: OBI:0002184 OBI:0002185: title: current clamp assay - description: The current clamp technique records the membrane potential by + description: + The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential @@ -4399,14 +5432,16 @@ enums: meaning: OBI:0002185 OBI:0002186: title: electroencephalography - description: An extracellular electrophysiology assay where electrodes are + description: + An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. meaning: OBI:0002186 OBI:0002187: title: single-unit recording - description: An extracellular electrophysiology assay where a single microelectrode + description: + An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their @@ -4414,97 +5449,114 @@ enums: meaning: OBI:0002187 OBI:0002188: title: multi-unit recording - description: An extracellular electrophysiology assay where a collection of + description: + An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. meaning: OBI:0002188 OBI:0002189: title: local field potential recording - description: An extracellular electrophysiology assay where a microelectrode + description: + An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. meaning: OBI:0002189 OBI:0002436: title: RNA interactome capture - description: An assay that identifies RNA binding proteins by cross-linking + description: + An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. meaning: OBI:0002436 OBI:0002437: title: widefield microscopy assay - description: A fluorescence microscopy technique where the specimen under + description: + A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. meaning: OBI:0002437 OBI:0002438: title: nuclear ligation assay - description: An assay that detects the proximity of chromosomal DNA through + description: + An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. meaning: OBI:0002438 OBI:0002439: title: chromosome conformation capture assay - description: A nuclear ligation assay that detects chromosomal interactions + description: + A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. meaning: OBI:0002439 OBI:0002440: title: Hi-C assay - description: A chromosome conformation capture assay that detects genome-wide + description: + A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. meaning: OBI:0002440 OBI:0002441: title: physical examination of an organism - description: An assay that produces a description of the qualities of an organism + description: + An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques. meaning: OBI:0002441 OBI:0002442: title: hydroxyl-radical footprinting assay - description: A footprinting assay that uses the reaction of hydroxyl radicals + description: + A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. meaning: OBI:0002442 OBI:0002443: title: methidiumpropyl-EDTA-iron(II) footprinting assay - description: A footprinting assay that determines protein-binding sites on + description: + A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. meaning: OBI:0002443 OBI:0002445: title: transcription start site mapping by primer extension assay - description: A transcription profiling assay in which the transcription start + description: + A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. meaning: OBI:0002445 OBI:0002449: title: footprinting assay measuring binding of a B cell epitope:antibody complex - description: A footprinting assay that detects the binding of an antigen with + description: + A footprinting assay that detects the binding of an antigen with an antibody. meaning: OBI:0002449 OBI:0002450: - title: hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody + title: + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex - description: A hydroxyl-radical footprinting assay that detects the binding + description: + A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. meaning: OBI:0002450 OBI:0002451: title: ELISA measuring epitope specific interferon-alpha production by T cells - description: An enzyme-linked immunosorbent assay that detects interferon-alpha + description: + An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. meaning: OBI:0002451 OBI:0002452: title: assay measuring epitope specific interferon-alpha production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. meaning: OBI:0002452 OBI:0002457: title: precision nuclear run-on sequencing assay - description: A transcription profiling by RNA sequencing assay that maps the + description: + A transcription profiling by RNA sequencing assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification @@ -4512,7 +5564,8 @@ enums: meaning: OBI:0002457 OBI:0002458: title: chromosome conformation capture-on-chip assay - description: A nuclear ligation assay which uses cross-linking of proteins + description: + A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites @@ -4520,177 +5573,217 @@ enums: meaning: OBI:0002458 OBI:0002459: title: genotype phasing by Hi-C assay - description: A genotyping assay in which carbon-copy chromosome conformation + description: + A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. meaning: OBI:0002459 OBI:0002485: title: transcript analysis by single-end sequencing assay - description: A sequencing assay that incorporates single-end reads and sequencing + description: + A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. meaning: OBI:0002485 OBI:0002489: title: differential medium assay - description: An organism detection assay that uses a differential medium to + description: + An organism detection assay that uses a differential medium to achieve its objective. meaning: OBI:0002489 OBI:0002564: title: histopathology assay - description: A histological assay that is intended to check for the presence + description: + A histological assay that is intended to check for the presence or level of a specific disease. meaning: OBI:0002564 OBI:0002571: title: polyA-selected RNA sequencing assay - description: A transcription profiling by RNA sequencing assay to study transcriptomes + description: + A transcription profiling by RNA sequencing assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. meaning: OBI:0002571 OBI:0002572: title: polyA-depleted RNA sequencing assay - description: A transcription profiling by RNA sequencing assay to study non-polyadenylated + description: + A transcription profiling by RNA sequencing assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. meaning: OBI:0002572 OBI:0002575: title: isoform sequencing - description: A transcription profiling by RNA sequencing assay for sequencing + description: + A transcription profiling by RNA sequencing assay for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. meaning: OBI:0002575 OBI:0002597: title: chromosome conformation capture sequencing assay - description: A chromosome conformation capture-on-chip assay quantitates the + description: + A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. meaning: OBI:0002597 OBI:0002621: title: reconstitution assay - description: An assay in which a cellular process is replicated from the bottom-up + description: + An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. meaning: OBI:0002621 OBI:0002622: title: in vitro transcription reconstitution assay - description: A reconstitution assay in which RNA synthesis is investigated + description: + A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. meaning: OBI:0002622 OBI:0002623: title: whole metagenome sequencing assay - description: A DNA sequencing assay that intends to provide information on + description: + A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. meaning: OBI:0002623 OBI:0002628: title: RNAi knockdown assay - description: A gene knockdown assay in which RNAi gene knockdown is used to + description: + A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. meaning: OBI:0002628 OBI:0002629: title: direct RNA sequencing assay - description: An assay to study transcription through direct RNA sequence determination, + description: + An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. meaning: OBI:0002629 OBI:0002631: title: single-cell transcription profiling by RNA sequencing assay - description: A transcription profiling by RNA sequencing assay that uses as + description: + A transcription profiling by RNA sequencing assay that uses as input RNA extracts that can be traced to a single cell of origin. These extracts may come from the entire cell or only a part of the cell such as the nucleus or the cytoplasm. meaning: OBI:0002631 OBI:0002634: - title: in vivo assay measuring B cell epitope specific disease exacerbation + title: + in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002634 OBI:0002635: - title: in vivo assay measuring T cell epitope specific disease reduction resulting + title: + in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that detects - a decrease in disease after adoptive transfer of epitope specfic T cells. + description: + An efficacy of T cell epitope intervention experiment that detects + a decrease in disease after adoptive transfer of epitope specific T cells. meaning: OBI:0002635 OBI:0002636: - title: in vivo assay measuring B cell epitope specific disease reduction resulting + title: + in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that detects + description: + An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002636 OBI:0002637: - title: in vivo assay measuring T cell epitope specific protection from challenge + title: + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that uses - a epitope protection experiment after adoptive transfer of epitope specfic + description: + An efficacy of T cell epitope intervention experiment that uses + a epitope protection experiment after adoptive transfer of epitope specific T cells. meaning: OBI:0002637 OBI:0002638: - title: in vivo assay measuring B cell epitope specific protection from challenge + title: + in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002638 OBI:0002639: - title: in vivo assay measuring T cell epitope specific protection from challenge + title: + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. meaning: OBI:0002639 OBI:0002640: - title: in vivo assay measuring B cell epitope specific protection from challenge + title: + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. meaning: OBI:0002640 OBI:0002641: - title: in vivo assay measuring T cell epitope specific protection from other + title: + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. meaning: OBI:0002641 OBI:0002642: - title: in vivo assay measuring B cell epitope specific protection from other + title: + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. meaning: OBI:0002642 OBI:0002643: - title: in vivo assay measuring T cell epitope specific protection from challenge + title: + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. meaning: OBI:0002643 OBI:0002644: - title: in vivo assay measuring B cell epitope specific protection from challenge + title: + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. meaning: OBI:0002644 OBI:0002645: - title: in vivo assay measuring T cell epitope specific tolerance induction + title: + in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that uses + description: + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of - epitope specfic T cells. + epitope specific T cells. meaning: OBI:0002645 OBI:0002646: - title: in vivo assay measuring B cell epitope specific tolerance induction + title: + in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that uses + description: + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002646 @@ -4700,171 +5793,212 @@ enums: meaning: OBI:0002647 OBI:0002649: title: blood microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a blood specimen. meaning: OBI:0002649 OBI:0002664: - title: cytometric bead array assay measuring epitope specific interleukin-15 + title: + cytometric bead array assay measuring epitope specific interleukin-15 production by T cells - description: A cytometric bead array assay that detects interleukin-15 production + description: + A cytometric bead array assay that detects interleukin-15 production by T cells. meaning: OBI:0002664 OBI:0002665: - title: cytometric bead array assay measuring epitope specific interleukin-16 + title: + cytometric bead array assay measuring epitope specific interleukin-16 production by T cells - description: A cytometric bead array assay that detects interleukin-16 production + description: + A cytometric bead array assay that detects interleukin-16 production by T cells. meaning: OBI:0002665 OBI:0002666: - title: in vivo assay measuring B cell epitope specific induction of hypersensitivity + title: + in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that detects + description: + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002666 OBI:0002667: - title: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity + title: + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that detects + description: + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope - specfic T cells. + specific T cells. meaning: OBI:0002667 OBI:0002668: - title: in vivo assay measuring epitope specific proliferation of T cells resulting + title: + in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells - description: A T cell epitope specific proliferation assay that is performed - in vivo after adoptive transfer of epitope specfic T cells. + description: + A T cell epitope specific proliferation assay that is performed + in vivo after adoptive transfer of epitope specific T cells. meaning: OBI:0002668 OBI:0002669: - title: assay measuring epitope specific helper T cell enhancement of a B cell + title: + assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - description: A T cell epitope specific helper activity assay that detects + description: + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive - transfer of epitope specfic T cells. + transfer of epitope specific T cells. meaning: OBI:0002669 OBI:0002670: - title: assay measuring epitope specific helper T cell enhancement of a T cell + title: + assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - description: A T cell epitope specific helper activity assay that detects + description: + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive - transfer of epitope specfic T cells. + transfer of epitope specific T cells. meaning: OBI:0002670 OBI:0002671: - title: in vivo assay measuring epitope specific T cell killing resulting from + title: + in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells - description: An in vivo cell killing assay that detects the killing of an + description: + An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. meaning: OBI:0002671 OBI:0002672: title: ELISA measuring epitope specific perforin release by T cells - description: An enzyme-linked immunosorbent assay that detects epitope specific + description: + An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. meaning: OBI:0002672 OBI:0002675: title: massively parallel reporter assay - description: An assay in which multiplexing the construction and interrogation + description: + An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. meaning: OBI:0002675 OBI:0002676: - title: in vivo assay measuring a T cell epitope specific response after adoptive + title: + in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that is - performed after adoptive transfer of epitope specfic T cells. + description: + An efficacy of T cell epitope intervention experiment that is + performed after adoptive transfer of epitope specific T cells. meaning: OBI:0002676 OBI:0002677: - title: in vivo assay measuring a B cell epitope specific response after adoptive + title: + in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells - description: An efficacy of B cell epitope intervention experiment that is + description: + An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0002677 OBI:0002678: - title: in vivo assay measuring T cell epitope specific disease exacerbation + title: + in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells - description: An efficacy of T cell epitope intervention experiment that uses + description: + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer - of epitope specfic T cells. + of epitope specific T cells. meaning: OBI:0002678 OBI:0002680: title: pseudovirus entry assay - description: An assay that measures the entry in target cells of reporter + description: + An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. meaning: OBI:0002680 OBI:0002692: title: polymerase chain reaction assay - description: An assay that uses polymerase chain reaction technique to amplify + description: + An assay that uses polymerase chain reaction technique to amplify DNA. meaning: OBI:0002692 OBI:0002693: title: restriction fragment length polymorphism assay - description: An assay that uses digestion of DNA with specific restriction + description: + An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. meaning: OBI:0002693 OBI:0002694: title: DNA fingerprinting assay - description: An assay to identify a specific individual organism from a DNA + description: + An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. meaning: OBI:0002694 OBI:0002695: title: insecticide resistance assay - description: An assay that aims to detect the presence and/or frequency of + description: + An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. meaning: OBI:0002695 OBI:0002696: title: insecticide resistance by monitoring known mutations assay - description: An insecticide resistance assay that detects, in a population, + description: + An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. meaning: OBI:0002696 OBI:0002697: title: insecticide resistance by detecting enzyme activity assay - description: An insecticide resistance assay that is based on determination + description: + An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. meaning: OBI:0002697 OBI:0002698: title: insecticide resistance bioassay - description: An insecticide resistance assay that is typically conducted to + description: + An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. meaning: OBI:0002698 OBI:0002699: title: insecticide resistance by detecting alpha esterase activity assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. meaning: OBI:0002699 OBI:0002700: title: insecticide resistance by detecting beta esterase activity assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. meaning: OBI:0002700 OBI:0002701: title: insecticide resistance by detecting acetylcholinesterase activity assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. meaning: OBI:0002701 OBI:0002702: - title: insecticide resistance by detecting glutathione S-transferase activity + title: + insecticide resistance by detecting glutathione S-transferase activity assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). meaning: OBI:0002702 OBI:0002703: - title: insecticide resistance by detecting carboxylic ester hydrolase activity + title: + insecticide resistance by detecting carboxylic ester hydrolase activity assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. meaning: OBI:0002703 OBI:0002704: title: insecticide resistance by detecting mixed-function oxidase assay - description: An insecticide resistance by detecting enzyme activity assay + description: + An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. meaning: OBI:0002704 OBI:0002705: @@ -4873,75 +6007,90 @@ enums: meaning: OBI:0002705 OBI:0002706: title: topical application insecticide resistance bioassay - description: An insecticide resistance bioassay by adding insecticide directly + description: + An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. meaning: OBI:0002706 OBI:0002707: title: direct insecticide resistance diagnostic assay - description: A direct insecticide resistance assay that at preset insecticide + description: + A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. meaning: OBI:0002707 OBI:0002708: title: insecticide resistance dose response assay - description: A direct insecticide resistance assay in which an insect population + description: + A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. meaning: OBI:0002708 OBI:0002709: title: insecticide resistance time response assay - description: A direct insecticide resistance assay to determine resistance + description: + A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. meaning: OBI:0002709 OBI:0002710: title: Centre for Disease Control and Prevention bottle bioassay - description: A direct insecticide resistance diagnostic assay performs in + description: + A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. meaning: OBI:0002710 OBI:0002711: title: WHO cone kit diagnostic assay - description: A direct insecticide resistance diagnostic assay uses WHO cone + description: + A direct insecticide resistance diagnostic assay uses WHO cone kit. meaning: OBI:0002711 OBI:0002712: title: WHO paper kit diagnostic assay - description: A direct insecticide resistance diagnostic assay uses WHO paper + description: + A direct insecticide resistance diagnostic assay uses WHO paper kit. meaning: OBI:0002712 OBI:0002713: title: WHO larvicide diagnostic assay - description: A direct insecticide resistance diagnostic assay tests survival + description: + A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. meaning: OBI:0002713 OBI:0002714: title: insecticide resistance dose response by bottle assay - description: An insecticide resistance dose response assay that performs in + description: + An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. meaning: OBI:0002714 OBI:0002715: title: insecticide resistance dose response by survival of larvae assay - description: An insecticide resistance dose response assay that tests survival + description: + An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. meaning: OBI:0002715 OBI:0002716: title: insecticide resistance dose response by WHO paper kit assay - description: An insecticide resistance dose response assay using WHO paper + description: + An insecticide resistance dose response assay using WHO paper kit. meaning: OBI:0002716 OBI:0002717: title: insecticide resistance time response by bottle assay - description: An insecticide resistance time response assay that is performed + description: + An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. meaning: OBI:0002717 OBI:0002718: title: insecticide resistance time response by WHO paper kit assay - description: An insecticide resistance time response assay using WHO paper + description: + An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. meaning: OBI:0002718 OBI:0002719: - title: insecticide resistance by amplification refractory mutation system + title: + insecticide resistance by amplification refractory mutation system assay - description: An insecticide resistance by monitoring known mutations assay + description: + An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of @@ -4951,50 +6100,60 @@ enums: human genomic DNA for one or more mutations. meaning: OBI:0002719 OBI:0002720: - title: insecticide resistance by primer introduced restriction analysis PCR + title: + insecticide resistance by primer introduced restriction analysis PCR assay - description: An insecticide resistance by monitoring known mutations assay + description: + An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. meaning: OBI:0002720 OBI:0002721: title: insecticide resistance by nested polymerase chain reaction assay - description: An insecticide resistance by monitoring known mutations assay + description: + An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. meaning: OBI:0002721 OBI:0002722: title: insecticide resistance by ligase detection reaction assay - description: An insecticide resistance assay that is based on monitoring known + description: + An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. meaning: OBI:0002722 OBI:0002723: - title: insecticide resistance by ligase detection reaction-fluorescent microsphere + title: + insecticide resistance by ligase detection reaction-fluorescent microsphere assay - description: An insecticide resistance by ligase detection reaction assay + description: + An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. meaning: OBI:0002723 OBI:0002724: title: insecticide resistance by PCR amplification of specific alleles assay - description: An insecticide resistance assay that is based on monitoring known + description: + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. meaning: OBI:0002724 OBI:0002725: title: insecticide resistance by fluorogenic PCR assay - description: An insecticide resistance assay that is based on monitoring known + description: + An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. meaning: OBI:0002725 OBI:0002726: title: insecticide resistance by PCR-RFLP assay - description: An insecticide resistance by monitoring known mutations assay + description: + An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. meaning: OBI:0002726 OBI:0002727: title: insecticide resistance by short interspersed elements PCR assay - description: An insecticide resistance assay that is based on monitoring known + description: + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). meaning: OBI:0002727 OBI:0002728: @@ -5003,34 +6162,40 @@ enums: meaning: OBI:0002728 OBI:0002729: title: VectorTest assay - description: A pathogen detection assay that identifies the presence or absence + description: + A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. meaning: OBI:0002729 OBI:0002730: title: pathogen detection by Rapid Analyte Measurement Platform assay - description: A pathogen detection assay that is based on Rapid Analyte Measurement + description: + A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. meaning: OBI:0002730 OBI:0002731: title: pathogen detection by loop-mediated isothermal amplification assay - description: A pathogen detection assay that is based on loop-mediated isothermal + description: + A pathogen detection assay that is based on loop-mediated isothermal amplification. meaning: OBI:0002731 OBI:0002732: title: blood meal assay - description: An assay that analyzes the specimen taken from blood meal fed + description: + An assay that analyzes the specimen taken from blood meal fed organism, such as insect. meaning: OBI:0002732 OBI:0002733: title: blood meal by counter current immunoelectrophoresis assay - description: A blood meal assay that uses a counter current immunoelectrophoresis + description: + A blood meal assay that uses a counter current immunoelectrophoresis technique. meaning: OBI:0002733 OBI:0002734: title: DNA based blood meal finger printing assay - description: A DNA fingerprinting assay that uses DNA extracted from blood + description: + A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. meaning: OBI:0002734 OBI:0002735: @@ -5039,25 +6204,29 @@ enums: meaning: OBI:0002735 OBI:0002736: title: organism detection by cross mating assay - description: An organism detection assay that is based on genetic crossings + description: + An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. meaning: OBI:0002736 OBI:0002737: title: organism detection by cytological chromosome examination assay - description: An organism detection assay that is based on analysis of polytene + description: + An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. meaning: OBI:0002737 OBI:0002738: title: organism detection by isoenzyme electrophoresis assay - description: An organism detection assay that is based on electrophoresis + description: + An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. meaning: OBI:0002738 OBI:0002739: title: organism detection by morphological examination assay - description: An organism detection assay that is based on examination of morphology + description: + An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen. meaning: OBI:0002739 OBI:0002740: @@ -5070,43 +6239,50 @@ enums: meaning: OBI:0002741 OBI:0002742: title: organism detection by salinity tolerance assay - description: An organism detection assay of mosquito species that is on the + description: + An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. meaning: OBI:0002742 OBI:0002753: title: PRO-cap - description: Precision nuclear run-on and sequencing to detect Pol II initiation + description: + Precision nuclear run-on and sequencing to detect Pol II initiation sites meaning: OBI:0002753 OBI:0002759: title: ribosomal RNA-depleted RNA sequencing assay - description: A transcription profiling by RNA sequencing assay in which highly + description: + A transcription profiling by RNA sequencing assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. meaning: OBI:0002759 OBI:0002760: title: metatranscriptome profiling assay - description: A transcription profiling by RNA sequencing assay that determines + description: + A transcription profiling by RNA sequencing assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. meaning: OBI:0002760 OBI:0002761: title: lipid profiling assay - description: An analyte assay assay that detects and identifies lipids resulting + description: + An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. meaning: OBI:0002761 OBI:0002762: title: single-nucleus ATAC-seq - description: An ATAC-seq assay in which single nuclei are isolated from frozen + description: + An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. meaning: OBI:0002762 OBI:0002763: title: 16s ribosomal gene sequencing assay - description: An amplicon sequencing assay in which the amplicon is derived + description: + An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or @@ -5114,150 +6290,177 @@ enums: meaning: OBI:0002763 OBI:0002764: title: single-cell ATAC-seq - description: An ATAC assay designed to robustly map the accessible genome + description: + An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. meaning: OBI:0002764 OBI:0002765: title: microbiome protein expression profiling assay - description: A protein expression profiling assay of microbial proteins extracted + description: + A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. meaning: OBI:0002765 OBI:0002766: title: cytokine assay - description: An analyte assay to study presence, concentration, or amount + description: + An analyte assay to study presence, concentration, or amount of cytokines. meaning: OBI:0002766 OBI:0002767: title: amplicon sequencing assay - description: A sequencing assay in which a DNA or RNA input molecule is amplified + description: + A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. meaning: OBI:0002767 OBI:0002768: title: whole virome sequencing assay - description: A whole metagenome sequencing assay that intends to provide information + description: + A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. meaning: OBI:0002768 OBI:0002773: title: single-value binding of antibody with reporter to antigen assay - description: An assay that detects the linking of antigens and antibodies + description: + An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest meaning: OBI:0002773 OBI:0002946: title: fluorescence imaging-based apoptosis assay - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. meaning: OBI:0002946 OBI:0002947: title: fluorescence imaging-based cell proliferation assay - description: A type of cell proliferation assay in which fluorescent dyes + description: + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. meaning: OBI:0002947 OBI:0002948: title: fluorescence imaging-based cell cycle state assay - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. meaning: OBI:0002948 OBI:0002949: title: fluorescence imaging-based cell viability assay - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. meaning: OBI:0002949 OBI:0002950: title: fluorescence imaging-based drug synergy assay - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. meaning: OBI:0002950 OBI:0002951: title: fluorescence imaging-based cell morphology assay - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. meaning: OBI:0002951 OBI:0002952: title: fluorescence imaging multiplex cytological profiling - description: A type of cytometry assay in which fluorescent dyes are used + description: + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. meaning: OBI:0002952 OBI:0002953: title: protein state assay - description: A type of assay that measures the quantity and/or identity of + description: + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. meaning: OBI:0002953 OBI:0002954: title: fluorescence imaging-based protein phosphorylation state assay - description: A type of protein state assay that employs high-throughput microscopy + description: + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. meaning: OBI:0002954 OBI:0002955: title: mass spectrometry-based protein state assay - description: A type of protein state assay that employs mass spectrometry + description: + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. meaning: OBI:0002955 OBI:0002956: - title: targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state + title: + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay - description: A type of mass spectrometry protein state assay that measures + description: + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. meaning: OBI:0002956 OBI:0002957: title: reverse phase protein array profiling assay - description: A type of protein state assay where tissue or cell samples are + description: + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. meaning: OBI:0002957 OBI:0002958: title: SWATH-MS protein profiling assay - description: A type of mass spectrometry assay using a data-independent acquisition + description: + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. meaning: OBI:0002958 OBI:0002959: title: tandem mass tag mass spectrometry assay - description: A type of tandem mass spectrometry where isotopomer labels are + description: + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. meaning: OBI:0002959 OBI:0002960: title: fluorescence imaging-based reporter gene assay - description: A type of reporter gene assay that employs fluorescence imaging + description: + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. meaning: OBI:0002960 OBI:0002961: title: global chromatin profiling by mass spectrometry assay - description: A type of epigenetic modification assay that employs targeted + description: + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. meaning: OBI:0002961 OBI:0002962: title: kinase inhibitor assay - description: A type of assay that identifies compounds that inhibit the activity + description: + A type of assay that identifies compounds that inhibit the activity of kinases. meaning: OBI:0002962 OBI:0002963: title: KINOMEscan assay - description: A type of proprietary kinase inhibitor assay that and employs + description: + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. meaning: OBI:0002963 OBI:0002964: - title: KiNativ assay - description: A type of proprietary in situ kinase inhibitor assay that employs + title: KiNative assay + description: + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. meaning: OBI:0002964 OBI:0002965: title: landmark transcript profiling assay - description: A type of transcription profiling assay in which a set of landmark + description: + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres @@ -5265,7 +6468,8 @@ enums: meaning: OBI:0002965 OBI:0002966: title: microenvironment microarray assay - description: A type of cytometry assay where cells are incubated for three + description: + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features @@ -5273,60 +6477,70 @@ enums: meaning: OBI:0002966 OBI:0002967: title: microwestern meso-scale quantitative western blot assay - description: A western blot assay that provides a high-throughput, sensitive, + description: + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. meaning: OBI:0002967 OBI:0002968: title: positive/negative ion switching metabolite profiling assay - description: A type of metabolic profiling assay which employs a hybrid dual + description: + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. meaning: OBI:0002968 OBI:0002969: title: cyclic immunofluoroescence assay - description: A type of microscopy assay resulting in highly multiplexed immunofluorescence + description: + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. meaning: OBI:0002969 OBI:0002970: title: multiplex bead-based protein state immunoassay - description: A type of protein state assay in which antibodies attached to + description: + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. meaning: OBI:0002970 OBI:0002984: title: capture Hi-C assay - description: A Hi-C assay in which a selection step is performed on ligated + description: + A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. meaning: OBI:0002984 OBI:0002985: title: magnetic resonance imaging assay - description: An imaging assay in which nuclear magnetic resonance is used + description: + An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. meaning: OBI:0002985 OBI:0002986: title: computed tomography imaging assay - description: An imaging assay that uses a series of X-ray images to produce + description: + An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. meaning: OBI:0002986 OBI:0002987: title: positron emission tomography imaging assay - description: An imaging assay in which positron-emitting radionuclides are + description: + An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. meaning: OBI:0002987 OBI:0002990: title: T cell receptor repertoire sequencing assay - description: A sequencing assay that determines the sequences of DNA or RNA + description: + A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. meaning: OBI:0002990 OBI:0002991: title: B cell receptor repertoire sequencing assay - description: A sequencing assay that determines the sequence of a DNA or RNA + description: + A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. meaning: OBI:0002991 @@ -5360,12 +6574,14 @@ enums: meaning: OBI:0003015 OBI:0003016: title: myelocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of myelocytes meaning: OBI:0003016 OBI:0003017: title: metamyelocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of metamyelocytes meaning: OBI:0003017 OBI:0003018: @@ -5374,52 +6590,62 @@ enums: meaning: OBI:0003018 OBI:0003019: title: promyelocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of promyelocytes meaning: OBI:0003019 OBI:0003021: title: basophil assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of basophils meaning: OBI:0003021 OBI:0003022: title: neutrophil assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of neutrophils meaning: OBI:0003022 OBI:0003023: title: eosinophil assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of eosinophils meaning: OBI:0003023 OBI:0003024: title: lymphocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of lymphocytes meaning: OBI:0003024 OBI:0003025: title: monocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of monocytes meaning: OBI:0003025 OBI:0003026: title: reticulocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of reticulocytes meaning: OBI:0003026 OBI:0003027: title: macrophage assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of macrophages meaning: OBI:0003027 OBI:0003028: title: platelet assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of platelets meaning: OBI:0003028 OBI:0003031: title: fluorogenic PCR assay - description: A polymerase chain reaction assay that uses target specific probes + description: + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. meaning: OBI:0003031 OBI:0003032: @@ -5428,13 +6654,15 @@ enums: meaning: OBI:0003032 OBI:0003033: title: cleavage under targets and release using nuclease assay - description: A type of DNA sequencing assay employing in situ chromatin profiling + description: + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. meaning: OBI:0003033 OBI:0003034: title: cleavage under targets and tagmentation - description: A type of DNA sequencing assay employing in situ chromatin profiling + description: + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted @@ -5442,7 +6670,8 @@ enums: meaning: OBI:0003034 OBI:0003035: title: coma severity assay - description: A physical examination of an organism that has the objective + description: + A physical examination of an organism that has the objective to determine the severity of coma in a patient. meaning: OBI:0003035 OBI:0003036: @@ -5451,7 +6680,8 @@ enums: meaning: OBI:0003036 OBI:0003037: title: malaria rapid diagnosis assay - description: An assay that is quick and easy in the diagnosis of malaria by + description: + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. meaning: OBI:0003037 OBI:0003038: @@ -5460,7 +6690,8 @@ enums: meaning: OBI:0003038 OBI:0003039: title: feces microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a feces specimen. meaning: OBI:0003039 OBI:0003040: @@ -5469,13 +6700,15 @@ enums: meaning: OBI:0003040 OBI:0003041: title: falcivax rapid diagnostic test - description: A parasite detection assay that can quickly establish the diagnosis + description: + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. meaning: OBI:0003041 OBI:0003042: title: optimal-IT rapid diagnostic test - description: A parasite detection assay that is rapid, sensitive, and able + description: + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. meaning: OBI:0003042 OBI:0003043: @@ -5484,7 +6717,8 @@ enums: meaning: OBI:0003043 OBI:0003044: title: parasite species identification by PCR assay - description: A parasite detection by PCR assay that identifies the species + description: + A parasite detection by PCR assay that identifies the species of parasite. meaning: OBI:0003044 OBI:0003045: @@ -5497,64 +6731,75 @@ enums: meaning: OBI:0003080 OBI:0003087: title: autofluorescence assay - description: A fluorescence detection assay in which the light that is naturally + description: + A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. meaning: OBI:0003087 OBI:0003088: title: autofluorescence microscopy assay - description: An autofluorescence assay in which the light that is naturally + description: + An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. meaning: OBI:0003088 OBI:0003089: title: bulk assay for transposase-accessible chromatin using sequencing - description: An assay for transposase-accessible chromatin using sequencing + description: + An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. meaning: OBI:0003089 OBI:0003090: title: bulk RNA-seq assay - description: A transcription profiling by RNA sequencing assay in which the + description: + A transcription profiling by RNA sequencing assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. meaning: OBI:0003090 OBI:0003091: title: multiplexed fluorescent antibody imaging assay - description: An imaging assay in which multiple cycles consisting of fluorescent + description: + An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. meaning: OBI:0003091 OBI:0003092: title: Cell DIVE multiplexed imaging assay - description: A multiplexed fluorescent antibody imaging assay that involves + description: + A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. meaning: OBI:0003092 OBI:0003093: title: co-detection by indexing assay - description: A multiplexed fluorescent antibody imaging assay that involves + description: + A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. meaning: OBI:0003093 OBI:0003094: title: fluorescence in-situ hybridization assay - description: An in-situ hybridization assay in which fluorescently labeled + description: + An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. meaning: OBI:0003094 OBI:0003095: - title: decoding amplified targeted transcripts with fluorescence in situ hybridization + title: + decoding amplified targeted transcripts with fluorescence in situ hybridization assay - description: A fluorescence in-situ hybridization assay which involves multiplex + description: + A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. meaning: OBI:0003095 OBI:0003096: title: imaging mass cytometry assay - description: A cytometry time of flight assay in which molecules of interest + description: + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time @@ -5562,22 +6807,26 @@ enums: meaning: OBI:0003096 OBI:0003097: title: liquid chromatography mass spectrometry assay - description: A mass spectrometry assay where a sample mixture is first separated + description: + A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. meaning: OBI:0003097 OBI:0003098: title: lightsheet fluorescence microscopy assay - description: A fluorescence microscopy that involves capturing of photons + description: + A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. meaning: OBI:0003098 OBI:0003099: - title: matrix assisted laser desorption ionization imaging mass spectrometry + title: + matrix assisted laser desorption ionization imaging mass spectrometry assay - description: A mass spectrometry assay that involves collection of spatially + description: + A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser @@ -5587,7 +6836,8 @@ enums: meaning: OBI:0003099 OBI:0003100: title: multiplexed ion beam imaging assay - description: A cytometry time of flight assay in which molecules of interest + description: + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary @@ -5595,7 +6845,8 @@ enums: meaning: OBI:0003100 OBI:0003101: title: nanospray desorption electrospray ionization assay - description: A mass spectrometry assay that analyzes organic and biological + description: + A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports @@ -5605,7 +6856,8 @@ enums: meaning: OBI:0003101 OBI:0003102: title: nanodroplet processing in one pot for trace samples assay - description: A protein expression profiling assay in which proteomics sample + description: + A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the @@ -5613,14 +6865,17 @@ enums: meaning: OBI:0003102 OBI:0003103: title: periodic acid-Schiff staining assay - description: A histological assay which is used on tissue samples to demonstrate + description: + A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. meaning: OBI:0003103 OBI:0003104: - title: single cell combinatorial indexing assay for transposase-accessessable + title: + single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing - description: An assay for transposase-accessible chromatin that uses sequencing + description: + An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells @@ -5628,46 +6883,54 @@ enums: meaning: OBI:0003104 OBI:0003105: title: single-cell combinatorial indexing RNA sequencing assay - description: A single-cell transcription profiling by RNA sequencing assay + description: + A single-cell transcription profiling by RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. meaning: OBI:0003105 OBI:0003106: title: sequential fluorescence in-situ hybridization assay - description: A fluorescence in-situ hybridization assay that involves ultra-resolution - imaging of cell activity by targetting thousands of single molecules with + description: + A fluorescence in-situ hybridization assay that involves ultra-resolution + imaging of cell activity by targeting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. meaning: OBI:0003106 OBI:0003107: title: slide-seq assay - description: A transcription profiling by RNA sequencing assay that involves + description: + A transcription profiling by RNA sequencing assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. meaning: OBI:0003107 OBI:0003108: - title: single-nucleus chromatin accessibility and mRNA expression sequencing + title: + single-nucleus chromatin accessibility and mRNA expression sequencing assay - description: An assay that involves joint profiling of accessible chromatin + description: + An assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. meaning: OBI:0003108 OBI:0003110: title: gas chromatography mass spectrometry assay - description: A mass spectrometry assay combining mass spectrometry and gas + description: + A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. meaning: OBI:0003110 OBI:0003111: - title: SOMAscan assay - description: An analyte assay that uses aptamers to detect protein analytes + title: SOMEAscan assay + description: + An analyte assay that uses aptamers to detect protein analytes in serum. meaning: OBI:0003111 OBI:0003112: title: Olink assay - description: A proximity extension assay that uses quantitative polymerase + description: + A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) @@ -5678,293 +6941,349 @@ enums: meaning: OBI:0003112 OBI:0003113: title: proximity extension assay - description: An analyte assay that uses quantitative polymerase chain reaction + description: + An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. meaning: OBI:0003113 OBI:0003115: title: antigen detection by cytometric bead array assay - description: A cytometric bead array assay in which a series of beads are + description: + A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. meaning: OBI:0003115 OBI:0003116: title: antibody detection by cytometric bead array assay - description: A cytometric bead array assay that detects antigen-specific antibodies. + description: + A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. meaning: OBI:0003116 OBI:0003117: title: 3D molecular structure determination assay - description: An assay that determines the 3-dimensional configuration of a + description: + An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. meaning: OBI:0003117 OBI:0003118: title: electron-microscopy 3D molecular structure determination assay - description: A 3D molecular structure determination assay that uses electron + description: + A 3D molecular structure determination assay that uses electron microscopy imaging. meaning: OBI:0003118 OBI:0003122: title: 3D cell structure determination assay - description: A 3D structure determination assay that determines the 3-dimensional + description: + A 3D structure determination assay that determines the 3-dimensional configuration of a cell. meaning: OBI:0003122 OBI:0003123: title: 3D neural cell structure determination assay - description: A 3D cell structure determination assay that determines the 3-dimensional + description: + A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. meaning: OBI:0003123 OBI:0003124: title: neuron morphology assay - description: A 3D neural cell structure determination assay that determines + description: + A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. meaning: OBI:0003124 OBI:0003125: title: mosaicism with repeat frameshift genetic sparse labeling - description: A 3D neural cell structure determination assay where sparse and + description: + A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. meaning: OBI:0003125 OBI:0003126: title: neuron morphology reconstruction assay - description: A neuron morphology assay where the morphology or structure of + description: + A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). meaning: OBI:0003126 OBI:0003127: title: B cell epitope assay - description: An immune epitope assay that characterizes the structrue of an + description: + An immune epitope assay that characterizes the structure of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. meaning: OBI:0003127 OBI:0003128: title: T cell epitope assay - description: An immune epitope assay that characterizes the structrue of an + description: + An immune epitope assay that characterizes the structure of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. meaning: OBI:0003128 OBI:0003145: title: assay measuring quantitative binding of a MHC:ligand complex - description: An assay that detects the binding of a MHC molecule with a ligand, + description: + An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. meaning: OBI:0003145 OBI:0003146: title: assay measuring quantitative binding of an antigen:antibody complex - description: An assay that detects the binding of an antigen with an antibody, + description: + An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. meaning: OBI:0003146 OBI:0003147: title: assay measuring quantitative binding of an epitope:MHC:TCR complex - description: An assay that detects the binding of a MHC:epitope complex with + description: + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output. meaning: OBI:0003147 OBI:0003148: title: albumin concentration assay - description: An albumin assay that measures the concentration of albumin in + description: + An albumin assay that measures the concentration of albumin in a specimen. meaning: OBI:0003148 OBI:0003149: title: basophil percentage assay - description: A basophil assay that measures the percentage of basophils in + description: + A basophil assay that measures the percentage of basophils in a specimen. meaning: OBI:0003149 OBI:0003150: title: calcium cation concentration assay - description: A calcium cation assay that measures the concentration of calcium + description: + A calcium cation assay that measures the concentration of calcium cations in a specimen. meaning: OBI:0003150 OBI:0003151: title: chloride concentration assay - description: A chloride assay that measures the concentration of chloride + description: + A chloride assay that measures the concentration of chloride in a specimen. meaning: OBI:0003151 OBI:0003152: title: cholesterol concentration assay - description: A cholesterol assay that measures the concentration of cholesterol + description: + A cholesterol assay that measures the concentration of cholesterol in a specimen. meaning: OBI:0003152 OBI:0003153: title: creatinine concentration assay - description: A creatinine assay that measures the concentration of creatinine + description: + A creatinine assay that measures the concentration of creatinine in a specimen. meaning: OBI:0003153 OBI:0003154: title: eosinophil percentage assay - description: An eosinophil assay that measures the percentage of eosinophils + description: + An eosinophil assay that measures the percentage of eosinophils in a specimen. meaning: OBI:0003154 OBI:0003155: title: globulin concentration assay - description: A globulin assay that measures the concentration of globulin + description: + A globulin assay that measures the concentration of globulin in a specimen. meaning: OBI:0003155 OBI:0003156: title: hemoglobin concentration assay - description: A hemoglobin assay that measures the amount of hemoglobin in + description: + A hemoglobin assay that measures the amount of hemoglobin in a specimen. meaning: OBI:0003156 OBI:0003157: title: high-density lipoprotein cholesterol concentration assay - description: A high-density lipoprotein cholesterol assay that measures the + description: + A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. meaning: OBI:0003157 OBI:0003158: title: iron concentration assay - description: An iron assay that measures the concentration of iron cation + description: + An iron assay that measures the concentration of iron cation in a specimen. meaning: OBI:0003158 OBI:0003159: title: low-density lipoprotein cholesterol concentration assay - description: A low-density lipoprotein cholesterol assay that measures the + description: + A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. meaning: OBI:0003159 OBI:0003160: title: lymphocyte percentage assay - description: A lymphocyte assay that measures the percentage of lymphocytes + description: + A lymphocyte assay that measures the percentage of lymphocytes in a specimen. meaning: OBI:0003160 OBI:0003161: title: metamyelocyte count assay - description: A metamyelocyte assay that measures the number of metamyelocytes + description: + A metamyelocyte assay that measures the number of metamyelocytes in a specimen. meaning: OBI:0003161 OBI:0003162: title: metamyelocyte percentage assay - description: A metamyelocyte assay that measures the percentage of metamyelocytes + description: + A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. meaning: OBI:0003162 OBI:0003163: title: methemoglobin percentage assay - description: A methemoglobin assay that measures the percentage of methemoglobin + description: + A methemoglobin assay that measures the percentage of methemoglobin in a specimen. meaning: OBI:0003163 OBI:0003164: title: monocyte percentage assay - description: A monocyte assay that measures the percentage of monocytes in + description: + A monocyte assay that measures the percentage of monocytes in a specimen. meaning: OBI:0003164 OBI:0003165: title: myelocyte count assay - description: A myelocyte assay that measures the number of myelocytes in a + description: + A myelocyte assay that measures the number of myelocytes in a specimen. meaning: OBI:0003165 OBI:0003166: title: neutrophil percentage assay - description: A neutrophil assay that measures the percentage of neutrophils + description: + A neutrophil assay that measures the percentage of neutrophils in a specimen. meaning: OBI:0003166 OBI:0003167: title: phosphate ion concentration assay - description: A phosphate ion assay that measures the concentration of phosphate + description: + A phosphate ion assay that measures the concentration of phosphate ions in a specimen. meaning: OBI:0003167 OBI:0003168: title: potassium(1+) concentration assay - description: A potassium(1+) assay that measures the concentration of potassium(1+) + description: + A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. meaning: OBI:0003168 OBI:0003170: title: reticulocyte percentage assay - description: A reticulocyte assay that measures the percentage of reticulocytes + description: + A reticulocyte assay that measures the percentage of reticulocytes in a specimen. meaning: OBI:0003170 OBI:0003171: title: sodium(1+) concentration assay - description: A sodium(1+) assay that measures the concentration of sodium(1+) + description: + A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. meaning: OBI:0003171 OBI:0003172: title: thyroid stimulating hormone concentration assay - description: A thyroid stimulating hormone assay that measures the concentration + description: + A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. meaning: OBI:0003172 OBI:0003173: title: triglyceride concentration assay - description: A triglyceride assay that measures the concentration of triglycerides + description: + A triglyceride assay that measures the concentration of triglycerides in a specimen. meaning: OBI:0003173 OBI:0003174: title: 3,3',5'-triiodothyronine concentration assay - description: A 3,3',5'-triiodothyronine assay that measures the concentration + description: + A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. meaning: OBI:0003174 OBI:0003175: title: fibrinogen concentration assay - description: A fibrinogen assay that measures the concentration of fibrinogen + description: + A fibrinogen assay that measures the concentration of fibrinogen in a specimen. meaning: OBI:0003175 OBI:0003176: title: free thyroxine concentration assay - description: A thyroxine assay that measures the concentration of free thyroxine + description: + A thyroxine assay that measures the concentration of free thyroxine in a specimen. meaning: OBI:0003176 OBI:0003177: title: total thyroxine concentration assay - description: A thyroxine assay that measures the concentration of total thyroxine + description: + A thyroxine assay that measures the concentration of total thyroxine in a specimen. meaning: OBI:0003177 OBI:0003180: title: direct bilirubin concentration assay - description: A bilirubin IXalpha assay that measures the concentration of + description: + A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. meaning: OBI:0003180 OBI:0003181: title: indirect bilirubin concentration assay - description: A bilirubin IXalpha assay that measures the concentration of + description: + A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. meaning: OBI:0003181 OBI:0003182: title: total bilirubin concentration assay - description: A bilirubin IXalpha assay that measures the concentration of + description: + A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. meaning: OBI:0003182 OBI:0003183: title: mean cell hemoglobin assay - description: A hemoglobin assay that measures the average concentration of + description: + A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. meaning: OBI:0003183 OBI:0003184: title: mean cell hemoglobin concentration assay - description: A hemoglobin assay that measures the concentration of hemoglobin + description: + A hemoglobin assay that measures the concentration of hemoglobin in a specimen. meaning: OBI:0003184 OBI:0003185: title: mean platelet volume assay - description: A platelet assay that measures the average volume of platelets + description: + A platelet assay that measures the average volume of platelets in a specimen. meaning: OBI:0003185 OBI:0003186: title: immature neutrophil count assay - description: A neutrophil assay that measures the number of immature neutrophils + description: + A neutrophil assay that measures the number of immature neutrophils in a specimen. meaning: OBI:0003186 OBI:0003187: title: immature neutrophil percentage assay - description: An neutrophil assay that measures the percentage of immature + description: + An neutrophil assay that measures the percentage of immature neutrophils in a specimen. meaning: OBI:0003187 OBI:0003188: title: nucleated erythrocyte percentage assay - description: An erythrocyte assay that measures the percentage of nucleated + description: + An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. meaning: OBI:0003188 OBI:0003189: title: mean cell volume assay - description: An erythrocyte assay that measures the average volume of erythrocytes + description: + An erythrocyte assay that measures the average volume of erythrocytes in a specimen. meaning: OBI:0003189 OBI:0003190: title: erythrocyte assay - description: A cytometry assay that measures the abundance and/or characteristics + description: + A cytometry assay that measures the abundance and/or characteristics of erythrocytes. meaning: OBI:0003190 OBI:0003191: title: manual hematocrit assay - description: A hematocrit assay that measures the percentage of erythrocytes + description: + A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. meaning: OBI:0003191 OBI:0003192: @@ -5973,7 +7292,8 @@ enums: meaning: OBI:0003192 OBI:0003193: title: adiponectin concentration assay - description: An adiponectin assay that measures the concentration of adiponectin + description: + An adiponectin assay that measures the concentration of adiponectin in a specimen. meaning: OBI:0003193 OBI:0003194: @@ -5982,7 +7302,8 @@ enums: meaning: OBI:0003194 OBI:0003195: title: creatine concentration assay - description: A creatine assay that measures the concentration of creatine + description: + A creatine assay that measures the concentration of creatine in a specimen. meaning: OBI:0003195 OBI:0003196: @@ -5991,7 +7312,8 @@ enums: meaning: OBI:0003196 OBI:0003197: title: estradiol concentration assay - description: An estradiol assay that measures the concentration of estradiol + description: + An estradiol assay that measures the concentration of estradiol in a specimen. meaning: OBI:0003197 OBI:0003202: @@ -6000,7 +7322,8 @@ enums: meaning: OBI:0003202 OBI:0003203: title: leptin concentration assay - description: An leptin assay that measures the concentration of leptin in + description: + An leptin assay that measures the concentration of leptin in a specimen. meaning: OBI:0003203 OBI:0003204: @@ -6009,17 +7332,20 @@ enums: meaning: OBI:0003204 OBI:0003205: title: high-density lipoprotein concentration assay - description: A lipoprotein concentration assay that measures the concentration + description: + A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. meaning: OBI:0003205 OBI:0003206: title: low-density lipoprotein concentration assay - description: A lipoprotein concentration assay that measures the concentration + description: + A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. meaning: OBI:0003206 OBI:0003207: title: very-low-density lipoprotein concentration assay - description: A lipoprotein concentration assay that measures the concentration + description: + A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. meaning: OBI:0003207 OBI:0003208: @@ -6028,7 +7354,8 @@ enums: meaning: OBI:0003208 OBI:0003209: title: luteinizing hormone concentration assay - description: A luteinizing hormone assay that measures the concentration of + description: + A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. meaning: OBI:0003209 OBI:0003210: @@ -6037,7 +7364,8 @@ enums: meaning: OBI:0003210 OBI:0003211: title: nitrite concentration assay - description: A nitrite assay that measures the concentration of nitrite in + description: + A nitrite assay that measures the concentration of nitrite in a specimen. meaning: OBI:0003211 OBI:0003212: @@ -6046,7 +7374,8 @@ enums: meaning: OBI:0003212 OBI:0003213: title: phospholipid concentration assay - description: A phospholipid assay that measures the concentration of phospholipids + description: + A phospholipid assay that measures the concentration of phospholipids in a specimen. meaning: OBI:0003213 OBI:0003214: @@ -6055,7 +7384,8 @@ enums: meaning: OBI:0003214 OBI:0003215: title: progesterone concentration assay - description: A progesterone assay that measures the concentration of progesterone + description: + A progesterone assay that measures the concentration of progesterone in a specimen. meaning: OBI:0003215 OBI:0003216: @@ -6064,7 +7394,8 @@ enums: meaning: OBI:0003216 OBI:0003217: title: testosterone concentration assay - description: A testosterone assay that measures the concentration of testosterone + description: + A testosterone assay that measures the concentration of testosterone in a specimen. meaning: OBI:0003217 OBI:0003218: @@ -6073,7 +7404,8 @@ enums: meaning: OBI:0003218 OBI:0003219: title: bile salt concentration assay - description: A bile salt assay that measures the concentration of bile salt + description: + A bile salt assay that measures the concentration of bile salt in a specimen. meaning: OBI:0003219 OBI:0003220: @@ -6082,7 +7414,8 @@ enums: meaning: OBI:0003220 OBI:0003221: title: free fatty acid concentration assay - description: A fatty acid assay that measures the concentration of free fatty + description: + A fatty acid assay that measures the concentration of free fatty acids in a specimen. meaning: OBI:0003221 OBI:0003222: @@ -6091,32 +7424,38 @@ enums: meaning: OBI:0003222 OBI:0003223: title: insulin concentration assay - description: A insulin assay that measures the concentration of insulin in + description: + A insulin assay that measures the concentration of insulin in a specimen. meaning: OBI:0003223 OBI:0003224: title: follicle stimulating hormone assay - description: An analyte assay that measures the abundance of follicle stimulating + description: + An analyte assay that measures the abundance of follicle stimulating hormone meaning: OBI:0003224 OBI:0003225: title: follicle stimulating hormone concentration assay - description: A follicle stimulating hormone assay that measures the concentration + description: + A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. meaning: OBI:0003225 OBI:0003226: title: total lymphocyte count assay - description: A lymphocyte assay that measures the number of lymphocytes and + description: + A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. meaning: OBI:0003226 OBI:0003227: title: total lymphocyte percentage assay - description: A lymphocyte assay that measures the percentage of lymphocytes + description: + A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. meaning: OBI:0003227 OBI:0003228: title: fluorescent immunospot assay - description: A cytometry assay that detects the presence of cells that secrete + description: + A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent @@ -6124,12 +7463,14 @@ enums: meaning: OBI:0003228 OBI:0003229: title: plasma proteomics assay - description: A proteomics profiling assay that detects proteins in a blood + description: + A proteomics profiling assay that detects proteins in a blood plasma specimen. meaning: OBI:0003229 OBI:0003230: title: T cell activation induced marker assay - description: A flow cytometry assay that detects the presence/amount of antigen-specific + description: + A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. @@ -6168,119 +7509,143 @@ enums: meaning: OBI:0003239 OBI:0003240: title: cerebrospinal fluid microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. meaning: OBI:0003240 OBI:0003241: title: endotracheal tube aspirate microbiology assay - description: An organism detection assay that detects microorganisms in an + description: + An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. meaning: OBI:0003241 OBI:0003242: title: induced sputum microbiology assay - description: An organism detection assay that detects microorganisms in an + description: + An organism detection assay that detects microorganisms in an induced sputum specimen. meaning: OBI:0003242 OBI:0003282: title: lung microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a lung specimen. meaning: OBI:0003282 OBI:0003283: title: pleural fluid microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a pleural fluid specimen. meaning: OBI:0003283 OBI:0003284: title: umbilical cord blood microbiology assay - description: An organism detection assay that detects microorganisms in an + description: + An organism detection assay that detects microorganisms in an umbilical cord blood specimen. meaning: OBI:0003284 OBI:0003285: title: nasopharyngeal or oropharyngeal swab microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. meaning: OBI:0003285 OBI:0003286: title: urine microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a urine specimen. meaning: OBI:0003286 OBI:0003287: title: multiplex real time polymerase chain reaction assay - description: A real time polymerase chain reaction assay in which multiple + description: + A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. meaning: OBI:0003287 OBI:0003288: - title: multiplex real time reverse-transcription polymerase chain reaction + title: + multiplex real time reverse-transcription polymerase chain reaction assay - description: A real time reverse-transcription polymerase chain reaction assay + description: + A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. meaning: OBI:0003288 OBI:0003290: title: mosquito membrane feeding assay - description: An assay that evaluates host-to-mosquito transmission of a parasite + description: + An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. meaning: OBI:0003290 OBI:0003292: - title: cytometric bead array assay measuring epitope specific granulysin release + title: + cytometric bead array assay measuring epitope specific granulysin release by T cells - description: A cytometric bead array assay that detects epitope specific granulysin + description: + A cytometric bead array assay that detects epitope specific granulysin release by T cells. meaning: OBI:0003292 OBI:0003293: - title: cytometric bead array assay measuring epitope specific perforin release + title: + cytometric bead array assay measuring epitope specific perforin release by T cells - description: A cytometric bead array assay that detects epitope specific perforin + description: + A cytometric bead array assay that detects epitope specific perforin release by T cells. meaning: OBI:0003293 OBI:0003294: title: modified acid-fast stain microscopy assay - description: A microscopy assay that uses staining to identify acid-fast organisms + description: + A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. meaning: OBI:0003294 OBI:0003296: title: antibodies from lymphocyte secretions assay - description: An assay that evaluates a blood specimen for antibodies currently + description: + An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. meaning: OBI:0003296 OBI:0003297: title: tyramide signal amplification sequencing assay - description: A DNA sequencing assay that uses tyramide signal amplification + description: + A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. meaning: OBI:0003297 OBI:0003298: title: DNA adenine methyltransferase identification assay - description: An assay for identifying DNA binding sites for a protein by fusing + description: + An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. meaning: OBI:0003298 OBI:0003299: title: DamID-seq - description: A DNA adenine methyltransferase identification (DamID) assay + description: + A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. meaning: OBI:0003299 OBI:0003300: title: nucleolus-associated domain sequencing assay - description: A DNA sequencing assay in which nucleoli are isolated and the + description: + A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. meaning: OBI:0003300 OBI:0003301: title: DNase Hi-C assay - description: A Hi-C assay in which DNase I is used for digesting DNA fragments + description: + A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. meaning: OBI:0003301 OBI:0003302: title: micro-C assay - description: A Hi-C assay which uses micrococcal nuclease digestion in place + description: + A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. meaning: OBI:0003302 OBI:0003303: @@ -6297,14 +7662,16 @@ enums: meaning: OBI:0003305 OBI:0003306: title: bulk Hi-C assay - description: A Hi-C assay in which the sample that is sequenced is derived + description: + A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. meaning: OBI:0003306 OBI:0003307: title: multi-contact Hi-C assay - description: A Hi-C assay that assesses interactions between multiple DNA + description: + A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read @@ -6313,14 +7680,16 @@ enums: meaning: OBI:0003307 OBI:0003309: title: transposase-mediated analysis of chromatin looping assay - description: A DNA sequencing assay designed to detect interacting genomic + description: + A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. meaning: OBI:0003309 OBI:0003310: title: split-pool recognition of interactions and tag extension assay - description: A sequencing assay designed to detect multi-way interactions + description: + A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates @@ -6331,18 +7700,21 @@ enums: meaning: OBI:0003310 OBI:0003311: title: DNA split-pool recognition of interactions and tag extension assay - description: A split-pool recognition of interactions and tag extension (SPRITE) + description: + A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. meaning: OBI:0003311 OBI:0003312: title: RNA-DNA split-pool recognition of interactions and tag extension assay - description: A split-pool recognition of interactions and tag extension (SPRITE) + description: + A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. meaning: OBI:0003312 OBI:0003313: title: genome architecture mapping assay - description: A DNA sequencing assay designed to analyze 3D chromatin structure + description: + A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput @@ -6351,70 +7723,86 @@ enums: meaning: OBI:0003313 OBI:0003314: title: mapping RNA-genome interactions assay - description: A nuclear ligation assay for probing RNA-DNA interactions in + description: + A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. meaning: OBI:0003314 OBI:0003315: title: assay measuring epitope specific amphiregulin production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. meaning: OBI:0003315 OBI:0003316: title: ELISA measuring epitope specific amphiregulin production by T cells - description: An enzyme-linked immunosorbent assay that detects amphiregulin + description: + An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. meaning: OBI:0003316 OBI:0003321: title: venous blood microbiology assay - description: A blood microbiology assay that detects a microorganism in a + description: + A blood microbiology assay that detects a microorganism in a venous blood specimen. meaning: OBI:0003321 OBI:0003323: - title: high throughput multiplexed assay measuring binding of a B cell epitope:antibody + title: + high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex - description: A B cell epitope assay that measures the binding of an antibody + description: + A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. meaning: OBI:0003323 OBI:0003324: - title: high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR + title: + high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex - description: A T cell epitope assay that measures the binding of T cell receptor + description: + A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. meaning: OBI:0003324 OBI:0003325: - title: high throughput multiplexed assay measuring binding of a MHC:ligand + title: + high throughput multiplexed assay measuring binding of a MHC:ligand complex - description: A MHC ligand assay that detects the binding of a ligand to an + description: + A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. meaning: OBI:0003325 OBI:0003326: - title: high throughput multiplexed assay measuring MHC ligand processing and + title: + high throughput multiplexed assay measuring MHC ligand processing and presentation - description: A MHC ligand assay that determines what ligands are processed + description: + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. meaning: OBI:0003326 OBI:0003368: title: detection technique - description: An assay (A) that is part of another assay (B), where the target + description: + An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. meaning: OBI:0003368 OBI:0003372: title: assay measuring epitope specific lymphotactin production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. meaning: OBI:0003372 OBI:0003373: title: ELISA measuring epitope specific lymphotactin production by T cells - description: An enzyme-linked immunosorbent assay that detects lymphotactin + description: + An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. meaning: OBI:0003373 OBI:0003375: title: patch-seq assay - description: An assay that combines electrophysiological, transcriptomic, + description: + An assay that combines electrophysiological, transcriptomic, and morphological characterization of individual neurons. In this approach, patch-clamp is used to generate an electrophysiological recording of the neuron, then the neuron's cytoplasm and/or nucleus is collected and processed @@ -6423,19 +7811,22 @@ enums: meaning: OBI:0003375 OBI:0003376: title: droplet-based single-cell RNA sequencing assay - description: 'A single-cell transcription profiling by RNA sequencing assay + description: + "A single-cell transcription profiling by RNA sequencing assay that analyzes mRNA transcripts from droplets of individual cells. The process involves the following steps: (1) prepare a single-cell suspension from a tissue; (2) co-encapsulate each cell with a distinctly barcoded microparticle (bead) in a nanoliter-scale droplet; (3) lyse cells after they have been isolated in droplets; (4) capture a cell’s mRNAs on its companion microparticle, forming STAMPs (single-cell transcriptomes attached to microparticles); - (5) reverse-transcribe, amplify, and sequence.' + (5) reverse-transcribe, amplify, and sequence." meaning: OBI:0003376 OBI:0003377: - title: single-nucleus chromatin accessibility and mRNA expression sequencing + title: + single-nucleus chromatin accessibility and mRNA expression sequencing 2 assay - description: An assay that uses combinatorial indexing to generate a library + description: + An assay that uses combinatorial indexing to generate a library of cDNA and open chromatin gDNA fragments by tagmenting a single nuclei and open chromatin, and encapsulating those in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which @@ -6444,7 +7835,8 @@ enums: meaning: OBI:0003377 OBI:0003378: title: switching mechanism at the 5' end of RNA template sequencing assay - description: A single cell transcription profiling by RNA sequencing assay + description: + A single cell transcription profiling by RNA sequencing assay wherein cells are lysed and their recovered RNA is hybridized to an oligo(dT) that primes a reverse transcription reaction, the outcome of which are cDNA’s that have PCR handles on both ends. The cDNA's are then amplified using @@ -6452,19 +7844,22 @@ enums: meaning: OBI:0003378 OBI:0003379: title: switching mechanism at the 5' end of RNA template sequencing 2 assay - description: A single cell transcription profiling by RNA sequencing assay + description: + A single cell transcription profiling by RNA sequencing assay that is a variation on the switching mechanism at the 5' end of RNA template sequencing assay (SMARTseq) that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. meaning: OBI:0003379 OBI:0003381: title: placental blood microbiology assay - description: A blood microbiology assay that detects microorganisms in a placental + description: + A blood microbiology assay that detects microorganisms in a placental blood specimen. meaning: OBI:0003381 OBI:0003412: title: linked-read sequencing assay - description: A DNA sequencing assay that uses microfluidics to partition and + description: + A DNA sequencing assay that uses microfluidics to partition and barcode high molecular weight DNA such that short reads derived from fragments of the large piece of DNA can be assembled within the context of the high molecular weight piece of DNA they are derived from, facilitating the use @@ -6472,304 +7867,379 @@ enums: meaning: OBI:0003412 OBI:0003418: title: antigen specific antibodies in blood assay - description: An antigen specific antibodies assay that has a blood specimen + description: + An antigen specific antibodies assay that has a blood specimen as evaluant. meaning: OBI:0003418 OBI:0003419: title: antigen specific antibodies in milk assay - description: An antigen specific antibodies assay that has a milk specimen + description: + An antigen specific antibodies assay that has a milk specimen as evaluant. meaning: OBI:0003419 OBI:0003422: title: enzymatic activity level assay - description: An assay in which the level of catalytic activity of an enzyme + description: + An assay in which the level of catalytic activity of an enzyme is determined. meaning: OBI:0003422 OBI:0003423: title: 5'-nucleotidase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. meaning: OBI:0003423 OBI:0003424: title: alanine aminotransferase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. meaning: OBI:0003424 OBI:0003425: title: alkaline phosphatase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. meaning: OBI:0003425 OBI:0003426: title: amylase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of amylase in a sample. meaning: OBI:0003426 OBI:0003427: title: aspartate aminotransferase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. meaning: OBI:0003427 OBI:0003428: title: cholinesterase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of cholinesterase in a sample. meaning: OBI:0003428 OBI:0003429: title: creatine kinase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of creatine kinase in a sample. meaning: OBI:0003429 OBI:0003430: title: gamma-glutamyltransferase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. meaning: OBI:0003430 OBI:0003431: title: glutamate dehydrogenase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. meaning: OBI:0003431 OBI:0003432: title: isocitrate dehydrogenase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. meaning: OBI:0003432 OBI:0003433: title: lactate dehydrogenase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. meaning: OBI:0003433 OBI:0003434: title: sorbitol dehydrogenase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. meaning: OBI:0003434 OBI:0003435: title: acyl-CoA oxidase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. meaning: OBI:0003435 OBI:0003436: title: N-acetyl-beta-glucosaminidase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. meaning: OBI:0003436 OBI:0003437: title: ribonuclease activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of ribonuclease in a sample. meaning: OBI:0003437 OBI:0003438: title: galactosidase activity level assay - description: An enzymatic activity level assay that measures the activity + description: + An enzymatic activity level assay that measures the activity of galactosidase in a sample. meaning: OBI:0003438 OBI:0003457: title: epitope protection from infectious challenge experiment based on survival - description: An epitope protection from infectious challenge experiment that + description: + An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. meaning: OBI:0003457 OBI:0003458: title: epitope protection from tumor challenge experiment based on burden - description: An epitope protection from tumor challenge experiment in which + description: + An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. meaning: OBI:0003458 OBI:0003459: title: epitope protection from tumor challenge experiment based on survival - description: An epitope protection from tumor challenge experiment that determines + description: + An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. meaning: OBI:0003459 OBI:0003460: - title: in vivo assay measuring T cell epitope specific protection from pathogen + title: + in vivo assay measuring T cell epitope specific protection from pathogen challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from pathogen challenge. meaning: OBI:0003460 OBI:0003461: - title: in vivo assay measuring T cell epitope specific protection from tumor + title: + in vivo assay measuring T cell epitope specific protection from tumor challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from tumor challenge. meaning: OBI:0003461 OBI:0003462: - title: in vivo assay measuring T cell epitope specific protection from other + title: + in vivo assay measuring T cell epitope specific protection from other challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. meaning: OBI:0003462 OBI:0003463: - title: in vivo assay measuring T cell epitope specific survival after tumor + title: + in vivo assay measuring T cell epitope specific survival after tumor challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. meaning: OBI:0003463 OBI:0003464: - title: in vivo assay measuring T cell epitope specific survival after pathogen + title: + in vivo assay measuring T cell epitope specific survival after pathogen challenge - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. meaning: OBI:0003464 OBI:0003465: - title: in vivo assay measuring B cell epitope specific protection from pathogen + title: + in vivo assay measuring B cell epitope specific protection from pathogen challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from pathogen challenge. meaning: OBI:0003465 OBI:0003466: - title: in vivo assay measuring B cell epitope specific protection from tumor + title: + in vivo assay measuring B cell epitope specific protection from tumor challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from tumor challenge. meaning: OBI:0003466 OBI:0003467: - title: in vivo assay measuring B cell epitope specific protection from other + title: + in vivo assay measuring B cell epitope specific protection from other challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. meaning: OBI:0003467 OBI:0003468: - title: in vivo assay measuring B cell epitope specific survival after pathogen + title: + in vivo assay measuring B cell epitope specific survival after pathogen challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. meaning: OBI:0003468 OBI:0003469: - title: in vivo assay measuring B cell epitope specific survival after tumor + title: + in vivo assay measuring B cell epitope specific survival after tumor challenge - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. meaning: OBI:0003469 OBI:0003470: - title: in vivo assay measuring T cell epitope specific protection from pathogen + title: + in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells - description: An in vivo assay measuring a T cell epitope specific protection + description: + An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0003470 OBI:0003471: - title: in vivo assay measuring T cell epitope specific pathogen protection + title: + in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. meaning: OBI:0003471 OBI:0003472: - title: in vivo assay measuring T cell epitope specific protection from tumor + title: + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells - description: An in vivo assay measuring a T cell epitope specific protection + description: + An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. meaning: OBI:0003472 OBI:0003473: - title: in vivo assay measuring T cell epitope specific protection from tumor + title: + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival - description: An in vivo assay measuring T cell epitope specific protection + description: + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. meaning: OBI:0003473 OBI:0003474: - title: in vivo assay measuring T cell epitope specific protection from other + title: + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells - description: An in vivo assay measuring a T cell epitope specific protection + description: + An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. meaning: OBI:0003474 OBI:0003475: - title: in vivo assay measuring B cell epitope specific protection from pathogen + title: + in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An in vivo assay measuring a B cell epitope specific protection + description: + An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0003475 OBI:0003476: - title: in vivo assay measuring B cell epitope specific pathogen protection + title: + in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. meaning: OBI:0003476 OBI:0003477: - title: in vivo assay measuring B cell epitope specific protection from tumor + title: + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An in vivo assay measuring a B cell epitope specific protection + description: + An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0003477 OBI:0003478: - title: in vivo assay measuring B cell epitope specific protection from tumor + title: + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - description: An in vivo assay measuring B cell epitope specific protection + description: + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. meaning: OBI:0003478 OBI:0003479: - title: in vivo assay measuring B cell epitope specific protection from other + title: + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - description: An in vivo assay measuring a B cell epitope specific protection + description: + An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. meaning: OBI:0003479 OBI:0003480: title: Gram stain assay - description: An organism detection assay that identifies bacteria based on + description: + An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. meaning: OBI:0003480 OBI:0003484: title: assay measuring epitope specific interleukin-25 production by T cells - description: A T cell epitope specific cytokine production assay that detects + description: + A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. meaning: OBI:0003484 OBI:0003485: - title: detection of specific nucleic acids with complementary probes assay + title: + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells - description: A detection of specific nucleic acid polymers with complementary + description: + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. meaning: OBI:0003485 OBI:0003486: - title: intracellular cytokine staining assay measuring epitope specific interleukin-25 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells - description: A flow cytometry assay that detects interleukin-25 production + description: + A flow cytometry assay that detects interleukin-25 production by T cells. meaning: OBI:0003486 OBI:0003487: title: ELISA measuring epitope specific interleukin-25 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-25 + description: + An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. meaning: OBI:0003487 OBI:0003488: - title: cell culture analyte detection bioassay measuring epitope specific + title: + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - description: A reporter cell line analyte detection bioassay that detects + description: + A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. meaning: OBI:0003488 OBI:0003498: title: organism detection assay - description: An assay that detects a type of organism and/or the quantity + description: + An assay that detects a type of organism and/or the quantity of individuals of a type of organism. meaning: OBI:0003498 OBI:0003501: title: functional assessment of individual - description: A physical examination of an organism's ability to perform functional + description: + A physical examination of an organism's ability to perform functional activities. meaning: OBI:0003501 OBI:0003502: title: facial atrophy assessment - description: An observational assessment of the loss of facial muscle tissue + description: + An observational assessment of the loss of facial muscle tissue due to inactivity or disease. meaning: OBI:0003502 OBI:0003503: title: tongue atrophy assessment - description: An observational assessment of the loss of muscle tissue related + description: + An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. meaning: OBI:0003503 OBI:0003504: @@ -6778,59 +8248,69 @@ enums: meaning: OBI:0003504 OBI:0003505: title: speech test assessment - description: A functional assessment of an individual's ability to understandably + description: + A functional assessment of an individual's ability to understandably repeat spoken sentences. meaning: OBI:0003505 OBI:0003506: title: finger to finger assessment - description: A functional assessment of an individual's ability to touch index + description: + A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time meaning: OBI:0003506 OBI:0003507: title: nose to finger assessment - description: A functional assessment of an individual's ability to touch their + description: + A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more. meaning: OBI:0003507 OBI:0003508: title: dysmetria assessment - description: A functional assessment of an individual's ability to accurately + description: + A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row. meaning: OBI:0003508 OBI:0003509: title: rapid alternating hands assessment - description: A functional assessment of an individual's ability to alternate + description: + A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time meaning: OBI:0003509 OBI:0003510: title: finger taps assessment - description: A functional assessment of an individual's ability to touch their + description: + A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time. meaning: OBI:0003510 OBI:0003511: title: heel along shin assessment - description: A functional assessment of an individual's ability to slide their + description: + A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended. meaning: OBI:0003511 OBI:0003512: title: heel to shin assessment - description: A functional assessment of an individual's ability to tap their + description: + A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times. meaning: OBI:0003512 OBI:0003513: title: muscle atrophy assessment - description: An observational assesment of an individual's muscle tissue loss + description: + An observational assessment of an individual's muscle tissue loss due to inactivity or disease. meaning: OBI:0003513 OBI:0003514: title: muscle weakness assessment - description: A functional assessment of an individual's ability to perform - muscle movement to overcome gravity or physical resistence. + description: + A functional assessment of an individual's ability to perform + muscle movement to overcome gravity or physical resistance. meaning: OBI:0003514 OBI:0003515: title: vibratory sense assessment @@ -6838,137 +8318,162 @@ enums: meaning: OBI:0003515 OBI:0003516: title: position sense assessment - description: A functional assessment of an individual's ability to sense the + description: + A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements. meaning: OBI:0003516 OBI:0003517: title: deep tendon reflex assessment - description: A functional assessment of an individual's muscle contraction + description: + A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body. meaning: OBI:0003517 OBI:0003518: title: limits of stability assessment - description: The functional assessment of an individual's ability to maintain + description: + The functional assessment of an individual's ability to maintain balance, posture or upright stability. meaning: OBI:0003518 OBI:0003519: title: sitting posture assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period. meaning: OBI:0003519 OBI:0003520: title: stance feet apart assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart. meaning: OBI:0003520 OBI:0003521: title: stance feet apart assessment, with eyes closed - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed. meaning: OBI:0003521 OBI:0003522: title: stance feet together assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together. meaning: OBI:0003522 OBI:0003523: title: stance feet together assessment, with eyes closed - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed. meaning: OBI:0003523 OBI:0003524: title: tandem stance assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement. meaning: OBI:0003524 OBI:0003525: title: stance on one foot assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot. meaning: OBI:0003525 OBI:0003526: title: tandem walk assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem. meaning: OBI:0003526 OBI:0003527: title: gait assessment - description: A limits of stability assessment designed to assess an individual's + description: + A limits of stability assessment designed to assess an individual's manner or pattern of walking. meaning: OBI:0003527 OBI:0003528: title: bulbar assessment - description: A functional assessment of an individual's lower cranial nerve + description: + A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance. meaning: OBI:0003528 OBI:0003529: title: spontaneous speech assessment - description: A functional assessment of an individual's ability to articulate + description: + A functional assessment of an individual's ability to articulate spoken words. meaning: OBI:0003529 OBI:0003530: title: limb coordination assessment - description: A functional assessment of an individual's ability to coordinate + description: + A functional assessment of an individual's ability to coordinate limb movement. meaning: OBI:0003530 OBI:0003531: title: upper limb coordination assessment - description: A limb coordination assessment designed to assess an individual's + description: + A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement. meaning: OBI:0003531 OBI:0003532: title: lower limb coordination assessment - description: A limb coordination assessment designed to assess an individual's + description: + A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement. meaning: OBI:0003532 OBI:0003533: title: nervous system functionality assessment - description: A functional assesment of an individual's nerve performance. + description: + A functional assessment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system. meaning: OBI:0003533 OBI:0003534: title: upright stability assessment - description: A functional assessment of an individual's ability to maintain + description: + A functional assessment of an individual's ability to maintain upright body posture. meaning: OBI:0003534 OBI:0003535: title: deep tendon reflex assessment of the knee joint - description: A deep tendon reflex assessment of an individual's reaction to + description: + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint. meaning: OBI:0003535 OBI:0003536: title: observational assessment of individual - description: A physical examination of an organism through visual assesment. + description: A physical examination of an organism through visual assessment. meaning: OBI:0003536 OBI:0003537: title: deep tendon reflex assessment of the ankle joint - description: A deep tendon reflex assessment of an individual's reaction to + description: + A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint. meaning: OBI:0003537 OBI:0003538: title: deep tendon reflex assessment of the tendon of biceps brachii - description: A deep tendon reflex assessment of an individual's reaction to + description: + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii. meaning: OBI:0003538 OBI:0003539: title: deep tendon reflex assessment of the brachioradialis - description: A deep tendon reflex assessment of an individual's reaction to + description: + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis. meaning: OBI:0003539 OBI:0003540: title: tandem mass spectrometry assay - description: A mass spectrometry assay that uses two or more analyzers separated + description: + A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). meaning: OBI:0003540 OBI:0003541: title: ELISA measuring Orientia tsutsugamushi IgM antibody - description: An enzyme-linked immunosorbent assay that detects the IgM antibody + description: + An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi. meaning: OBI:0003541 OBI:0003542: @@ -6981,22 +8486,26 @@ enums: meaning: OBI:0003543 OBI:0003544: title: analytical chromatography measuring Chikungunya IgM antibody - description: Analytical chromatography that detects the IgM antibody that + description: + Analytical chromatography that detects the IgM antibody that binds Chikungunya. meaning: OBI:0003544 OBI:0003545: title: ELISA measuring Chikungunya IgM antibody - description: An enzyme-linked immunosorbent assay that detects the IgM antibody + description: + An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya. meaning: OBI:0003545 OBI:0003546: title: microarray ELISA measuring Chikungunya IgM antibody - description: An enzyme-linked immunosorbent assay that uses a microarray as + description: + An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya. meaning: OBI:0003546 OBI:0003552: title: proximity ligation-assisted ChIP-seq - description: A chromosome conformation capture assay in which proximity ligation + description: + A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific @@ -7004,33 +8513,40 @@ enums: meaning: OBI:0003552 OBI:0003576: title: skin of body microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a skin of body specimen. meaning: OBI:0003576 OBI:0003578: title: bone marrow microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a bone marrow specimen. meaning: OBI:0003578 OBI:0003580: title: nasal aspirate microbiology assay - description: An organism detection assay that detects microorganisms in a + description: + An organism detection assay that detects microorganisms in a nasal aspirate specimen. meaning: OBI:0003580 OBI:0003582: - title: cell proliferation assay using carboxyfluorescein succinimidyl ester + title: + cell proliferation assay using carboxyfluorescein succinimidyl ester staining - description: A cell proliferation assay that uses carboxyfluorescein succinimidyl + description: + A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division. meaning: OBI:0003582 OBI:0003583: title: cell viability assay - description: A cytometry assay which measures the number of living cells in + description: + A cytometry assay which measures the number of living cells in a population. meaning: OBI:0003583 OBI:0003584: title: cell viability assay using Annexin V staining - description: A cell viability assay that uses Annexin V staining to detect + description: + A cell viability assay that uses Annexin V staining to detect apoptotic cells. meaning: OBI:0003584 OBI:0003587: @@ -7039,7 +8555,8 @@ enums: meaning: OBI:0003587 OBI:0003589: title: serum anti-Epstein-Barr virus antibody level assay - description: An antigen specific antibodies assay that is meant to detect + description: + An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. meaning: OBI:0003589 OBI:0003590: @@ -7048,103 +8565,123 @@ enums: meaning: OBI:0003590 OBI:0003598: title: single cell B cell receptor repertoire sequencing assay - description: A B cell receptor repertoire sequencing assay that determines + description: + A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. meaning: OBI:0003598 OBI:0003599: title: single cell T cell receptor repertoire sequencing assay - description: A T cell receptor repertoire sequencing assay that determines + description: + A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. meaning: OBI:0003599 OBI:0003601: title: quartz crystal microbalance assay - description: An assay that measures the change in frequency of a quartz crystal + description: + An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. meaning: OBI:0003601 OBI:0003602: - title: quartz crystal microbalance assay measuring the dissociation constant + title: + quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - description: A quartz crystal microbalance assay that measures the dissociation + description: + A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. meaning: OBI:0003602 OBI:0003604: title: multiplexed error-robust fluorescence in situ hybridization assay - description: A fluorescence in-situ hybridization assay that uses combinatorial + description: + A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. meaning: OBI:0003604 OBI:0003605: title: single molecule fluorescence in situ hybridization - description: A fluorescence in-situ hybridization assay that detects single + description: + A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. meaning: OBI:0003605 OBI:0003612: - title: electron microscopy assay determining the 3D structure of a T cell + title: + electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex - description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR + description: + An electron-microscopy 3D molecular structure determination assay + that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. meaning: OBI:0003612 OBI:0003613: - title: electron microscopy assay determining the 3D structure of a MHC:ligand + title: + electron microscopy assay determining the 3D structure of a MHC:ligand complex - description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a MHC:ligand + description: + An electron-microscopy 3D molecular structure determination assay + that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. meaning: OBI:0003613 OBI:0003659: title: in vitro CRISPR screen assay - description: An assay in which cells expressing a Cas system are infected + description: + An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. meaning: OBI:0003659 OBI:0003660: title: in vitro CRISPR screen using single-cell RNA-seq - description: An in vitro CRISPR screen assay that uses single-cell RNA-Seq + description: + An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. meaning: OBI:0003660 OBI:0003661: title: in vitro CRISPR screen using flow cytometry - description: An in vitro CRISPR screen assay that uses flow cytometry to detect + description: + An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. meaning: OBI:0003661 OBI:0003662: title: single-nucleus methylcytosine and transcriptome sequencing assay - description: A DNA methylation profiling by high throughput sequencing assay + description: + A DNA methylation profiling by high throughput sequencing assay that measures the cytosine DNA methylation and gene expression signature of single nuclei. meaning: OBI:0003662 OBI:0003686: title: chromatin accessibility assay - description: An assay that determines which regions of a DNA molecule are + description: + An assay that determines which regions of a DNA molecule are in the form of euchromatin and thus able to make direct physical contact with (i.e. are accessible to) other molecules such as RNA polymerase, transcription factors, etc. meaning: OBI:0003686 OBI:0003687: title: m6A-MTase sequencing assay - description: A DNA methylation profiling assay in which chromatin stencils + description: + A DNA methylation profiling assay in which chromatin stencils are created by treating nuclei with m6A methyltransferase (MTase) and then sequenced using single-molecule circular consensus sequencing to identify regions of accessible DNA at nucleotide resolution. meaning: OBI:0003687 OBI:0003709: title: assessment of learning and/or memory response in an organism - description: A nervous system functionality assessment of learning or memory + description: + A nervous system functionality assessment of learning or memory in an organism meaning: OBI:0003709 OBI:0003710: title: assessment of startle response in an organism - description: A nervous system functionality assessment of auditory startle + description: + A nervous system functionality assessment of auditory startle response in an organism in an anechoic chamber by exposing to sound. meaning: OBI:0003710 OBI:0003711: title: grip strength assay - description: A nervous system functionality assessment that uses the grip + description: + A nervous system functionality assessment that uses the grip strength of a lab animal to measure neuromuscular function. meaning: OBI:0003711 OBI:0003712: @@ -7153,27 +8690,32 @@ enums: meaning: OBI:0003712 OBI:0003713: title: organism development assay - description: A physical examination of an organism that provides information + description: + A physical examination of an organism that provides information about some developmental process in that organism. meaning: OBI:0003713 OBI:0003714: title: reproductive assay - description: A physical examination of an organism that provides information + description: + A physical examination of an organism that provides information about some reproductive process in that organism. meaning: OBI:0003714 OBI:0003715: title: vital sign assay - description: An assay of a organism to measure basic physiological functions + description: + An assay of a organism to measure basic physiological functions such as breathing, pulse, etc. (phylum bilateral). meaning: OBI:0003715 OBI:0003716: title: blood pressure assay - description: A vital sign assay that determines the blood pressure (force + description: + A vital sign assay that determines the blood pressure (force of blood against the artery walls) of an organism. meaning: OBI:0003716 OBI:0003717: title: heart rate variability assay - description: A pulse rate assay that measures beat to beat variability in + description: + A pulse rate assay that measures beat to beat variability in heart beats. meaning: OBI:0003717 OBI:0003718: @@ -7182,12 +8724,14 @@ enums: meaning: OBI:0003718 OBI:0003719: title: respiratory assay - description: A vital sign assay that measures the quality of respiration / + description: + A vital sign assay that measures the quality of respiration / respiratory system of an organism meaning: OBI:0003719 OBI:0003720: title: cell differentiation assay - description: A cytometry assay that monitors the differentiation stage of + description: + A cytometry assay that monitors the differentiation stage of cells in culture. meaning: OBI:0003720 OBI:0003721: @@ -7196,12 +8740,14 @@ enums: meaning: OBI:0003721 OBI:0003722: title: natural killer cell count assay - description: A cytometry assay to determine the number of natural killer cells + description: + A cytometry assay to determine the number of natural killer cells in a specimen meaning: OBI:0003722 OBI:0003723: title: natural killer cell percentage assay - description: A cytometry assay that measures the percentage of natural killer + description: + A cytometry assay that measures the percentage of natural killer cells in a specimen. meaning: OBI:0003723 OBI:0003724: @@ -7210,12 +8756,14 @@ enums: meaning: OBI:0003724 OBI:0003725: title: survey administration assay - description: An assay that obtains data from one or more participants by using + description: + An assay that obtains data from one or more participants by using a survey or questionnaire meaning: OBI:0003725 OBI:0003734: title: clinical history collection assay - description: A clinical assay that produces a data item indicating whether + description: + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. meaning: OBI:0003734 @@ -7225,137 +8773,165 @@ enums: meaning: OBI:0003735 OBI:0003736: title: genetic characteristic assay - description: An assay that produces information about a genetic characteristic + description: + An assay that produces information about a genetic characteristic of an organism. meaning: OBI:0003736 OBI:0003738: title: blood type assay - description: An assay that classifies an organism's blood within one or more + description: + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. meaning: OBI:0003738 OBI:0003741: title: capillary electrophoresis mass spectrometry assay - description: A mass spectrometry assay where a sample mixture is first separated + description: + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. meaning: OBI:0003741 OBI:0003750: title: neurite outgrowth assay - description: A cell differentiation assay that detects neurite outgrowth and/or + description: + A cell differentiation assay that detects neurite outgrowth and/or branching meaning: OBI:0003750 OBI:0003751: title: neuronal differentiation assay - description: A cell differentiation assay that measures differentiation of + description: + A cell differentiation assay that measures differentiation of neurons. meaning: OBI:0003751 OBI:0003752: title: oligodendrocyte differentiation assay - description: A cell differentiation assay that measures differentiation of + description: + A cell differentiation assay that measures differentiation of oligodendrocytes. meaning: OBI:0003752 OBI:0003753: title: regulation of synapse maturation assay - description: A cell differentiation assay that measures synapse formation + description: + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. meaning: OBI:0003753 OBI:0003754: title: Ames assay - description: A cell based DNA damage assay that uses several constructed bacterial + description: + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. meaning: OBI:0003754 OBI:0003755: title: micronucleus assay - description: A cell based DNA damage assay in eukaryotic cells that detects + description: + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. meaning: OBI:0003755 OBI:0003756: title: PIG-a assay - description: A cell based DNA damage assay in eukaryotic cells that detects + description: + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. meaning: OBI:0003756 OBI:0003757: title: cell viability assay based on detection of resorufin - description: A cell viability assay using the NAD(P)H-aided conversion of + description: + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. meaning: OBI:0003757 OBI:0003758: title: cell death assay using caspase abundance to detect apoptosis - description: A cell death assay that uses fluorescence imaging-based detection + description: + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis meaning: OBI:0003758 OBI:0003759: title: cell death assay - description: A cell viability assay which measures the number or proportion + description: + A cell viability assay which measures the number or proportion of dead cells in a population. meaning: OBI:0003759 OBI:0003760: - title: cell viability assay based on detection of resorufin using fluorescence + title: + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. - description: A cell viability assay based on detection of resorufin that uses + description: + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin meaning: OBI:0003760 OBI:0003761: title: cell death assay detecting lactate dehydrogenase (LDH) release - description: A cell death assay that measures the release of intracellular + description: + A cell death assay that measures the release of intracellular LDH. meaning: OBI:0003761 OBI:0003762: - title: cell death assay detecting lactate dehydrogenase (LDH) release using + title: + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. - description: A cell death assay detecting lactate dehydrogenase (LDH) release + description: + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate meaning: OBI:0003762 OBI:0003763: title: ovulation assessment in rodent assay - description: A histological assay that measures the number of corpora lutea + description: + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. meaning: OBI:0003763 OBI:0003764: title: macroscopic examination of material anatomical entity assay - description: An assay that performs a macroscopic assessment of a material + description: + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. meaning: OBI:0003764 OBI:0003765: title: pathological macroscopic examination of specimen assay - description: A macroscopic examination of material anatomical entity assay + description: + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. meaning: OBI:0003765 OBI:0003766: title: estrous cycle assay based on tissue morphology - description: A histological assay that evaluates cells in the vaginal endometrium + description: + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. meaning: OBI:0003766 OBI:0003767: title: organism development assay in late embryo - description: An organism development assay performed with a late embryo stage + description: + An organism development assay performed with a late embryo stage subject. meaning: OBI:0003767 OBI:0003768: title: pregnancy assessment based on tissue morphology assay - description: A histological assay that measures the number of implantation + description: + A histological assay that measures the number of implantation sites in an organism. meaning: OBI:0003768 OBI:0003769: title: cell death assay using vital dye - description: A cell death assay that uses the Trypan blue vital dye to stain + description: + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. meaning: OBI:0003769 OBI:0003770: title: neurite length assay - description: A cytometry assay that uses a distance measurement assay to determine + description: + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. meaning: OBI:0003770 OBI:0003771: title: neurite degree of arborization assay - description: A cytometry assay that measures the degree of arborization, or + description: + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes meaning: OBI:0003771 OBI:0003772: title: neurite count assay - description: A cytometry assay that measures the number of neurites in a cultured + description: + A cytometry assay that measures the number of neurites in a cultured specimen. meaning: OBI:0003772 OBI:0003773: @@ -7364,17 +8940,20 @@ enums: meaning: OBI:0003773 OBI:0003774: title: cell-body-associated presynaptic puncta count assay - description: A regulation of synapse maturation assay that determines the + description: + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. meaning: OBI:0003774 OBI:0003775: title: dendrite-associated presynaptic puncta count assay - description: A regulation of synapse maturation assay that determines the + description: + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. meaning: OBI:0003775 OBI:0003776: title: synapse per neuron assay - description: A regulation of synapse maturation assay that determines the + description: + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. meaning: OBI:0003776 @@ -7384,17 +8963,20 @@ enums: meaning: OBI:0003777 OBI:0003778: title: hormone assay - description: The analyte assay that measures the abundance of a hormone in + description: + The analyte assay that measures the abundance of a hormone in a specimen. meaning: OBI:0003778 OBI:0003779: title: chemiluminescent assay - description: An analyte assay that detects a substance by measuring the release + description: + An analyte assay that detects a substance by measuring the release of light triggered by a chemical reaction. meaning: OBI:0003779 OBI:0003780: title: electrochemiluminescence assay - description: A chemiluminescent assay that detects a substance by measuring + description: + A chemiluminescent assay that detects a substance by measuring the release of light triggered by an electrochemical reaction. meaning: OBI:0003780 OBI:0003781: @@ -7407,14 +8989,16 @@ enums: meaning: OBI:0003782 OBI:0003788: title: cellular indexing of transcriptomes and epitopes by sequencing - description: An assay performed on single cells that simultaneously measures + description: + An assay performed on single cells that simultaneously measures transcript expression via single-cell RNA sequencing and profiles surface proteins via sequencing of DNA-barcodes attached to antibodies recognizing particular surface proteins from individual cells. meaning: OBI:0003788 OBI:0003789: title: immune receptor repertoire profiling assay - description: An assay that determines the sequence of a DNA or RNA molecules + description: + An assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors or T cell receptors within an input sample. meaning: OBI:0003789 @@ -7432,17 +9016,20 @@ enums: meaning: OBI:0003792 OBI:0003793: title: bacterial lipopolysaccharide detection in plasma assay - description: An analyte assay measuring bacterial lipopolysaccharide in a + description: + An analyte assay measuring bacterial lipopolysaccharide in a plasma sample. meaning: OBI:0003793 OBI:0003794: title: bacterial lipopolysaccharide detection in feces assay - description: An analyte assay measuring bacterial lipopolysaccharide in a + description: + An analyte assay measuring bacterial lipopolysaccharide in a feces sample. meaning: OBI:0003794 OBI:0003795: title: adenosine deaminase activity assay - description: An analyte assay measuring adenosine deaminase activity in a + description: + An analyte assay measuring adenosine deaminase activity in a sample. meaning: OBI:0003795 OBI:0003796: @@ -7459,12 +9046,14 @@ enums: meaning: OBI:0003798 OBI:0003799: title: analyte detection by flow based bead assay - description: An analyte assay that uses beads to measure the concentration + description: + An analyte assay that uses beads to measure the concentration of an analyte with a flow cytometer. meaning: OBI:0003799 OBI:0003801: title: urine opacity assay - description: A histological assay with urine evaluant that measures opacity + description: + A histological assay with urine evaluant that measures opacity of the urine meaning: OBI:0003801 OBI:0003802: @@ -7485,30 +9074,38 @@ enums: meaning: OBI:0003805 OBI:0003811: title: estrous cycle count assay - description: An estrous cycle assay based on tissue morphology that determines + description: + An estrous cycle assay based on tissue morphology that determines the number of estrous cycles observed in a defined time. meaning: OBI:0003811 OBI:0003812: title: estrous cycle duration assay - description: An estrous cycle assay based on tissue morphology that determines + description: + An estrous cycle assay based on tissue morphology that determines the average length of a full estrous cycle observed in a defined time. meaning: OBI:0003812 OBI:0003813: - title: organism development assay in late embryo based on examination of surface + title: + organism development assay in late embryo based on examination of surface structure - description: An organism development assay in late embryo that evaluates only + description: + An organism development assay in late embryo that evaluates only the external surface structure of the organism meaning: OBI:0003813 OBI:0003814: - title: organism development assay in late embryo based on examination of skeletal + title: + organism development assay in late embryo based on examination of skeletal system - description: An organism development assay in late embryo that evaluates the + description: + An organism development assay in late embryo that evaluates the skeletal system of the organism meaning: OBI:0003814 OBI:0003815: - title: organism development assay in late embryo based on examination of anatomical + title: + organism development assay in late embryo based on examination of anatomical system - description: An organism development assay in late embryo that evaluates the + description: + An organism development assay in late embryo that evaluates the anatomical system of the organism meaning: OBI:0003815 OBI:0003816: @@ -7521,17 +9118,20 @@ enums: meaning: OBI:0003817 OBI:0003818: title: crown rump length - description: A length measurement assay that measures the length of a neonate + description: + A length measurement assay that measures the length of a neonate or fetus from crown of head to base of torso (rump) meaning: OBI:0003818 OBI:0003819: title: path length assay - description: An assay that measures the distance traveled in a defined period + description: + An assay that measures the distance traveled in a defined period of time. meaning: OBI:0003819 OBI:0003820: title: cell migration assay - description: A distance measurement assay in which the migration of cells + description: + A distance measurement assay in which the migration of cells in culture is monitored by measuring the distance between the start position and the cell's location when observed. meaning: OBI:0003820 @@ -7541,7 +9141,8 @@ enums: meaning: OBI:0003821 OBI:0003822: title: radial glial migration assay - description: A cell migration assay that measures migration of a radial glia + description: + A cell migration assay that measures migration of a radial glia cell meaning: OBI:0003822 OBI:0003823: @@ -7550,7 +9151,8 @@ enums: meaning: OBI:0003823 OBI:0003824: title: neural crest cell migration assay - description: A cell migration assay that measures migration of a neural crest + description: + A cell migration assay that measures migration of a neural crest cell meaning: OBI:0003824 OBI:0003825: @@ -7575,47 +9177,56 @@ enums: meaning: OBI:0003829 OBI:0003830: title: cell viability assay using luciferase to detect ATP in the cell - description: A cell viability assay that uses an ATP bioluminescence assay + description: + A cell viability assay that uses an ATP bioluminescence assay to detect ATP in the living cell meaning: OBI:0003830 OBI:0003831: title: population count assay - description: An assay that measures the number of elements in a portion of + description: + An assay that measures the number of elements in a portion of a population meaning: OBI:0003831 OBI:0003832: title: hemolysis assay - description: A hematology assay that measures the fragility of red blood cells + description: + A hematology assay that measures the fragility of red blood cells by observing spillage of hemoglobin from burst cells. meaning: OBI:0003832 OBI:0003833: title: neuron action potential rate assay - description: An electrophysiology assay that measures action potential events + description: + An electrophysiology assay that measures action potential events in neurons during a time period. meaning: OBI:0003833 OBI:0003834: title: neuron burst rate assay - description: An electrophysiology assay that measures the number of action + description: + An electrophysiology assay that measures the number of action potential bursts in neurons during a time period. meaning: OBI:0003834 OBI:0003835: title: neuron interburst interval assay - description: An electrophysiology assay that measures the elapsed time between + description: + An electrophysiology assay that measures the elapsed time between consecutive action potential bursts in neurons. meaning: OBI:0003835 OBI:0003836: title: neuron burst duration assay - description: An electrophysiology assay that measures the time elapsed between + description: + An electrophysiology assay that measures the time elapsed between the first action potential in a neuron burst and the last in that burst. meaning: OBI:0003836 OBI:0003837: title: action potential interval assay - description: An electrophysiology assay that measures the time elapsed between + description: + An electrophysiology assay that measures the time elapsed between the peaks of consecutive action potential spikes in a neuron burst. meaning: OBI:0003837 OBI:0003838: title: rate of action potentials in neuron burst assay - description: An electrophysiology assay that measures the number of action + description: + An electrophysiology assay that measures the number of action potential spikes occurring within a neuron burst meaning: OBI:0003838 OBI:0003839: @@ -7624,208 +9235,244 @@ enums: meaning: OBI:0003839 OBI:0003840: title: body mass change assay - description: A body mass assay that measures the change in body mass for a + description: + A body mass assay that measures the change in body mass for a subject over a period of time. meaning: OBI:0003840 OBI:0003841: title: body weight assay at death - description: A body weight assay with evaluant individual organism specimen + description: + A body weight assay with evaluant individual organism specimen with quality dead. meaning: OBI:0003841 OBI:0003842: title: tissue mass assay - description: A mass measurement assay with evaluant tissue or bodily fluid + description: + A mass measurement assay with evaluant tissue or bodily fluid specimen. meaning: OBI:0003842 OBI:0003843: title: tissue mass percent of body mass assay - description: A mass measurement assay with evaluant tissue expressed as a + description: + A mass measurement assay with evaluant tissue expressed as a percentage of the body weight of the organism from which the specimen was derived. meaning: OBI:0003843 OBI:0003844: title: developmental marker age of attainment assessment - description: An age determination assay which determines the age of the subject + description: + An age determination assay which determines the age of the subject at the time of the change from a state where it did not have a developmental stage marker to one in which it does. meaning: OBI:0003844 OBI:0003850: title: cytochrome P450 assay - description: A protein assay that measures the abundance of cytochrome P450 + description: + A protein assay that measures the abundance of cytochrome P450 in a specimen. meaning: OBI:0003850 OBI:0003851: title: growth factor assay - description: An analyte assay to measure the abundance of one or more growth + description: + An analyte assay to measure the abundance of one or more growth factors in a volume of sample. meaning: OBI:0003851 OBI:0003852: title: Hoechst dye assay - description: A fluorescence imaging-based cell morphology assay that uses + description: + A fluorescence imaging-based cell morphology assay that uses Hoechst dye 33342 meaning: OBI:0003852 OBI:0003853: title: hypersensitivity assay - description: An immune response assay to assess the hypersensitivity response + description: + An immune response assay to assess the hypersensitivity response in an organism or cell culture. meaning: OBI:0003853 OBI:0003882: title: super-resolution microscopy assay - description: A type of light microscopy assay where the images are taken with + description: + A type of light microscopy assay where the images are taken with a resolution higher than the diffraction limit. meaning: OBI:0003882 OBI:0003885: title: 1M7 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-7-nitroisatoic anhydride as reagent and chemical probe meaning: OBI:0003885 OBI:0003886: title: NAI RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-methylnicotinic acid imidazolide as reagent and chemical probe meaning: OBI:0003886 OBI:0003887: title: NAI-N3 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-(azidomethyl)nicotinic acid imidazolide as reagent and chemical probe meaning: OBI:0003887 OBI:0003888: title: 2A3 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe meaning: OBI:0003888 OBI:0003889: title: I5 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using indoline-5-carboxylic acid imidazolide as reagent and chemical probe meaning: OBI:0003889 OBI:0003890: title: 1M4 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methylimidazole-4-carboxylic acid imidazolide as reagent and chemical probe meaning: OBI:0003890 OBI:0003891: title: 6A3 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 6-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe meaning: OBI:0003891 OBI:0003892: title: B5 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzotriazole-5-carboxylic acid imidazolide as reagent and chemical probe meaning: OBI:0003892 OBI:0003893: title: NIC RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using nicotinic acid imidazolide as reagent and chemical probe meaning: OBI:0003893 OBI:0003894: title: BzCN RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzoyl cyanide as reagent and chemical probe meaning: OBI:0003894 OBI:0003895: title: 1M6 RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-6-nitroisatoic anhydride as reagent and chemical probe meaning: OBI:0003895 OBI:0003896: title: 5NIA RNA structure mapping assay - description: A single-nucleotide-resolution ribonucleic acid structure mapping + description: + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 5-nitroisatoic anhydride as reagent and chemical probe meaning: OBI:0003896 OBI:0003897: title: cell count assay - description: An assay that measures the number of cells in a portion of a + description: + An assay that measures the number of cells in a portion of a cell culture or tissue or bodily fluid meaning: OBI:0003897 OBI:0003898: title: differential leukocyte count assay - description: A hematology assay that measures the percentage of classes of + description: + A hematology assay that measures the percentage of classes of leukocytes in a sample. meaning: OBI:0003898 OBI:0003899: title: electrocardiogram assay - description: An electrophysiology assay that measures heart activity using + description: + An electrophysiology assay that measures heart activity using electrodes placed to detect electrical signals from the heart. meaning: OBI:0003899 OBI:0003900: title: telemeter sensor detection assay - description: An assay which uses an implanted telemeter to measure physiological + description: + An assay which uses an implanted telemeter to measure physiological data in a living organism and transmit the measures via radio waves to a recording device. meaning: OBI:0003900 OBI:0003901: title: multi-electrode array assay - description: A multi-unit recording assay using a multi-electrode array (MEA) + description: + A multi-unit recording assay using a multi-electrode array (MEA) on the surface of a well on a cell culture plate. meaning: OBI:0003901 OBI:0003902: title: transepithelial / transendothelial electrical resistance (TEER) assay - description: An extracellular electrophysiology recording assay to measure + description: + An extracellular electrophysiology recording assay to measure the integrity of a cell monolayer meaning: OBI:0003902 OBI:0003903: - title: count of multi-electrode plate electrodes detecting action potential + title: + count of multi-electrode plate electrodes detecting action potential assay - description: A multi-electrode array assay that measures the number of electrodes + description: + A multi-electrode array assay that measures the number of electrodes in a well where the mean rate of action potentials is at least 5 spikes per minute. meaning: OBI:0003903 OBI:0003904: title: count of multi-electrode plate electrodes detecting neuron burst assay - description: A multi-electrode array assay that measures the number of electrodes + description: + A multi-electrode array assay that measures the number of electrodes in a well where the burst rate is at least 0.5 bursts per minute. meaning: OBI:0003904 OBI:0003905: title: neural network spike rate assay - description: An multi-electrode assay that measures the number of events when + description: + An multi-electrode assay that measures the number of events when multiple electrodes simultaneously detect an action potential during a time period. meaning: OBI:0003905 OBI:0003906: title: neural network spike duration assay - description: A multi-electrode assay that measures the mean duration of events + description: + A multi-electrode assay that measures the mean duration of events when multiple electrodes detect an action potential meaning: OBI:0003906 OBI:0003907: title: count of multi-electrode plate electrodes detecting spike peak assay - description: A multi-electrode array assay that measures the average number + description: + A multi-electrode array assay that measures the average number of electrodes detecting a network spike, measured at the peak of a network spike. meaning: OBI:0003907 OBI:0003908: title: mean interspike interval in network spike - description: A multi-electrode assay that measures the average interval between + description: + A multi-electrode assay that measures the average interval between network spikes, events where multiple electrodes simultaneously detect an action potential. meaning: OBI:0003908 OBI:0003909: title: bile acid concentration assay - description: An analyte assay that measures the abundance of bile acid in + description: + An analyte assay that measures the abundance of bile acid in a volume of sample. meaning: OBI:0003909 OBI:0003910: @@ -7834,31 +9481,37 @@ enums: meaning: OBI:0003910 OBI:0003911: title: urea nitrogen concentration assay - description: A urea nitrogen assay that measures the abundance of urea nitrogen + description: + A urea nitrogen assay that measures the abundance of urea nitrogen in a specimen meaning: OBI:0003911 OBI:0003912: title: in vitro CRISPR screen using single-cell ATAC-seq - description: An in vitro CRISPR screen assay that uses single-cell ATAC-Seq + description: + An in vitro CRISPR screen assay that uses single-cell ATAC-Seq to detect induced changes in chromatin accessibility meaning: OBI:0003912 OBI:0003913: title: single-cell metabolically labeled new RNA tagging sequencing - description: A single-cell transcription profiling by RNA sequencing assay + description: + A single-cell transcription profiling by RNA sequencing assay in which mRNA transcripts are metabolically labeled with 4-thiouridine to investigate temporal RNA dynamics. meaning: OBI:0003913 OBI:0003914: title: single cell massively parallel reporter assay - description: A massively parallel reporter assay in which libraries of reporter + description: + A massively parallel reporter assay in which libraries of reporter constructs are transfected into samples and then measured via single cell transcriptomic methods to enable discovery of cell-specific transcriptional regulatory activity meaning: OBI:0003914 OBI:0003915: - title: ultra high throughput single-cell combinatorial indexing RNA sequencing + title: + ultra high throughput single-cell combinatorial indexing RNA sequencing 3 assay - description: A single-cell transcription profiling by RNA sequencing assay + description: + A single-cell transcription profiling by RNA sequencing assay that involves single cell combinatorial indexing ('sci-') to profile the transcriptomes of single cells or nuclei in an ultra high-throughput manor via changes to the method, as compared to sci-RNA-seq, that include extraction @@ -7868,32 +9521,37 @@ enums: meaning: OBI:0003915 OBI:0302736: title: DNA damage comet assay - description: A cell based DNA damage assay that measures DNA damage (DNA breakage) + description: + A cell based DNA damage assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis meaning: OBI:0302736 OBI:0302737: title: PCR-SSCP assay - description: An assay that identifies DNA sequence variation (mutation, deletion, + description: + An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions meaning: OBI:0302737 OBI:0600002: title: tumor grading - description: An assay that determines the grade (severity/stage) of a tumor + description: + An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. meaning: OBI:0600002 OBI:0600017: title: assay detecting a molecular label - description: An assay that detects the presence or a quality of a molecular + description: + An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached meaning: OBI:0600017 OBI:0600020: title: histological assay - description: An assay that uses visual examination of cells or tissue (or + description: + An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. meaning: OBI:0600020 @@ -7903,240 +9561,299 @@ enums: meaning: OBI:0600025 OBI:0600026: title: longitudinal mass measurement assay - description: An assay that measures the mass of a material at two or more + description: + An assay that measures the mass of a material at two or more time points meaning: OBI:0600026 OBI:0600031: title: enzyme-linked immunospot assay - description: A cytometry assay in which cells are cultured on a surface coated + description: + A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. meaning: OBI:0600031 OBI:0600045: title: 3D structure determination assay - description: An assay that determines the 3-dimensional configuration of an + description: + An assay that determines the 3-dimensional configuration of an input material. meaning: OBI:0600045 OBI:0600047: title: sequencing assay - description: An assay the uses chemical or biochemical means to infer the + description: + An assay the uses chemical or biochemical means to infer the sequence of a biomaterial meaning: OBI:0600047 OBI:1110013: - title: ELISPOT assay measuring epitope specific interleukin-2 production by + title: + ELISPOT assay measuring epitope specific interleukin-2 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-2 + description: + An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. meaning: OBI:1110013 OBI:1110037: title: assay measuring binding of a T cell epitope:MHC:TCR complex - description: A T cell epitope assay that measures the binding of T cell receptor + description: + A T cell epitope assay that measures the binding of T cell receptor to an epitope. meaning: OBI:1110037 OBI:1110059: - title: ELISPOT assay measuring epitope specific interferon-gamma production + title: + ELISPOT assay measuring epitope specific interferon-gamma production by T cells - description: An enzyme-linked immunospot assay that detects interferon-gamma + description: + An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. meaning: OBI:1110059 OBI:1110124: title: assay measuring qualitative binding of a T cell epitope:MHC:TCR complex - description: An assay that detects the binding of a MHC:epitope complex with + description: + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. meaning: OBI:1110124 OBI:1110125: title: assay measuring MHC ligand processing and presentation - description: A MHC ligand assay that determines what ligands are processed + description: + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. meaning: OBI:1110125 OBI:1110126: title: assay measuring binding of a MHC:ligand complex - description: A MHC ligand assay that detects the binding of a ligand to an + description: + A MHC ligand assay that detects the binding of a ligand to an MHC molecule. meaning: OBI:1110126 OBI:1110127: title: assay measuring binding of a B cell epitope:antibody complex - description: A B cell epitope assay that measures the binding of an antibody + description: + A B cell epitope assay that measures the binding of an antibody receptor to an epitope. meaning: OBI:1110127 OBI:1110128: title: immune epitope assay - description: An assay that detects the binding of an epitope to an adaptive + description: + An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, - or characterizes the structrue of the complex resulting from such a binding + or characterizes the structure of the complex resulting from such a binding event. meaning: OBI:1110128 OBI:1110129: title: assay measuring epitope specific cytokine production by T cells - description: A T cell epitope assay that detects cytokine production by T + description: + A T cell epitope assay that detects cytokine production by T cells. meaning: OBI:1110129 OBI:1110130: title: assay measuring epitope specific T cell killing - description: A T cell epitope dependent biological activity assay that detects + description: + A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. meaning: OBI:1110130 OBI:1110131: title: assay measuring epitope specific proliferation of T cells - description: A T cell epitope dependent biological activity assay that detects + description: + A T cell epitope dependent biological activity assay that detects T cell proliferation. meaning: OBI:1110131 OBI:1110150: title: 51 chromium assay measuring epitope specific T cell killing - description: A chromium release assay that detects the killing of an antigen + description: + A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. meaning: OBI:1110150 OBI:1110151: title: ELISA measuring epitope specific interferon-gamma production by T cells - description: An enzyme-linked immunosorbent assay that detects interferon-gamma + description: + An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. meaning: OBI:1110151 OBI:1110152: title: ELISA measuring epitope specific interleukin-2 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-2 + description: + An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. meaning: OBI:1110152 OBI:1110153: title: ELISA measuring epitope specific interleukin-4 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-4 + description: + An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. meaning: OBI:1110153 OBI:1110154: title: ELISA measuring epitope specific interleukin-5 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-5 + description: + An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. meaning: OBI:1110154 OBI:1110155: - title: ELISA measuring epitope specific tumor necrosis factor alpha production + title: + ELISA measuring epitope specific tumor necrosis factor alpha production by T cells - description: An enzyme-linked immunosorbent assay that detects tumor necrosis + description: + An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells. meaning: OBI:1110155 OBI:1110156: title: ELISA measuring epitope specific interleukin-10 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-10 + description: + An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells. meaning: OBI:1110156 OBI:1110157: - title: ELISA measuring epitope specific granulocyte macrophage colony-stimulating + title: + ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - description: An enzyme-linked immunosorbent assay that detects granulocyte + description: + An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells. meaning: OBI:1110157 OBI:1110158: title: ELISA measuring epitope specific interleukin-6 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-6 + description: + An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells. meaning: OBI:1110158 OBI:1110159: title: ELISA measuring epitope specific interleukin-13 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-13 + description: + An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells. meaning: OBI:1110159 OBI:1110160: title: ELISA measuring epitope specific interleukin-12 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-12 + description: + An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells. meaning: OBI:1110160 OBI:1110161: - title: ELISA measuring epitope specific interleukin-1 beta production by T + title: + ELISA measuring epitope specific interleukin-1 beta production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-1 + description: + An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells. meaning: OBI:1110161 OBI:1110162: title: ELISA measuring epitope specific interleukin-17 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-17 + description: + An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. meaning: OBI:1110162 OBI:1110163: title: ELISA measuring epitope specific interleukin-18 production by T cells - description: An enzyme-linked immunosorbent assay that detects interleukin-18 + description: + An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. meaning: OBI:1110163 OBI:1110167: - title: ELISPOT assay measuring epitope specific interleukin-4 production by + title: + ELISPOT assay measuring epitope specific interleukin-4 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-4 + description: + An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. meaning: OBI:1110167 OBI:1110168: - title: ELISPOT assay measuring epitope specific tumor necrosis factor alpha + title: + ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells - description: An enzyme-linked immunospot assay that detects tumor necrosis + description: + An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells meaning: OBI:1110168 OBI:1110170: - title: ELISPOT assay measuring epitope specific interleukin-10 production + title: + ELISPOT assay measuring epitope specific interleukin-10 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-10 + description: + An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. meaning: OBI:1110170 OBI:1110171: - title: ELISPOT assay measuring epitope specific interleukin-13 production + title: + ELISPOT assay measuring epitope specific interleukin-13 production by T cells - description: An enzyme-linked immunospot assay that detects interleukin-13 + description: + An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. meaning: OBI:1110171 OBI:1110172: - title: intracellular cytokine staining assay measuring epitope specific interferon-gamma + title: + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells - description: A flow cytometry assay that detects interferon-gamma production + description: + A flow cytometry assay that detects interferon-gamma production by T cells. meaning: OBI:1110172 OBI:1110173: - title: intracellular cytokine staining assay measuring epitope specific interleukin-2 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells - description: A flow cytometry assay that detects interleukin-2 production + description: + A flow cytometry assay that detects interleukin-2 production by T cells. meaning: OBI:1110173 OBI:1110174: - title: intracellular cytokine staining assay measuring epitope specific tumor + title: + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells - description: A flow cytometry assay that detects tumor necrosis factor alpha + description: + A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. meaning: OBI:1110174 OBI:1110175: - title: intracellular cytokine staining assay measuring epitope specific interleukin-4 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells - description: A flow cytometry assay that detects interleukin-4 production + description: + A flow cytometry assay that detects interleukin-4 production by T cells. meaning: OBI:1110175 OBI:1110177: - title: intracellular cytokine staining assay measuring epitope specific interleukin-10 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells - description: A flow cytometry assay that detects interleukin-10 production + description: + A flow cytometry assay that detects interleukin-10 production by T cells. meaning: OBI:1110177 OBI:1110178: - title: intracellular cytokine staining assay measuring epitope specific interleukin-17 + title: + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - description: A flow cytometry assay that detects interleukin-17 production + description: + A flow cytometry assay that detects interleukin-17 production by T cells. meaning: OBI:1110178 OBI:1110179: - title: MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR + title: + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - description: A MHC tetramer/multimer assay that measures the binding of an + description: + A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. meaning: OBI:1110179 OBI:1110180: title: 3H-thymidine assay measuring epitope specific proliferation of T cells - description: A tritiated thymidine incorporation assay that detects T cell + description: + A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro. meaning: OBI:1110180 OBI:1110181: title: BrdU assay measuring epitope specific proliferation of T cells - description: A BrdU incorporation assay that detects T cell epitope specific + description: + A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro. meaning: OBI:1110181 OBI:1110207: title: assay detecting IFN-gamma production - description: An assay that determines information about the production of + description: + An assay that determines information about the production of the cytokine interferon gamma meaning: OBI:1110207 OBI:2100001: @@ -8205,7 +9922,8 @@ enums: meaning: OBI:2100016 OBI:2100017: title: alkaline phosphatase (human) assay - description: An analyte assay that measures the abundance of alkaline phosphatase + description: + An analyte assay that measures the abundance of alkaline phosphatase (human) meaning: OBI:2100017 OBI:2100018: @@ -8214,7 +9932,8 @@ enums: meaning: OBI:2100018 OBI:2100019: title: aspartate aminotransferase (human) assay - description: An analyte assay that measures the abundance of aspartate aminotransferase + description: + An analyte assay that measures the abundance of aspartate aminotransferase (human) meaning: OBI:2100019 OBI:2100020: @@ -8247,7 +9966,8 @@ enums: meaning: OBI:2100026 OBI:2100027: title: segmented neutrophil of bone marrow count assay - description: A cytometry assay that measures the count of segmented neutrophil + description: + A cytometry assay that measures the count of segmented neutrophil of bone marrows meaning: OBI:2100027 OBI:2100028: @@ -8260,7 +9980,8 @@ enums: meaning: OBI:2100029 OBI:2100030: title: high-density lipoprotein cholesterol assay - description: An analyte assay that measures the abundance of high-density + description: + An analyte assay that measures the abundance of high-density lipoprotein cholesterol meaning: OBI:2100030 OBI:2100031: @@ -8269,17 +9990,20 @@ enums: meaning: OBI:2100031 OBI:2100032: title: low-density lipoprotein cholesterol assay - description: An analyte assay that measures the abundance of low-density lipoprotein + description: + An analyte assay that measures the abundance of low-density lipoprotein cholesterol meaning: OBI:2100032 OBI:2100033: title: thyroid stimulating hormone assay - description: An analyte assay that measures the abundance of thyroid stimulating + description: + An analyte assay that measures the abundance of thyroid stimulating hormone meaning: OBI:2100033 OBI:2100034: title: prostate-specific antigen assay - description: An analyte assay that measures the abundance of prostate-specific + description: + An analyte assay that measures the abundance of prostate-specific antigen meaning: OBI:2100034 OBI:2100035: @@ -8348,227 +10072,272 @@ enums: meaning: OBI:2100050 OBI:2100051: title: 3-hydroxybutyric acid assay - description: An analyte assay that measures the abundance of 3-hydroxybutyric + description: + An analyte assay that measures the abundance of 3-hydroxybutyric acid meaning: OBI:2100051 OBI:2100052: title: panel5 venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order meaning: OBI:2100052 OBI:2100053: title: panel5 venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order meaning: OBI:2100053 OBI:2100054: title: panel5 venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order meaning: OBI:2100054 OBI:2100055: title: panel5 venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order meaning: OBI:2100055 OBI:2100056: title: automated differential venous blood basophil count assay - description: A cytometry assay that measures the count of basophils in venous + description: + A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order meaning: OBI:2100056 OBI:2100057: title: automated differential venous blood neutrophil count assay - description: A cytometry assay that measures the count of neutrophils in venous + description: + A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order meaning: OBI:2100057 OBI:2100058: title: automated differential venous blood eosinophil count assay - description: A cytometry assay that measures the count of eosinophils in venous + description: + A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order meaning: OBI:2100058 OBI:2100059: title: automated differential venous blood lymphocyte count assay - description: A cytometry assay that measures the count of lymphocytes in venous + description: + A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order meaning: OBI:2100059 OBI:2100060: title: automated differential venous blood monocyte count assay - description: A cytometry assay that measures the count of monocytes in venous + description: + A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order meaning: OBI:2100060 OBI:2100061: title: venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous + description: + An analyte assay that measures the abundance of chloride in venous blood meaning: OBI:2100061 OBI:2100062: title: CBC with automated differential venous blood RBC count assay - description: A cytometry assay that measures the count of RBCs in venous blood + description: + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order meaning: OBI:2100062 OBI:2100063: title: CBC with automated differential venous blood platelet count assay - description: A cytometry assay that measures the count of platelets in venous + description: + A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order meaning: OBI:2100063 OBI:2100064: title: CBC with automated differential venous blood WBC count assay - description: A cytometry assay that measures the count of WBCs in venous blood + description: + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order meaning: OBI:2100064 OBI:2100065: title: CBC with automated differential venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order meaning: OBI:2100065 OBI:2100066: title: CBC with automated differential venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order meaning: OBI:2100066 OBI:2100067: title: venous blood phosphate assay - description: An analyte assay that measures the abundance of phosphate in + description: + An analyte assay that measures the abundance of phosphate in venous blood meaning: OBI:2100067 OBI:2100068: title: liver injury venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order meaning: OBI:2100068 OBI:2100069: title: liver injury venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order meaning: OBI:2100069 OBI:2100070: title: liver injury venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order meaning: OBI:2100070 OBI:2100071: title: liver injury venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order meaning: OBI:2100071 OBI:2100072: title: venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood meaning: OBI:2100072 OBI:2100073: title: venous blood magnesium assay - description: An analyte assay that measures the abundance of magnesium in + description: + An analyte assay that measures the abundance of magnesium in venous blood meaning: OBI:2100073 OBI:2100074: title: CBC venous blood RBC count assay - description: A cytometry assay that measures the count of RBCs in venous blood + description: + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order meaning: OBI:2100074 OBI:2100075: title: CBC venous blood WBC count assay - description: A cytometry assay that measures the count of WBCs in venous blood + description: + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order meaning: OBI:2100075 OBI:2100076: title: CBC venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order meaning: OBI:2100076 OBI:2100077: title: CBC venous blood platelet count assay - description: A cytometry assay that measures the count of platelets in venous + description: + A cytometry assay that measures the count of platelets in venous blood as part of a CBC order meaning: OBI:2100077 OBI:2100078: title: CBC venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order meaning: OBI:2100078 OBI:2100079: title: corrected venous blood leukocyte count assay - description: A cytometry assay that measures the count of leukocytes in venous + description: + A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order meaning: OBI:2100079 OBI:2100080: title: liver evaluation venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order meaning: OBI:2100080 OBI:2100081: title: liver evaluation venous blood globulin assay - description: An analyte assay that measures the abundance of globulin in venous + description: + An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order meaning: OBI:2100081 OBI:2100082: title: liver evaluation venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order meaning: OBI:2100082 OBI:2100083: title: liver evaluation venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order meaning: OBI:2100083 OBI:2100084: title: liver evaluation venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order meaning: OBI:2100084 OBI:2100085: title: liver evaluation venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order meaning: OBI:2100085 OBI:2100086: title: liver evaluation venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order meaning: OBI:2100086 OBI:2100087: title: basic metabolic panel venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous + description: + An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order meaning: OBI:2100087 OBI:2100088: title: basic metabolic panel venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order meaning: OBI:2100088 OBI:2100089: title: basic metabolic panel venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order meaning: OBI:2100089 OBI:2100090: title: basic metabolic panel venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order meaning: OBI:2100090 OBI:2100091: title: basic metabolic panel venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order meaning: OBI:2100091 OBI:2100092: title: basic metabolic panel venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order meaning: OBI:2100092 OBI:2100093: title: basic metabolic panel venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order meaning: OBI:2100093 OBI:2100094: title: venous blood creatine kinase assay - description: An analyte assay that measures the abundance of creatine kinase + description: + An analyte assay that measures the abundance of creatine kinase in venous blood meaning: OBI:2100094 OBI:2100095: title: venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood meaning: OBI:2100095 OBI:2100096: @@ -8577,68 +10346,82 @@ enums: meaning: OBI:2100096 OBI:2100097: title: total venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a total order meaning: OBI:2100097 OBI:2100098: title: venous blood iron assay - description: An analyte assay that measures the abundance of iron in venous + description: + An analyte assay that measures the abundance of iron in venous blood meaning: OBI:2100098 OBI:2100099: title: CBC with manual differential venous blood band neutrophil count assay - description: A cytometry assay that measures the count of band neutrophils + description: + A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order meaning: OBI:2100099 OBI:2100100: title: CBC with manual differential venous blood WBC count assay - description: A cytometry assay that measures the count of WBCs in venous blood + description: + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order meaning: OBI:2100100 OBI:2100101: title: CBC with manual differential venous blood eosinophil count assay - description: A cytometry assay that measures the count of eosinophils in venous + description: + A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order meaning: OBI:2100101 OBI:2100102: title: CBC with manual differential venous blood lymphocyte count assay - description: A cytometry assay that measures the count of lymphocytes in venous + description: + A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100102 OBI:2100103: title: CBC with manual differential venous blood nucleated RBC count assay - description: A cytometry assay that measures the count of nucleated RBCs in + description: + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order meaning: OBI:2100103 OBI:2100104: title: CBC with manual differential venous blood monocyte count assay - description: A cytometry assay that measures the count of monocytes in venous + description: + A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100104 OBI:2100105: - title: CBC with manual differential venous blood segmented neutrophil count + title: + CBC with manual differential venous blood segmented neutrophil count assay - description: A cytometry assay that measures the count of segmented neutrophils + description: + A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order meaning: OBI:2100105 OBI:2100106: title: CBC with manual differential venous blood basophil count assay - description: A cytometry assay that measures the count of basophils in venous + description: + A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order meaning: OBI:2100106 OBI:2100107: title: venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood meaning: OBI:2100107 OBI:2100108: title: cardiac enzymes venous blood creatine kinase assay - description: An analyte assay that measures the abundance of creatine kinase + description: + An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order meaning: OBI:2100108 OBI:2100109: title: venous blood haptoglobin assay - description: An analyte assay that measures the abundance of haptoglobin in + description: + An analyte assay that measures the abundance of haptoglobin in venous blood meaning: OBI:2100109 OBI:2100110: @@ -8647,27 +10430,32 @@ enums: meaning: OBI:2100110 OBI:2100111: title: venous blood prealbunin assay - description: An analyte assay that measures the abundance of prealbunin in + description: + An analyte assay that measures the abundance of prealbunin in venous blood meaning: OBI:2100111 OBI:2100112: title: lipid panel venous blood triglyceride assay - description: An analyte assay that measures the abundance of triglyceride + description: + An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order meaning: OBI:2100112 OBI:2100113: title: lipid panel venous blood high density lipoprotein assay - description: An analyte assay that measures the abundance of high density + description: + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order meaning: OBI:2100113 OBI:2100114: title: lipid panel venous blood cholesterol assay - description: An analyte assay that measures the abundance of cholesterol in + description: + An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order meaning: OBI:2100114 OBI:2100115: title: lipid panel venous blood low density lipoprotein assay - description: An analyte assay that measures the abundance of low density lipoprotein + description: + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order meaning: OBI:2100115 OBI:2100116: @@ -8676,117 +10464,140 @@ enums: meaning: OBI:2100116 OBI:2100117: title: venous blood uric acid assay - description: An analyte assay that measures the abundance of uric acid in + description: + An analyte assay that measures the abundance of uric acid in venous blood meaning: OBI:2100117 OBI:2100118: title: total venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a total order meaning: OBI:2100118 OBI:2100119: title: venous blood thyroid stimulating hormone assay - description: An analyte assay that measures the abundance of thyroid stimulating + description: + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood meaning: OBI:2100119 OBI:2100120: title: venous blood prostate specific antigen assay - description: An analyte assay that measures the abundance of prostate specific + description: + An analyte assay that measures the abundance of prostate specific antigen in venous blood meaning: OBI:2100120 OBI:2100121: title: 24 hour total urine volume assay - description: An assay that measures volume in urine as part of a 24 hour total + description: + An assay that measures volume in urine as part of a 24 hour total order meaning: OBI:2100121 OBI:2100122: title: T4 uptake venous blood T4 assay - description: An analyte assay that measures the abundance of T4 in venous + description: + An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order meaning: OBI:2100122 OBI:2100123: title: arterial blood glucose assay - description: An analyte assay that measures the abundance of glucose in arterial + description: + An analyte assay that measures the abundance of glucose in arterial blood meaning: OBI:2100123 OBI:2100124: title: CBC with manual differential venous blood cell count assay - description: A cytometry assay that measures the count of cells in venous + description: + A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order meaning: OBI:2100124 OBI:2100125: title: hemoglobin oxygen saturation arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order meaning: OBI:2100125 OBI:2100126: title: hemoglobin oxygen saturation arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order meaning: OBI:2100126 OBI:2100127: title: inpatient profile venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order meaning: OBI:2100127 OBI:2100128: title: inpatient profile venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order meaning: OBI:2100128 OBI:2100129: title: inpatient profile venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order meaning: OBI:2100129 OBI:2100130: title: inpatient profile venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order meaning: OBI:2100130 OBI:2100131: title: venous blood folic acid assay - description: An analyte assay that measures the abundance of folic acid in + description: + An analyte assay that measures the abundance of folic acid in venous blood meaning: OBI:2100131 OBI:2100132: title: count venous blood reticulocyte count assay - description: A cytometry assay that measures the count of reticulocytes in + description: + A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order meaning: OBI:2100132 OBI:2100133: title: venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood meaning: OBI:2100133 OBI:2100134: title: venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood meaning: OBI:2100134 OBI:2100135: title: venous blood transferrin assay - description: An analyte assay that measures the abundance of transferrin in + description: + An analyte assay that measures the abundance of transferrin in venous blood meaning: OBI:2100135 OBI:2100136: title: venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood meaning: OBI:2100136 OBI:2100137: title: random electrolytes urine sodium assay - description: An analyte assay that measures the abundance of sodium in urine + description: + An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order meaning: OBI:2100137 OBI:2100138: title: random electrolytes urine potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order meaning: OBI:2100138 OBI:2100139: title: urine creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in urine meaning: OBI:2100139 OBI:2100140: @@ -8795,32 +10606,38 @@ enums: meaning: OBI:2100140 OBI:2100141: title: cooximitery arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order meaning: OBI:2100141 OBI:2100142: title: cooximitery arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order meaning: OBI:2100142 OBI:2100143: title: cooximitery arterial blood methemoglobin assay - description: An analyte assay that measures the abundance of methemoglobin + description: + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order meaning: OBI:2100143 OBI:2100144: title: electrolytes urine sodium assay - description: An analyte assay that measures the abundance of sodium in urine + description: + An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order meaning: OBI:2100144 OBI:2100145: title: electrolytes urine potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order meaning: OBI:2100145 OBI:2100146: title: Biosite cardiac panel arterial blood creatine kinase MB assay - description: An assay that measures creatine kinase MB in arterial blood as + description: + An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order meaning: OBI:2100146 OBI:2100147: @@ -8829,71 +10646,87 @@ enums: meaning: OBI:2100147 OBI:2100148: title: comprehensive metabolic panel venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100148 OBI:2100149: title: comprehensive metabolic panel venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100149 OBI:2100150: title: comprehensive metabolic panel venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100150 OBI:2100151: title: comprehensive metabolic panel venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100151 OBI:2100152: title: comprehensive metabolic panel venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100152 OBI:2100153: title: comprehensive metabolic panel venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100153 OBI:2100154: - title: comprehensive metabolic panel venous blood human alkaline phosphatase + title: + comprehensive metabolic panel venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100154 OBI:2100155: title: comprehensive metabolic panel venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100155 OBI:2100156: title: comprehensive metabolic panel venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous + description: + An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100156 OBI:2100157: - title: comprehensive metabolic panel venous blood human aspartate aminotransferase + title: + comprehensive metabolic panel venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100157 OBI:2100158: title: comprehensive metabolic panel venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100158 OBI:2100159: title: comprehensive metabolic panel venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100159 OBI:2100160: - title: comprehensive metabolic panel venous blood alanine aminotransferase + title: + comprehensive metabolic panel venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order meaning: OBI:2100160 OBI:2100161: @@ -8910,192 +10743,230 @@ enums: meaning: OBI:2100163 OBI:2100164: title: venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in venous blood meaning: OBI:2100164 OBI:2100165: title: venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood meaning: OBI:2100165 OBI:2100166: title: blood gas venous blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in venous + description: + An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order meaning: OBI:2100166 OBI:2100167: title: ionized venous blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order meaning: OBI:2100167 OBI:2100168: title: blood gas venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order meaning: OBI:2100168 OBI:2100169: title: blood gas venous blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order meaning: OBI:2100169 OBI:2100170: title: arterial blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in arterial blood meaning: OBI:2100170 OBI:2100171: title: venous blood tacrolimus assay - description: An analyte assay that measures the abundance of tacrolimus in + description: + An analyte assay that measures the abundance of tacrolimus in venous blood meaning: OBI:2100171 OBI:2100172: title: random venous blood vancomycin assay - description: An analyte assay that measures the abundance of vancomycin in + description: + An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order meaning: OBI:2100172 OBI:2100173: title: venous blood mycophenolic acid assay - description: An analyte assay that measures the abundance of mycophenolic + description: + An analyte assay that measures the abundance of mycophenolic acid in venous blood meaning: OBI:2100173 OBI:2100174: title: non-vented blood gas arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order meaning: OBI:2100174 OBI:2100175: title: non-vented blood gas arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order meaning: OBI:2100175 OBI:2100176: title: non-vented blood gas arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order meaning: OBI:2100176 OBI:2100177: title: quantitative venous blood IgG assay - description: An assay that measures IgG in venous blood as part of a quantitative + description: + An assay that measures IgG in venous blood as part of a quantitative order meaning: OBI:2100177 OBI:2100178: title: quantitative venous blood IgM assay - description: An assay that measures IgM in venous blood as part of a quantitative + description: + An assay that measures IgM in venous blood as part of a quantitative order meaning: OBI:2100178 OBI:2100179: title: quantitative venous blood IgA assay - description: An assay that measures IgA in venous blood as part of a quantitative + description: + An assay that measures IgA in venous blood as part of a quantitative order meaning: OBI:2100179 OBI:2100180: title: arterial blood sodium assay - description: An analyte assay that measures the abundance of sodium in arterial + description: + An analyte assay that measures the abundance of sodium in arterial blood meaning: OBI:2100180 OBI:2100181: title: arterial blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in arterial blood meaning: OBI:2100181 OBI:2100182: title: ionized arterial blood calcium assay - description: An analyte assay that measures the abundance of calcium in arterial + description: + An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order meaning: OBI:2100182 OBI:2100183: title: vented blood gas arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order meaning: OBI:2100183 OBI:2100184: title: vented blood gas arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order meaning: OBI:2100184 OBI:2100185: title: vented blood gas arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order meaning: OBI:2100185 OBI:2100186: title: arterial blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in arterial blood meaning: OBI:2100186 OBI:2100187: title: arterial blood chloride assay - description: An analyte assay that measures the abundance of chloride in arterial + description: + An analyte assay that measures the abundance of chloride in arterial blood meaning: OBI:2100187 OBI:2100188: title: arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in arterial blood meaning: OBI:2100188 OBI:2100189: title: GEM premier blood gas venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order meaning: OBI:2100189 OBI:2100190: title: GEM premier blood gas venous blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order meaning: OBI:2100190 OBI:2100191: title: GEM premier blood gas venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order meaning: OBI:2100191 OBI:2100192: title: GEM premier blood gas venous blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in venous + description: + An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order meaning: OBI:2100192 OBI:2100193: title: GEM premier blood gas venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order meaning: OBI:2100193 OBI:2100194: title: GEM premier blood gas venous blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order meaning: OBI:2100194 OBI:2100195: title: GEM premier blood gas venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order meaning: OBI:2100195 OBI:2100196: title: GEM premier blood gas venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order meaning: OBI:2100196 OBI:2100197: title: GEM premier blood gas venous blood lactic acid assay - description: An assay that measures lactic acid in venous blood as part of + description: + An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order meaning: OBI:2100197 OBI:2100198: title: GEM premier blood gas venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order meaning: OBI:2100198 OBI:2100199: title: trough venous blood tobramycin assay - description: An analyte assay that measures the abundance of tobramycin in + description: + An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order meaning: OBI:2100199 OBI:2100200: title: random venous blood tobramycin assay - description: An analyte assay that measures the abundance of tobramycin in + description: + An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order meaning: OBI:2100200 OBI:2100201: title: CBC with manual differential venous blood metamyelocyte count assay - description: A cytometry assay that measures the count of metamyelocytes in + description: + A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100201 OBI:2100202: @@ -9104,12 +10975,14 @@ enums: meaning: OBI:2100202 OBI:2100203: title: venous blood 25-hydroxyvitamin D2 assay - description: An analyte assay that measures the abundance of 25-hydroxyvitamin + description: + An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood meaning: OBI:2100203 OBI:2100204: title: venous blood digoxin assay - description: An analyte assay that measures the abundance of digoxin in venous + description: + An analyte assay that measures the abundance of digoxin in venous blood meaning: OBI:2100204 OBI:2100205: @@ -9118,458 +10991,549 @@ enums: meaning: OBI:2100205 OBI:2100206: title: venous blood tobramycin assay - description: An analyte assay that measures the abundance of tobramycin in + description: + An analyte assay that measures the abundance of tobramycin in venous blood meaning: OBI:2100206 OBI:2100207: title: CBC with manual differential venous blood myelocyte count assay - description: A cytometry assay that measures the count of myelocytes in venous + description: + A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100207 OBI:2100208: title: SPEP protein electrophoresis venous blood beta-globin assay - description: An analyte assay that measures the abundance of beta-globin in + description: + An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order meaning: OBI:2100208 OBI:2100209: title: SPEP protein electrophoresis venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order meaning: OBI:2100209 OBI:2100210: title: SPEP protein electrophoresis venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order meaning: OBI:2100210 OBI:2100211: title: trough venous blood vancomycin assay - description: An analyte assay that measures the abundance of vancomycin in + description: + An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order meaning: OBI:2100211 OBI:2100212: title: hepatic panel venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order meaning: OBI:2100212 OBI:2100213: title: hepatic panel venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order meaning: OBI:2100213 OBI:2100214: title: hepatic panel venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order meaning: OBI:2100214 OBI:2100215: title: hepatic panel venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order meaning: OBI:2100215 OBI:2100216: title: hepatic panel venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order meaning: OBI:2100216 OBI:2100217: title: hepatic panel venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order meaning: OBI:2100217 OBI:2100218: title: estimated venous blood glomerular filtration assay - description: An assay that measures glomerular filtration in venous blood + description: + An assay that measures glomerular filtration in venous blood as part of a estimated order meaning: OBI:2100218 OBI:2100219: title: DT60 venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order meaning: OBI:2100219 OBI:2100220: title: fasting venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order meaning: OBI:2100220 OBI:2100221: title: random venous blood amikacin assay - description: An analyte assay that measures the abundance of amikacin in venous + description: + An analyte assay that measures the abundance of amikacin in venous blood as part of a random order meaning: OBI:2100221 OBI:2100222: title: venous blood ammonia assay - description: An analyte assay that measures the abundance of ammonia in venous + description: + An analyte assay that measures the abundance of ammonia in venous blood meaning: OBI:2100222 OBI:2100223: title: venous blood GGT assay - description: An analyte assay that measures the abundance of GGT in venous + description: + An analyte assay that measures the abundance of GGT in venous blood meaning: OBI:2100223 OBI:2100224: title: chem11 venous blood phosphate assay - description: An analyte assay that measures the abundance of phosphate in + description: + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order meaning: OBI:2100224 OBI:2100225: title: chem11 venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order meaning: OBI:2100225 OBI:2100226: title: chem11 venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order meaning: OBI:2100226 OBI:2100227: title: chem11 venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order meaning: OBI:2100227 OBI:2100228: title: chem11 venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order meaning: OBI:2100228 OBI:2100229: title: chem11 venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order meaning: OBI:2100229 OBI:2100230: title: chem11 venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order meaning: OBI:2100230 OBI:2100231: title: chem11 venous blood magnesium assay - description: An analyte assay that measures the abundance of magnesium in + description: + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order meaning: OBI:2100231 OBI:2100232: title: chem11 venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order meaning: OBI:2100232 OBI:2100233: title: chem11 venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous + description: + An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order meaning: OBI:2100233 OBI:2100234: title: total venous blood IgE assay - description: An assay that measures IgE in venous blood as part of a total + description: + An assay that measures IgE in venous blood as part of a total order meaning: OBI:2100234 OBI:2100235: title: chem16 venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order meaning: OBI:2100235 OBI:2100236: title: chem16 venous blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order meaning: OBI:2100236 OBI:2100237: title: chem16 venous blood magnesium assay - description: An analyte assay that measures the abundance of magnesium in + description: + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order meaning: OBI:2100237 OBI:2100238: title: chem16 venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order meaning: OBI:2100238 OBI:2100239: title: chem16 venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous + description: + An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order meaning: OBI:2100239 OBI:2100240: title: chem16 venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order meaning: OBI:2100240 OBI:2100241: title: chem16 venous blood triglyceride assay - description: An analyte assay that measures the abundance of triglyceride + description: + An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order meaning: OBI:2100241 OBI:2100242: title: chem16 venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous + description: + An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order meaning: OBI:2100242 OBI:2100243: title: chem16 venous blood phosphate assay - description: An analyte assay that measures the abundance of phosphate in + description: + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order meaning: OBI:2100243 OBI:2100244: title: chem16 venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order meaning: OBI:2100244 OBI:2100245: title: chem16 venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order meaning: OBI:2100245 OBI:2100246: title: chem16 venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order meaning: OBI:2100246 OBI:2100247: title: chem16 venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous + description: + An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order meaning: OBI:2100247 OBI:2100248: title: chem16 venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order meaning: OBI:2100248 OBI:2100249: title: chem16 venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order meaning: OBI:2100249 OBI:2100250: title: POC chem8 arterial blood glucose assay - description: An analyte assay that measures the abundance of glucose in arterial + description: + An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order meaning: OBI:2100250 OBI:2100251: title: POC chem8 arterial blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order meaning: OBI:2100251 OBI:2100252: title: POC chem8 arterial blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order meaning: OBI:2100252 OBI:2100253: title: POC chem8 arterial blood sodium assay - description: An analyte assay that measures the abundance of sodium in arterial + description: + An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order meaning: OBI:2100253 OBI:2100254: title: POC chem8 arterial blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order meaning: OBI:2100254 OBI:2100255: title: POC chem8 arterial blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order meaning: OBI:2100255 OBI:2100256: title: POC chem8 arterial blood chloride assay - description: An analyte assay that measures the abundance of chloride in arterial + description: + An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order meaning: OBI:2100256 OBI:2100257: title: peak venous blood tobramycin assay - description: An analyte assay that measures the abundance of tobramycin in + description: + An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order meaning: OBI:2100257 OBI:2100258: title: 24 hour urine creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order meaning: OBI:2100258 OBI:2100259: title: intact venous blood PTH assay - description: An analyte assay that measures the abundance of PTH in venous + description: + An analyte assay that measures the abundance of PTH in venous blood as part of a intact order meaning: OBI:2100259 OBI:2100260: title: total venous blood PSA assay - description: An analyte assay that measures the abundance of PSA in venous + description: + An analyte assay that measures the abundance of PSA in venous blood as part of a total order meaning: OBI:2100260 OBI:2100261: title: total venous blood T3 assay - description: An analyte assay that measures the abundance of T3 in venous + description: + An analyte assay that measures the abundance of T3 in venous blood as part of a total order meaning: OBI:2100261 OBI:2100262: title: 24 hour urine protein assay - description: An analyte assay that measures the abundance of protein in urine + description: + An analyte assay that measures the abundance of protein in urine as part of a 24 hour order meaning: OBI:2100262 OBI:2100263: title: total venous blood cholesterol assay - description: An analyte assay that measures the abundance of cholesterol in + description: + An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order meaning: OBI:2100263 OBI:2100264: title: venous blood triglyceride assay - description: An analyte assay that measures the abundance of triglyceride + description: + An analyte assay that measures the abundance of triglyceride in venous blood meaning: OBI:2100264 OBI:2100265: title: tube 4 count cerebrospinal fluid cell count assay - description: A cytometry assay that measures the count of cells in cerebrospinal + description: + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order meaning: OBI:2100265 OBI:2100266: title: cerebrospinal fluid protein assay - description: An analyte assay that measures the abundance of protein in cerebrospinal + description: + An analyte assay that measures the abundance of protein in cerebrospinal fluid meaning: OBI:2100266 OBI:2100267: title: cerebrospinal fluid glucose assay - description: An analyte assay that measures the abundance of glucose in cerebrospinal + description: + An analyte assay that measures the abundance of glucose in cerebrospinal fluid meaning: OBI:2100267 OBI:2100268: title: tube 1 count cerebrospinal fluid cell count assay - description: A cytometry assay that measures the count of cells in cerebrospinal + description: + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order meaning: OBI:2100268 OBI:2100269: title: venous blood dehydroepiandrosterone assay - description: An analyte assay that measures the abundance of dehydroepiandrosterone + description: + An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood meaning: OBI:2100269 OBI:2100270: title: venous blood cortisol assay - description: An analyte assay that measures the abundance of cortisol in venous + description: + An analyte assay that measures the abundance of cortisol in venous blood meaning: OBI:2100270 OBI:2100271: - title: ABL90 panel arterial blood sodium assay - description: An analyte assay that measures the abundance of sodium in arterial - blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood sodium assay + description: + An analyte assay that measures the abundance of sodium in arterial + blood as part of a ABLE90 panel order meaning: OBI:2100271 OBI:2100272: - title: ABL90 panel arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial - blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood oxygen assay + description: + An analyte assay that measures the abundance of oxygen in arterial + blood as part of a ABLE90 panel order meaning: OBI:2100272 OBI:2100273: - title: ABL90 panel arterial blood glucose assay - description: An analyte assay that measures the abundance of glucose in arterial - blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood glucose assay + description: + An analyte assay that measures the abundance of glucose in arterial + blood as part of a ABLE90 panel order meaning: OBI:2100273 OBI:2100274: - title: ABL90 panel arterial blood lactic acid assay - description: An assay that measures lactic acid in arterial blood as part - of a ABL90 panel order + title: ABLE90 panel arterial blood lactic acid assay + description: + An assay that measures lactic acid in arterial blood as part + of a ABLE90 panel order meaning: OBI:2100274 OBI:2100275: - title: ABL90 panel arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in - arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood hemoglobin assay + description: + An analyte assay that measures the abundance of hemoglobin in + arterial blood as part of a ABLE90 panel order meaning: OBI:2100275 OBI:2100276: - title: ABL90 panel arterial blood chloride assay - description: An analyte assay that measures the abundance of chloride in arterial - blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood chloride assay + description: + An analyte assay that measures the abundance of chloride in arterial + blood as part of a ABLE90 panel order meaning: OBI:2100276 OBI:2100277: - title: ABL90 panel arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide - in arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood carbon dioxide assay + description: + An analyte assay that measures the abundance of carbon dioxide + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100277 OBI:2100278: - title: ABL90 panel arterial blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells - in arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood hematocrit assay + description: + A cytometry assay that measures the proportion of red blood cells + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100278 OBI:2100279: - title: ABL90 panel arterial blood calcium assay - description: An analyte assay that measures the abundance of calcium in arterial - blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood calcium assay + description: + An analyte assay that measures the abundance of calcium in arterial + blood as part of a ABLE90 panel order meaning: OBI:2100279 OBI:2100280: - title: ABL90 panel arterial blood temperature assay - description: An assay that measures temperature in arterial blood as part - of a ABL90 panel order + title: ABLE90 panel arterial blood temperature assay + description: + An assay that measures temperature in arterial blood as part + of a ABLE90 panel order meaning: OBI:2100280 OBI:2100281: - title: ABL90 panel arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in - arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood bicarbonate assay + description: + An analyte assay that measures the abundance of bicarbonate in + arterial blood as part of a ABLE90 panel order meaning: OBI:2100281 OBI:2100282: - title: ABL90 panel arterial blood potassium assay - description: An analyte assay that measures the abundance of potassium in - arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood potassium assay + description: + An analyte assay that measures the abundance of potassium in + arterial blood as part of a ABLE90 panel order meaning: OBI:2100282 OBI:2100283: title: CBC with manual differential venous blood promyelocyte count assay - description: A cytometry assay that measures the count of promyelocytes in + description: + A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100283 OBI:2100284: - title: ABL90 panel venous blood glucose assay - description: An analyte assay that measures the abundance of glucose in venous - blood as part of a ABL90 panel order + title: ABLE90 panel venous blood glucose assay + description: + An analyte assay that measures the abundance of glucose in venous + blood as part of a ABLE90 panel order meaning: OBI:2100284 OBI:2100285: - title: ABL90 panel venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in - venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood hemoglobin assay + description: + An analyte assay that measures the abundance of hemoglobin in + venous blood as part of a ABLE90 panel order meaning: OBI:2100285 OBI:2100286: - title: ABL90 panel venous blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium - in venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood ionized calcium assay + description: + An analyte assay that measures the abundance of ionized calcium + in venous blood as part of a ABLE90 panel order meaning: OBI:2100286 OBI:2100287: - title: ABL90 panel venous blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide - in venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood carbon dioxide assay + description: + An analyte assay that measures the abundance of carbon dioxide + in venous blood as part of a ABLE90 panel order meaning: OBI:2100287 OBI:2100288: - title: ABL90 panel venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells - in venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood hematocrit assay + description: + A cytometry assay that measures the proportion of red blood cells + in venous blood as part of a ABLE90 panel order meaning: OBI:2100288 OBI:2100289: - title: ABL90 panel venous blood sodium assay - description: An analyte assay that measures the abundance of sodium in venous - blood as part of a ABL90 panel order + title: ABLE90 panel venous blood sodium assay + description: + An analyte assay that measures the abundance of sodium in venous + blood as part of a ABLE90 panel order meaning: OBI:2100289 OBI:2100290: - title: ABL90 panel venous blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in venous - blood as part of a ABL90 panel order + title: ABLE90 panel venous blood oxygen assay + description: + An analyte assay that measures the abundance of oxygen in venous + blood as part of a ABLE90 panel order meaning: OBI:2100290 OBI:2100291: - title: ABL90 panel venous blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in - venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood bicarbonate assay + description: + An analyte assay that measures the abundance of bicarbonate in + venous blood as part of a ABLE90 panel order meaning: OBI:2100291 OBI:2100292: - title: ABL90 panel venous blood lactic acid assay - description: An assay that measures lactic acid in venous blood as part of - a ABL90 panel order + title: ABLE90 panel venous blood lactic acid assay + description: + An assay that measures lactic acid in venous blood as part of + a ABLE90 panel order meaning: OBI:2100292 OBI:2100293: - title: ABL90 panel venous blood chloride assay - description: An analyte assay that measures the abundance of chloride in venous - blood as part of a ABL90 panel order + title: ABLE90 panel venous blood chloride assay + description: + An analyte assay that measures the abundance of chloride in venous + blood as part of a ABLE90 panel order meaning: OBI:2100293 OBI:2100294: title: venous blood T4 assay - description: An analyte assay that measures the abundance of T4 in venous + description: + An analyte assay that measures the abundance of T4 in venous blood meaning: OBI:2100294 OBI:2100295: title: free venous blood T4 assay - description: An analyte assay that measures the abundance of T4 in venous + description: + An analyte assay that measures the abundance of T4 in venous blood as part of a free order meaning: OBI:2100295 OBI:2100296: - title: ABL90 panel venous blood potassium assay - description: An analyte assay that measures the abundance of potassium in - venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood potassium assay + description: + An analyte assay that measures the abundance of potassium in + venous blood as part of a ABLE90 panel order meaning: OBI:2100296 OBI:2100297: title: urine sodium assay @@ -9577,292 +11541,350 @@ enums: meaning: OBI:2100297 OBI:2100298: title: bone profile venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order meaning: OBI:2100298 OBI:2100299: title: bone profile venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order meaning: OBI:2100299 OBI:2100300: title: bone profile venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order meaning: OBI:2100300 OBI:2100301: title: bone profile venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order meaning: OBI:2100301 OBI:2100302: title: bone profile venous blood phosphate assay - description: An analyte assay that measures the abundance of phosphate in + description: + An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order meaning: OBI:2100302 OBI:2100303: title: ABG/electrolytes arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order meaning: OBI:2100303 OBI:2100304: title: ABG/electrolytes arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order meaning: OBI:2100304 OBI:2100305: title: ABG/electrolytes arterial blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order meaning: OBI:2100305 OBI:2100306: title: CBC with automated differential venous blood nucleated RBC count assay - description: A cytometry assay that measures the count of nucleated RBCs in + description: + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order meaning: OBI:2100306 OBI:2100307: - title: ABL90 panel venous blood methemoglobin assay - description: An analyte assay that measures the abundance of methemoglobin - in venous blood as part of a ABL90 panel order + title: ABLE90 panel venous blood methemoglobin assay + description: + An analyte assay that measures the abundance of methemoglobin + in venous blood as part of a ABLE90 panel order meaning: OBI:2100307 OBI:2100308: - title: ABL90 panel arterial blood methemoglobin assay - description: An analyte assay that measures the abundance of methemoglobin - in arterial blood as part of a ABL90 panel order + title: ABLE90 panel arterial blood methemoglobin assay + description: + An analyte assay that measures the abundance of methemoglobin + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100308 OBI:2100309: title: venous blood valproic acid assay - description: An analyte assay that measures the abundance of valproic acid + description: + An analyte assay that measures the abundance of valproic acid in venous blood meaning: OBI:2100309 OBI:2100310: title: high sensitivity cardiac/neonatal venous blood c-reactive protein assay - description: An analyte assay that measures the abundance of c-reactive protein + description: + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order meaning: OBI:2100310 OBI:2100311: title: POC arterial blood creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order meaning: OBI:2100311 OBI:2100312: title: GEM4000 ANLCOOX arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100312 OBI:2100313: title: GEM4000 ANLCOOX arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100313 OBI:2100314: title: GEM4000 ANLCOOX arterial blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100314 OBI:2100315: title: GEM4000 ANLCOOX arterial blood temperature assay - description: An assay that measures temperature in arterial blood as part + description: + An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100315 OBI:2100316: title: GEM4000 ANLCOOX arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100316 OBI:2100317: title: GEM4000 ANLCOOX arterial blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100317 OBI:2100318: title: GEM4000 ANLCOOX arterial blood glucose assay - description: An analyte assay that measures the abundance of glucose in arterial + description: + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100318 OBI:2100319: title: GEM4000 ANLCOOX arterial blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100319 OBI:2100320: title: GEM4000 ANLCOOX arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100320 OBI:2100321: title: GEM4000 ANLCOOX arterial blood sodium assay - description: An analyte assay that measures the abundance of sodium in arterial + description: + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order meaning: OBI:2100321 OBI:2100322: title: ionized venous blood calcium assay - description: An analyte assay that measures the abundance of calcium in venous + description: + An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order meaning: OBI:2100322 OBI:2100323: title: venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in venous blood meaning: OBI:2100323 OBI:2100324: title: CBC with manual differential venous blood megakaryocyte count assay - description: A cytometry assay that measures the count of megakaryocytes in + description: + A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order meaning: OBI:2100324 OBI:2100325: title: non-cardiac venous blood c-reactive protein assay - description: An analyte assay that measures the abundance of c-reactive protein + description: + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order meaning: OBI:2100325 OBI:2100326: title: intraoperative venous blood PTH assay - description: An analyte assay that measures the abundance of PTH in venous + description: + An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order meaning: OBI:2100326 OBI:2100327: title: venous blood parathyroid hormone assay - description: An analyte assay that measures the abundance of parathyroid hormone + description: + An analyte assay that measures the abundance of parathyroid hormone in venous blood meaning: OBI:2100327 OBI:2100328: title: total bodily fluid protein assay - description: An analyte assay that measures the abundance of protein in bodily + description: + An analyte assay that measures the abundance of protein in bodily fluid as part of a total order meaning: OBI:2100328 OBI:2100329: title: bodily fluid glucose assay - description: An analyte assay that measures the abundance of glucose in bodily + description: + An analyte assay that measures the abundance of glucose in bodily fluid meaning: OBI:2100329 OBI:2100330: title: count bodily fluid cell count assay - description: A cytometry assay that measures the count of cells in bodily + description: + A cytometry assay that measures the count of cells in bodily fluid as part of a count order meaning: OBI:2100330 OBI:2100331: title: manual differential bodily fluid segmented neutrophil count assay - description: A cytometry assay that measures the count of segmented neutrophils + description: + A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order meaning: OBI:2100331 OBI:2100332: title: manual differential bodily fluid mesothelial cell count assay - description: A cytometry assay that measures the count of mesothelial cells + description: + A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order meaning: OBI:2100332 OBI:2100333: title: manual differential bodily fluid monocyte count assay - description: A cytometry assay that measures the count of monocytes in bodily + description: + A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order meaning: OBI:2100333 OBI:2100334: title: manual differential bodily fluid lymphocyte count assay - description: A cytometry assay that measures the count of lymphocytes in bodily + description: + A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order meaning: OBI:2100334 OBI:2100335: title: manual differential bodily fluid macrophage count assay - description: A cytometry assay that measures the count of macrophages in bodily + description: + A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order meaning: OBI:2100335 OBI:2100336: title: manual differential bodily fluid basophil count assay - description: A cytometry assay that measures the count of basophils in bodily + description: + A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order meaning: OBI:2100336 OBI:2100337: title: manual differential bodily fluid eosinophil count assay - description: A cytometry assay that measures the count of eosinophils in bodily + description: + A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order meaning: OBI:2100337 OBI:2100338: title: liver function venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order meaning: OBI:2100338 OBI:2100339: title: liver function venous blood alanine aminotransferase assay - description: An analyte assay that measures the abundance of alanine aminotransferase + description: + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order meaning: OBI:2100339 OBI:2100340: title: liver function venous blood human aspartate aminotransferase assay - description: An analyte assay that measures the abundance of human aspartate + description: + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order meaning: OBI:2100340 OBI:2100341: title: liver function venous blood albumin assay - description: An analyte assay that measures the abundance of albumin in venous + description: + An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order meaning: OBI:2100341 OBI:2100342: title: liver function venous blood protein assay - description: An analyte assay that measures the abundance of protein in venous + description: + An analyte assay that measures the abundance of protein in venous blood as part of a liver function order meaning: OBI:2100342 OBI:2100343: title: liver function venous blood human alkaline phosphatase assay - description: An analyte assay that measures the abundance of human alkaline + description: + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order meaning: OBI:2100343 OBI:2100344: title: vitamin B12 and Folate venous blood folic acid assay - description: An analyte assay that measures the abundance of folic acid in + description: + An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order meaning: OBI:2100344 OBI:2100345: title: bodily fluid cell count assay - description: A cytometry assay that measures the count of cells in bodily + description: + A cytometry assay that measures the count of cells in bodily fluid meaning: OBI:2100345 OBI:2100346: title: venous blood reticulocyte count assay - description: A cytometry assay that measures the count of reticulocytes in + description: + A cytometry assay that measures the count of reticulocytes in venous blood meaning: OBI:2100346 OBI:2100347: title: bodily fluid cholesterol assay - description: An analyte assay that measures the abundance of cholesterol in + description: + An analyte assay that measures the abundance of cholesterol in bodily fluid meaning: OBI:2100347 OBI:2100348: title: TSH reflex Free T4 venous blood thyroid stimulating hormone assay - description: An analyte assay that measures the abundance of thyroid stimulating + description: + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order meaning: OBI:2100348 OBI:2100349: title: direct venous blood bilirubin assay - description: An analyte assay that measures the abundance of bilirubin in + description: + An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order meaning: OBI:2100349 OBI:2100350: title: free venous blood T3 assay - description: An analyte assay that measures the abundance of T3 in venous + description: + An analyte assay that measures the abundance of T3 in venous blood as part of a free order meaning: OBI:2100350 OBI:2100351: title: bodily fluid albumin assay - description: An analyte assay that measures the abundance of albumin in bodily + description: + An analyte assay that measures the abundance of albumin in bodily fluid meaning: OBI:2100351 OBI:2100352: title: bodily fluid triglyceride assay - description: An analyte assay that measures the abundance of triglyceride + description: + An analyte assay that measures the abundance of triglyceride in bodily fluid meaning: OBI:2100352 OBI:2100353: title: hemoglobin and hematocrit venous blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order meaning: OBI:2100353 OBI:2100354: title: hemoglobin and hematocrit venous blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order meaning: OBI:2100354 OBI:2100355: title: venous blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in venous blood meaning: OBI:2100355 OBI:2100356: @@ -9871,12 +11893,14 @@ enums: meaning: OBI:2100356 OBI:2100357: title: venous blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in venous blood meaning: OBI:2100357 OBI:2100358: title: venous blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in venous + description: + An analyte assay that measures the abundance of oxygen in venous blood meaning: OBI:2100358 OBI:2100359: @@ -9884,39 +11908,47 @@ enums: description: An assay that measures osmolality in venous blood meaning: OBI:2100359 OBI:2100360: - title: liver fibrosis (chronic viral hepatitis) venous blood platelet count + title: + liver fibrosis (chronic viral hepatitis) venous blood platelet count assay - description: A cytometry assay that measures the count of platelets in venous + description: + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order meaning: OBI:2100360 OBI:2100361: title: venous blood T3 assay - description: An analyte assay that measures the abundance of T3 in venous + description: + An analyte assay that measures the abundance of T3 in venous blood meaning: OBI:2100361 OBI:2100362: title: CBC with manual differential venous blood neutrophil count assay - description: A cytometry assay that measures the count of neutrophils in venous + description: + A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order meaning: OBI:2100362 OBI:2100363: title: creatinine clearance urine creatinine assay - description: An analyte assay that measures the abundance of creatinine in + description: + An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order meaning: OBI:2100363 OBI:2100364: title: venous blood beta hydroxybutryic acid assay - description: An analyte assay that measures the abundance of beta hydroxybutryic + description: + An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood meaning: OBI:2100364 OBI:2100365: title: venous blood megakaryocyte count assay - description: A cytometry assay that measures the count of megakaryocytes in + description: + A cytometry assay that measures the count of megakaryocytes in venous blood meaning: OBI:2100365 OBI:2100366: title: venous blood nucleated RBC count assay - description: A cytometry assay that measures the count of nucleated RBCs in + description: + A cytometry assay that measures the count of nucleated RBCs in venous blood meaning: OBI:2100366 OBI:2100367: @@ -9925,182 +11957,218 @@ enums: meaning: OBI:2100367 OBI:2100368: title: automated count venous blood reticulocyte count assay - description: A cytometry assay that measures the count of reticulocytes in + description: + A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order meaning: OBI:2100368 OBI:2100369: title: total venous blood homocysteine assay - description: An analyte assay that measures the abundance of homocysteine + description: + An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order meaning: OBI:2100369 OBI:2100370: title: venous blood Ceruloplasmin assay - description: An analyte assay that measures the abundance of Ceruloplasmin + description: + An analyte assay that measures the abundance of Ceruloplasmin in venous blood meaning: OBI:2100370 OBI:2100371: title: GEM4 arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order meaning: OBI:2100371 OBI:2100372: title: GEM4 arterial blood lactic acid assay - description: An assay that measures lactic acid in arterial blood as part + description: + An assay that measures lactic acid in arterial blood as part of a GEM4 order meaning: OBI:2100372 OBI:2100373: title: GEM4 arterial blood hemoglobin assay - description: An analyte assay that measures the abundance of hemoglobin in + description: + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order meaning: OBI:2100373 OBI:2100374: title: GEM4 arterial blood sodium assay - description: An analyte assay that measures the abundance of sodium in arterial + description: + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order meaning: OBI:2100374 OBI:2100375: title: GEM4 arterial blood potassium assay - description: An analyte assay that measures the abundance of potassium in + description: + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order meaning: OBI:2100375 OBI:2100376: title: GEM4 arterial blood temperature assay - description: An assay that measures temperature in arterial blood as part + description: + An assay that measures temperature in arterial blood as part of a GEM4 order meaning: OBI:2100376 OBI:2100377: title: GEM4 arterial blood glucose assay - description: An analyte assay that measures the abundance of glucose in arterial + description: + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order meaning: OBI:2100377 OBI:2100378: title: GEM4 arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order meaning: OBI:2100378 OBI:2100379: title: GEM4 arterial blood hematocrit assay - description: A cytometry assay that measures the proportion of red blood cells + description: + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order meaning: OBI:2100379 OBI:2100380: title: GEM4 arterial blood ionized calcium assay - description: An analyte assay that measures the abundance of ionized calcium + description: + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order meaning: OBI:2100380 OBI:2100381: title: GEM4 arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order meaning: OBI:2100381 OBI:2100382: title: liver fibrosis (NAFLD) venous blood platelet count assay - description: A cytometry assay that measures the count of platelets in venous + description: + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order meaning: OBI:2100382 OBI:2100383: title: venous blood beta hydroxybutric acid assay - description: An analyte assay that measures the abundance of beta hydroxybutric + description: + An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood meaning: OBI:2100383 OBI:2100384: title: CBC with manual differential venous blood plasma cell count assay - description: A cytometry assay that measures the count of plasma cells in + description: + A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order meaning: OBI:2100384 OBI:2100385: title: venous blood erythropoietin assay - description: An analyte assay that measures the abundance of erythropoietin + description: + An analyte assay that measures the abundance of erythropoietin in venous blood meaning: OBI:2100385 OBI:2100386: title: blood gas arterial blood oxygen assay - description: An analyte assay that measures the abundance of oxygen in arterial + description: + An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order meaning: OBI:2100386 OBI:2100387: title: blood gas arterial blood bicarbonate assay - description: An analyte assay that measures the abundance of bicarbonate in + description: + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order meaning: OBI:2100387 OBI:2100388: title: blood gas arterial blood carbon dioxide assay - description: An analyte assay that measures the abundance of carbon dioxide + description: + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order meaning: OBI:2100388 OBI:2100389: title: free/total venous blood PSA assay - description: An analyte assay that measures the abundance of PSA in venous + description: + An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order meaning: OBI:2100389 OBI:2100390: title: cerebrospinal fluid lymphocyte count assay - description: A cytometry assay that measures the count of lymphocytes in cerebrospinal + description: + A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid meaning: OBI:2100390 OBI:2100391: title: cerebrospinal fluid segmented neutrophil count assay - description: A cytometry assay that measures the count of segmented neutrophils + description: + A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid meaning: OBI:2100391 OBI:2100392: title: cerebrospinal fluid mesothelial cell count assay - description: A cytometry assay that measures the count of mesothelial cells + description: + A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid meaning: OBI:2100392 OBI:2100393: title: cerebrospinal fluid macrophage count assay - description: A cytometry assay that measures the count of macrophages in cerebrospinal + description: + A cytometry assay that measures the count of macrophages in cerebrospinal fluid meaning: OBI:2100393 OBI:2100394: title: cerebrospinal fluid basophil count assay - description: A cytometry assay that measures the count of basophils in cerebrospinal + description: + A cytometry assay that measures the count of basophils in cerebrospinal fluid meaning: OBI:2100394 OBI:2100395: title: cerebrospinal fluid monocyte count assay - description: A cytometry assay that measures the count of monocytes in cerebrospinal + description: + A cytometry assay that measures the count of monocytes in cerebrospinal fluid meaning: OBI:2100395 OBI:2100396: title: cerebrospinal fluid eosinophil count assay - description: A cytometry assay that measures the count of eosinophils in cerebrospinal + description: + A cytometry assay that measures the count of eosinophils in cerebrospinal fluid meaning: OBI:2100396 OBI:2100397: title: venous blood beta-2-microglobulin assay - description: An analyte assay that measures the abundance of beta-2-microglobulin + description: + An analyte assay that measures the abundance of beta-2-microglobulin in venous blood meaning: OBI:2100397 OBI:2100398: title: lipid panel reflex direct venous blood low density lipoprotein assay - description: An analyte assay that measures the abundance of low density lipoprotein + description: + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order meaning: OBI:2100398 OBI:2100399: title: lipid panel reflex direct venous blood triglyceride assay - description: An analyte assay that measures the abundance of triglyceride + description: + An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order meaning: OBI:2100399 OBI:2100400: title: lipid panel reflex direct venous blood cholesterol assay - description: An analyte assay that measures the abundance of cholesterol in + description: + An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order meaning: OBI:2100400 OBI:2100401: title: lipid panel reflex direct venous blood high density lipoprotein assay - description: An analyte assay that measures the abundance of high density + description: + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order meaning: OBI:2100401 OBI:2100402: title: pooled clone sequencing assay - description: A DNA sequencing assay in which the DNA input is derived from + description: + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. meaning: OBI:2100402 OBI:9999994: title: chromium release assay - description: An in vitro cell killing assay in which radioactive chromium + description: + An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. diff --git a/src/common_access_model/schema/enums/EnumAsserterType.yaml b/src/common_access_model/schema/enums/EnumAsserterType.yaml index 8d9b64a..51188f1 100644 --- a/src/common_access_model/schema/enums/EnumAsserterType.yaml +++ b/src/common_access_model/schema/enums/EnumAsserterType.yaml @@ -16,17 +16,17 @@ enums: title: Research Staff Asserted description: Assertion made by research staff. aliases: - - investigator_assessment + - investigator_assessment CAMO:0000017: title: Healthcare Asserted description: Assertion documented by a healthcare system or provider. aliases: - - medical_record + - medical_record CAMO:0000018: title: Participant or Representative Asserted description: Assertion made by a study participant, their representative, or some combination. aliases: - - participant_or_caregiver_report + - participant_or_caregiver_report CAMO:0000019: title: Participant Asserted description: Assertion made by a study participant. @@ -35,4 +35,4 @@ enums: description: Assertion made by a study participant's representative or representatives. CAMO:0000021: title: Caregiver Asserted - description: Assertion made by a study participant's caregiver or caregivers. \ No newline at end of file + description: Assertion made by a study participant's caregiver or caregivers. diff --git a/src/common_access_model/schema/enums/EnumAvailabilityStatus.yaml b/src/common_access_model/schema/enums/EnumAvailabilityStatus.yaml index 76d4a7a..1eeee2b 100644 --- a/src/common_access_model/schema/enums/EnumAvailabilityStatus.yaml +++ b/src/common_access_model/schema/enums/EnumAvailabilityStatus.yaml @@ -11,4 +11,4 @@ enums: snomedct:103329007: title: Unavailable meaning: snomedct:103329007 - description: The item is not available to users. \ No newline at end of file + description: The item is not available to users. diff --git a/src/common_access_model/schema/enums/EnumDataCategory.yaml b/src/common_access_model/schema/enums/EnumDataCategory.yaml index 3fd26b8..d796160 100644 --- a/src/common_access_model/schema/enums/EnumDataCategory.yaml +++ b/src/common_access_model/schema/enums/EnumDataCategory.yaml @@ -15,29 +15,34 @@ enums: permissible_values: edam:topic_0077: title: Nucleic acids - description: The processing and analysis of nucleic acid sequence, structural + description: + The processing and analysis of nucleic acid sequence, structural and other data. meaning: edam:topic_0077 edam:topic_0078: title: Proteins - description: Archival, processing and analysis of protein data, typically + description: + Archival, processing and analysis of protein data, typically molecular sequence and structural data. meaning: edam:topic_0078 edam:topic_0080: title: Sequence analysis - description: The archival, processing and analysis of molecular sequences + description: + The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. meaning: edam:topic_0080 edam:topic_0081: title: Structure analysis - description: The curation, processing, analysis and prediction of data about + description: + The curation, processing, analysis and prediction of data about the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. meaning: edam:topic_0081 edam:topic_0082: title: Structure prediction - description: The prediction of molecular structure, including the prediction, + description: + The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with @@ -49,29 +54,34 @@ enums: meaning: edam:topic_0084 edam:topic_0085: title: Functional genomics - description: The study of gene or protein functions and their interactions + description: + The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. meaning: edam:topic_0085 edam:topic_0089: title: Ontology and terminology - description: The conceptualisation, categorisation and nomenclature (naming) + description: + The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. meaning: edam:topic_0089 edam:topic_0091: title: Bioinformatics - description: The archival, curation, processing and analysis of complex biological + description: + The archival, curation, processing and analysis of complex biological data. meaning: edam:topic_0091 edam:topic_0092: title: Data visualisation - description: Rendering (drawing on a computer screen) or visualisation of + description: + Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. meaning: edam:topic_0092 edam:topic_0097: title: Nucleic acid structure analysis - description: The archival, curation, processing and analysis of nucleic acid + description: + The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. meaning: edam:topic_0097 @@ -81,7 +91,8 @@ enums: meaning: edam:topic_0099 edam:topic_0102: title: Mapping - description: The mapping of complete (typically nucleotide) sequences. Mapping + description: + The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping @@ -89,17 +100,20 @@ enums: meaning: edam:topic_0102 edam:topic_0108: title: Protein expression - description: The translation of mRNA into protein and subsequent protein processing + description: + The translation of mRNA into protein and subsequent protein processing in the cell. meaning: edam:topic_0108 edam:topic_0114: title: Gene structure - description: Gene structure, regions which make an RNA product and features + description: + Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. meaning: edam:topic_0114 edam:topic_0121: title: Proteomics - description: Proteomics is in the narrow sense (sensu stricto) the application + description: + Proteomics is in the narrow sense (sensu stricto) the application of methods to separate, characterise, identify, and quantify all proteins (the proteome) - or a substantial set of proteins - that are present in a sample. Proteomics in the broad sense is the science of proteins and peptides @@ -107,23 +121,27 @@ enums: meaning: edam:topic_0121 edam:topic_0122: title: Structural genomics - description: The elucidation of the three dimensional structure for all (available) + description: + The elucidation of the three dimensional structure for all (available) proteins in a given organism. meaning: edam:topic_0122 edam:topic_0123: title: Protein properties - description: The study of the physical and biochemical properties of peptides + description: + The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. meaning: edam:topic_0123 edam:topic_0128: title: Protein interactions - description: Protein-protein, protein-DNA/RNA and protein-ligand interactions, + description: + Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. meaning: edam:topic_0128 edam:topic_0130: title: Protein folding, stability and design - description: Protein stability, folding (in 3D space) and protein sequence-structure-function + description: + Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes @@ -131,7 +149,8 @@ enums: meaning: edam:topic_0130 edam:topic_0140: title: Protein targeting and localisation - description: The study of how proteins are transported within and without + description: + The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export. meaning: edam:topic_0140 @@ -145,48 +164,56 @@ enums: meaning: edam:topic_0153 edam:topic_0154: title: Small molecules - description: Small molecules of biological significance, typically archival, + description: + Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. meaning: edam:topic_0154 edam:topic_0157: title: Sequence composition, complexity and repeats - description: The archival, processing and analysis of the basic character + description: + The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. meaning: edam:topic_0157 edam:topic_0160: title: Sequence sites, features and motifs - description: The archival, detection, prediction and analysis of positional + description: + The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. meaning: edam:topic_0160 edam:topic_0166: title: Protein structural motifs and surfaces - description: Structural features or common 3D motifs within protein structures, + description: + Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. meaning: edam:topic_0166 edam:topic_0176: title: Molecular dynamics - description: The study and simulation of molecular (typically protein) conformation + description: + The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. meaning: edam:topic_0176 edam:topic_0194: title: Phylogenomics - description: The integrated study of evolutionary relationships and whole + description: + The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. meaning: edam:topic_0194 edam:topic_0196: title: Sequence assembly - description: The assembly of fragments of a DNA sequence to reconstruct the + description: + The assembly of fragments of a DNA sequence to reconstruct the original sequence. meaning: edam:topic_0196 edam:topic_0199: title: Genetic variation - description: Stable, naturally occurring mutations in a nucleotide sequence + description: + Stable, naturally occurring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. meaning: edam:topic_0199 @@ -196,7 +223,8 @@ enums: meaning: edam:topic_0202 edam:topic_0203: title: Gene expression - description: The analysis of levels and patterns of synthesis of gene products + description: + The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. meaning: edam:topic_0203 @@ -206,30 +234,35 @@ enums: meaning: edam:topic_0204 edam:topic_0208: title: Pharmacogenomics - description: The influence of genotype on drug response, for example by correlating + description: + The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. meaning: edam:topic_0208 edam:topic_0209: title: Medicinal chemistry - description: The design and chemical synthesis of bioactive molecules, for + description: + The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. meaning: edam:topic_0209 edam:topic_0218: title: Natural language processing - description: The processing and analysis of natural language, such as scientific + description: + The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction. meaning: edam:topic_0218 edam:topic_0219: title: Data curation and archival - description: Data curation and archival includes the preservation of data + description: + Data curation and archival includes the preservation of data in a repository, archive, or a deposition database; and curation of data and metadata, database accessions, annotation, and data provenance. meaning: edam:topic_0219 edam:topic_0593: title: NMR - description: An analytical technique that exploits the magenetic properties + description: + An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. meaning: edam:topic_0593 @@ -239,44 +272,52 @@ enums: meaning: edam:topic_0601 edam:topic_0602: title: Molecular interactions, pathways and networks - description: Molecular interactions, biological pathways, networks and other + description: + Molecular interactions, biological pathways, networks and other models. meaning: edam:topic_0602 edam:topic_0605: title: Informatics - description: The study and practice of information processing and use of computer + description: + The study and practice of information processing and use of computer information systems. meaning: edam:topic_0605 edam:topic_0607: title: Laboratory information management - description: Laboratory management and resources, for example, catalogues + description: + Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. meaning: edam:topic_0607 edam:topic_0610: title: Ecology - description: The ecological and environmental sciences and especially the + description: + The ecological and environmental sciences and especially the application of information technology (ecoinformatics). meaning: edam:topic_0610 edam:topic_0611: title: Electron microscopy - description: The study of matter by studying the interference pattern from + description: + The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. meaning: edam:topic_0611 edam:topic_0621: title: Model organisms - description: A specific organism, or group of organisms, used to study a particular + description: + A specific organism, or group of organisms, used to study a particular aspect of biology. meaning: edam:topic_0621 edam:topic_0622: title: Genomics - description: Whole genomes of one or more organisms, or genomes in general, + description: + Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. meaning: edam:topic_0622 edam:topic_0623: title: Gene and protein families - description: Particular gene(s), gene family or other gene group or system + description: + Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have @@ -284,7 +325,8 @@ enums: meaning: edam:topic_0623 edam:topic_0625: title: Genotype and phenotype - description: The study of genetic constitution of a living entity, such as + description: + The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, @@ -292,12 +334,14 @@ enums: meaning: edam:topic_0625 edam:topic_0632: title: Probes and primers - description: Molecular probes (e.g. a peptide probe or DNA microarray probe) + description: + Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. meaning: edam:topic_0632 edam:topic_0634: title: Pathology - description: Diseases, including diseases in general and the genes, gene variations + description: + Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. meaning: edam:topic_0634 edam:topic_0637: @@ -306,22 +350,26 @@ enums: meaning: edam:topic_0637 edam:topic_0654: title: DNA - description: DNA sequences and structure, including processes such as methylation + description: + DNA sequences and structure, including processes such as methylation and replication. meaning: edam:topic_0654 edam:topic_0659: title: Functional, regulatory and non-coding RNA - description: Non-coding or functional RNA sequences, including regulatory + description: + Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). meaning: edam:topic_0659 edam:topic_0736: title: Protein folds and structural domains - description: Protein tertiary structural domains and folds in a protein or + description: + Protein tertiary structural domains and folds in a protein or polypeptide chain. meaning: edam:topic_0736 edam:topic_0749: title: Transcription factors and regulatory sites - description: Proteins that bind to DNA and control transcription of DNA to + description: + Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. @@ -332,49 +380,58 @@ enums: meaning: edam:topic_0769 edam:topic_0780: title: Plant biology - description: Plants, e.g. information on a specific plant genome including + description: + Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. meaning: edam:topic_0780 edam:topic_0781: title: Virology - description: Study of viruses, e.g. sequence and structural data, interactions + description: + Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. meaning: edam:topic_0781 edam:topic_0797: title: Comparative genomics - description: The study (typically comparison) of the sequence, structure or + description: + The study (typically comparison) of the sequence, structure or function of multiple genomes. meaning: edam:topic_0797 edam:topic_0798: title: Mobile genetic elements - description: Mobile genetic elements, such as transposons, Plasmids, Bacteriophage + description: + Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. meaning: edam:topic_0798 edam:topic_0804: title: Immunology - description: The application of information technology to immunology such + description: + The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. meaning: edam:topic_0804 edam:topic_0820: title: Membrane and lipoproteins - description: Lipoproteins (protein-lipid assemblies), and proteins or region + description: + Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. meaning: edam:topic_0820 edam:topic_0821: title: Enzymes - description: Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed + description: + Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. meaning: edam:topic_0821 edam:topic_1317: title: Structural biology - description: The molecular structure of biological molecules, particularly + description: + The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. meaning: edam:topic_1317 edam:topic_1775: title: Function analysis - description: The study of gene and protein function including the prediction + description: + The study of gene and protein function including the prediction of functional properties of a protein. meaning: edam:topic_1775 edam:topic_2229: @@ -383,12 +440,14 @@ enums: meaning: edam:topic_2229 edam:topic_2258: title: Cheminformatics - description: The application of information technology to chemistry in biological + description: + The application of information technology to chemistry in biological research environment. meaning: edam:topic_2258 edam:topic_2259: title: Systems biology - description: The holistic modelling and analysis of complex biological systems + description: + The holistic modelling and analysis of complex biological systems and the interactions therein. meaning: edam:topic_2259 edam:topic_2269: @@ -397,7 +456,8 @@ enums: meaning: edam:topic_2269 edam:topic_2275: title: Molecular modelling - description: The construction, analysis, evaluation, refinement etc. of models + description: + The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). meaning: edam:topic_2275 @@ -407,22 +467,26 @@ enums: meaning: edam:topic_2533 edam:topic_2640: title: Oncology - description: The study of cancer, for example, genes and proteins implicated + description: + The study of cancer, for example, genes and proteins implicated in cancer. meaning: edam:topic_2640 edam:topic_2814: title: Protein structure analysis - description: Protein secondary or tertiary structural data and/or associated + description: + Protein secondary or tertiary structural data and/or associated annotation. meaning: edam:topic_2814 edam:topic_2815: title: Human biology - description: The study of human beings in general, including the human genome + description: + The study of human beings in general, including the human genome and proteome. meaning: edam:topic_2815 edam:topic_2828: title: X-ray diffraction - description: The study of matter and their structure by means of the diffraction + description: + The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. meaning: edam:topic_2828 @@ -432,7 +496,8 @@ enums: meaning: edam:topic_2830 edam:topic_2840: title: Toxicology - description: Toxins and the adverse effects of these chemical substances on + description: + Toxins and the adverse effects of these chemical substances on living organisms. meaning: edam:topic_2840 edam:topic_2885: @@ -441,33 +506,39 @@ enums: meaning: edam:topic_2885 edam:topic_3047: title: Molecular biology - description: The molecular basis of biological activity, particularly the + description: + The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. meaning: edam:topic_3047 edam:topic_3050: title: Biodiversity - description: The degree of variation of life forms within a given ecosystem, + description: + The degree of variation of life forms within a given ecosystem, biome or an entire planet. meaning: edam:topic_3050 edam:topic_3053: title: Genetics - description: The study of genes, genetic variation and heredity in living + description: + The study of genes, genetic variation and heredity in living organisms. meaning: edam:topic_3053 edam:topic_3055: title: Quantitative genetics - description: The genes and genetic mechanisms such as Mendelian inheritance + description: + The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). meaning: edam:topic_3055 edam:topic_3056: title: Population genetics - description: The distribution of allele frequencies in a population of organisms + description: + The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. meaning: edam:topic_3056 edam:topic_3063: title: Medical informatics - description: The application of information technology to health, disease + description: + The application of information technology to health, disease and biomedicine. meaning: edam:topic_3063 edam:topic_3064: @@ -476,7 +547,8 @@ enums: meaning: edam:topic_3064 edam:topic_3065: title: Embryology - description: The development of organisms between the one-cell stage (typically + description: + The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. meaning: edam:topic_3065 edam:topic_3067: @@ -485,29 +557,34 @@ enums: meaning: edam:topic_3067 edam:topic_3068: title: Literature and language - description: The scientific literature, language processing, reference information, + description: + The scientific literature, language processing, reference information, and documentation. meaning: edam:topic_3068 edam:topic_3070: title: Biology - description: The study of life and living organisms, including their morphology, + description: + The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on. meaning: edam:topic_3070 edam:topic_3071: title: Data management - description: Data management comprises the practices and principles of taking + description: + Data management comprises the practices and principles of taking care of data, other than analysing them. This includes for example taking care of the associated metadata, data formats, storage, preservation/archiving, access, and legal aspects related to using and sharing data. meaning: edam:topic_3071 edam:topic_3077: title: Data acquisition - description: The acquisition of data, typically measurements of physical systems + description: + The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means. meaning: edam:topic_3077 edam:topic_3120: title: Protein variants - description: Protein sequence variants produced e.g. from alternative splicing, + description: + Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. meaning: edam:topic_3120 edam:topic_3125: @@ -520,53 +597,62 @@ enums: meaning: edam:topic_3127 edam:topic_3168: title: Sequencing - description: The determination of complete (typically nucleotide) sequences, + description: + The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. meaning: edam:topic_3168 edam:topic_3169: title: ChIP-seq - description: The analysis of protein-DNA interactions where chromatin immunoprecipitation + description: + The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. meaning: edam:topic_3169 edam:topic_3170: title: RNA-Seq - description: A topic concerning high-throughput sequencing of cDNA to measure + description: + A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. meaning: edam:topic_3170 edam:topic_3172: title: Metabolomics - description: The systematic study of metabolites, the chemical processes they + description: + The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. meaning: edam:topic_3172 edam:topic_3173: title: Epigenomics - description: The study of the epigenetic modifications of a whole cell, tissue, + description: + The study of the epigenetic modifications of a whole cell, tissue, organism etc. meaning: edam:topic_3173 edam:topic_3174: title: Metagenomics - description: The study of genetic material recovered from environmental samples, + description: + The study of genetic material recovered from environmental samples, and associated environmental data. meaning: edam:topic_3174 edam:topic_3175: title: Structural variation - description: Variation in chromosome structure including microscopic and submicroscopic + description: + Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. meaning: edam:topic_3175 edam:topic_3176: title: DNA packaging - description: DNA-histone complexes (chromatin), organisation of chromatin + description: + DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. meaning: edam:topic_3176 edam:topic_3179: title: ChIP-on-chip - description: Experimental techniques that combine chromatin immunoprecipitation + description: + Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. meaning: edam:topic_3179 @@ -576,35 +662,41 @@ enums: meaning: edam:topic_3277 edam:topic_3292: title: Biochemistry - description: Chemical substances and physico-chemical processes and that occur + description: + Chemical substances and physico-chemical processes and that occur within living organisms. meaning: edam:topic_3292 edam:topic_3293: title: Phylogenetics - description: The study of evolutionary relationships amongst organisms from + description: + The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). meaning: edam:topic_3293 edam:topic_3295: title: Epigenetics - description: Topic concerning the study of heritable changes, for example + description: + Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. meaning: edam:topic_3295 edam:topic_3297: title: Biotechnology - description: The exploitation of biological process, structure and function + description: + The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. meaning: edam:topic_3297 edam:topic_3298: title: Phenomics - description: Phenomes, or the study of the change in phenotype (the physical + description: + Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. meaning: edam:topic_3298 edam:topic_3299: title: Evolutionary biology - description: The evolutionary processes, from the genetic to environmental + description: + The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. meaning: edam:topic_3299 edam:topic_3300: @@ -621,17 +713,20 @@ enums: meaning: edam:topic_3302 edam:topic_3303: title: Medicine - description: Research in support of healing by diagnosis, treatment, and prevention + description: + Research in support of healing by diagnosis, treatment, and prevention of disease. meaning: edam:topic_3303 edam:topic_3304: title: Neurobiology - description: The study of the nervous system and brain; its anatomy, physiology + description: + The study of the nervous system and brain; its anatomy, physiology and function. meaning: edam:topic_3304 edam:topic_3305: title: Public health and epidemiology - description: Topic concerning the the patterns, cause, and effect of disease + description: + Topic concerning the the patterns, cause, and effect of disease within populations. meaning: edam:topic_3305 edam:topic_3306: @@ -640,22 +735,26 @@ enums: meaning: edam:topic_3306 edam:topic_3307: title: Computational biology - description: The development and application of theory, analytical methods, + description: + The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. meaning: edam:topic_3307 edam:topic_3308: title: Transcriptomics - description: The analysis of transcriptomes, or a set of all the RNA molecules + description: + The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. meaning: edam:topic_3308 edam:topic_3314: title: Chemistry - description: The composition and properties of matter, reactions, and the + description: + The composition and properties of matter, reactions, and the use of reactions to create new substances. meaning: edam:topic_3314 edam:topic_3315: title: Mathematics - description: The study of numbers (quantity) and other topics including structure, + description: + The study of numbers (quantity) and other topics including structure, space, and change. meaning: edam:topic_3315 edam:topic_3316: @@ -664,12 +763,14 @@ enums: meaning: edam:topic_3316 edam:topic_3318: title: Physics - description: The study of matter, space and time, and related concepts such + description: + The study of matter, space and time, and related concepts such as energy and force. meaning: edam:topic_3318 edam:topic_3320: title: RNA splicing - description: RNA splicing; post-transcription RNA modification involving the + description: + RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. meaning: edam:topic_3320 edam:topic_3321: @@ -682,7 +783,8 @@ enums: meaning: edam:topic_3322 edam:topic_3324: title: Infectious disease - description: The branch of medicine that deals with the prevention, diagnosis + description: + The branch of medicine that deals with the prevention, diagnosis and management of transmissible disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). @@ -693,12 +795,14 @@ enums: meaning: edam:topic_3325 edam:topic_3332: title: Computational chemistry - description: Topic concerning the development and application of theory, analytical + description: + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. meaning: edam:topic_3332 edam:topic_3334: title: Neurology - description: The branch of medicine that deals with the anatomy, functions + description: + The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. meaning: edam:topic_3334 edam:topic_3335: @@ -711,81 +815,95 @@ enums: meaning: edam:topic_3336 edam:topic_3337: title: Biobank - description: Repositories of biological samples, typically human, for basic + description: + Repositories of biological samples, typically human, for basic biological and clinical research. meaning: edam:topic_3337 edam:topic_3338: title: Mouse clinic - description: Laboratory study of mice, for example, phenotyping, and mutagenesis + description: + Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. meaning: edam:topic_3338 edam:topic_3339: title: Microbial collection - description: Collections of microbial cells including bacteria, yeasts and + description: + Collections of microbial cells including bacteria, yeasts and moulds. meaning: edam:topic_3339 edam:topic_3340: title: Cell culture collection - description: Collections of cells grown under laboratory conditions, specifically, + description: + Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. meaning: edam:topic_3340 edam:topic_3341: title: Clone library - description: Collections of DNA, including both collections of cloned molecules, + description: + Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. meaning: edam:topic_3341 edam:topic_3342: title: Translational medicine - description: '''translating'' the output of basic and biomedical research + description: "'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and - advice.' + advice." meaning: edam:topic_3342 edam:topic_3343: title: Compound libraries and screening - description: Collections of chemicals, typically for use in high-throughput + description: + Collections of chemicals, typically for use in high-throughput screening experiments. meaning: edam:topic_3343 edam:topic_3344: title: Biomedical science - description: Topic concerning biological science that is (typically) performed + description: + Topic concerning biological science that is (typically) performed in the context of medicine. meaning: edam:topic_3344 edam:topic_3345: title: Data identity and mapping - description: Topic concerning the identity of biological entities, or reports + description: + Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. meaning: edam:topic_3345 edam:topic_3360: title: Biomarkers - description: Objective indicators of biological state often used to assess + description: + Objective indicators of biological state often used to assess health, and determinate treatment. meaning: edam:topic_3360 edam:topic_3365: title: Data architecture, analysis and design - description: The development of policies, models and standards that cover + description: + The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data. meaning: edam:topic_3365 edam:topic_3366: title: Data integration and warehousing - description: The combination and integration of data from different sources, + description: + The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. meaning: edam:topic_3366 edam:topic_3368: title: Biomaterials - description: Any matter, surface or construct that interacts with a biological + description: + Any matter, surface or construct that interacts with a biological system. meaning: edam:topic_3368 edam:topic_3369: title: Chemical biology - description: The use of synthetic chemistry to study and manipulate biological + description: + The use of synthetic chemistry to study and manipulate biological systems. meaning: edam:topic_3369 edam:topic_3370: title: Analytical chemistry - description: The study of the separation, identification, and quantification + description: + The study of the separation, identification, and quantification of the chemical components of natural and artificial materials. meaning: edam:topic_3370 edam:topic_3371: @@ -794,17 +912,20 @@ enums: meaning: edam:topic_3371 edam:topic_3372: title: Software engineering - description: The process that leads from an original formulation of a computing + description: + The process that leads from an original formulation of a computing problem to executable programs. meaning: edam:topic_3372 edam:topic_3373: title: Drug development - description: The process of bringing a new drug to market once a lead compounds + description: + The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. meaning: edam:topic_3373 edam:topic_3374: title: Biotherapeutics - description: The process of formulating and administering a pharmaceutical + description: + The process of formulating and administering a pharmaceutical compound to achieve a therapeutic effect. meaning: edam:topic_3374 edam:topic_3375: @@ -821,12 +942,14 @@ enums: meaning: edam:topic_3377 edam:topic_3378: title: Pharmacovigilance - description: The detection, assessment, understanding and prevention of adverse + description: + The detection, assessment, understanding and prevention of adverse effects of medicines. meaning: edam:topic_3378 edam:topic_3379: title: Preclinical and clinical studies - description: The testing of new medicines, vaccines or procedures on animals + description: + The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. meaning: edam:topic_3379 @@ -840,7 +963,8 @@ enums: meaning: edam:topic_3383 edam:topic_3384: title: Medical imaging - description: The use of imaging techniques for clinical purposes for medical + description: + The use of imaging techniques for clinical purposes for medical research. meaning: edam:topic_3384 edam:topic_3385: @@ -857,68 +981,80 @@ enums: meaning: edam:topic_3387 edam:topic_3388: title: Molecular medicine - description: The identification of molecular and genetic causes of disease + description: + The identification of molecular and genetic causes of disease and the development of interventions to correct them. meaning: edam:topic_3388 edam:topic_3390: title: Nutritional science - description: The study of the effects of food components on the metabolism, + description: + The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. meaning: edam:topic_3390 edam:topic_3391: title: Omics - description: The collective characterisation and quantification of pools of + description: + The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. meaning: edam:topic_3391 edam:topic_3393: title: Quality affairs - description: The processes that need to be in place to ensure the quality + description: + The processes that need to be in place to ensure the quality of products for human or animal use. meaning: edam:topic_3393 edam:topic_3394: title: Regulatory affairs - description: The protection of public health by controlling the safety and + description: + The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. meaning: edam:topic_3394 edam:topic_3395: title: Regenerative medicine - description: Biomedical approaches to clinical interventions that involve + description: + Biomedical approaches to clinical interventions that involve the use of stem cells. meaning: edam:topic_3395 edam:topic_3396: title: Systems medicine - description: An interdisciplinary field of study that looks at the dynamic + description: + An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incorporating biochemical, physiological, and environmental interactions that sustain life. meaning: edam:topic_3396 edam:topic_3397: title: Veterinary medicine - description: Topic concerning the branch of medicine that deals with the prevention, + description: + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. meaning: edam:topic_3397 edam:topic_3398: title: Bioengineering - description: The application of biological concepts and methods to the analytical + description: + The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. meaning: edam:topic_3398 edam:topic_3399: title: Geriatric medicine - description: The branch of medicine dealing with the diagnosis, treatment + description: + The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. meaning: edam:topic_3399 edam:topic_3400: title: Allergy, clinical immunology and immunotherapeutics - description: Health issues related to the immune system and their prevention, + description: + Health issues related to the immune system and their prevention, diagnosis and management. meaning: edam:topic_3400 edam:topic_3401: title: Pain medicine - description: The prevention of pain and the evaluation, treatment and rehabilitation + description: + The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. meaning: edam:topic_3401 edam:topic_3402: @@ -927,173 +1063,204 @@ enums: meaning: edam:topic_3402 edam:topic_3403: title: Critical care medicine - description: The multidisciplinary that cares for patients with acute, life-threatening + description: + The multidisciplinary that cares for patients with acute, life-threatening illness or injury. meaning: edam:topic_3403 edam:topic_3404: title: Dermatology - description: The branch of medicine that deals with prevention, diagnosis + description: + The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. meaning: edam:topic_3404 edam:topic_3405: title: Dentistry - description: The study, diagnosis, prevention and treatments of disorders + description: + The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. meaning: edam:topic_3405 edam:topic_3406: title: Ear, nose and throat medicine - description: The branch of medicine that deals with the prevention, diagnosis, + description: + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. meaning: edam:topic_3406 edam:topic_3407: title: Endocrinology and metabolism - description: The branch of medicine dealing with diseases of endocrine organs, + description: + The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. meaning: edam:topic_3407 edam:topic_3408: title: Haematology - description: The branch of medicine that deals with the blood, blood-forming + description: + The branch of medicine that deals with the blood, blood-forming organs and blood diseases. meaning: edam:topic_3408 edam:topic_3409: title: Gastroenterology - description: The branch of medicine that deals with disorders of the oesophagus, + description: + The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. meaning: edam:topic_3409 edam:topic_3410: title: Gender medicine - description: The study of the biological and physiological differences between + description: + The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. meaning: edam:topic_3410 edam:topic_3411: title: Gynaecology and obstetrics - description: The branch of medicine that deals with the health of the female + description: + The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. meaning: edam:topic_3411 edam:topic_3412: title: Hepatic and biliary medicine - description: The branch of medicine that deals with the liver, gallbladder, + description: + The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. meaning: edam:topic_3412 edam:topic_3414: title: Trauma medicine - description: The branch of medicine that treats body wounds or shock produced + description: + The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. meaning: edam:topic_3414 edam:topic_3415: title: Medical toxicology - description: The branch of medicine that deals with the diagnosis, management + description: + The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. meaning: edam:topic_3415 edam:topic_3416: title: Musculoskeletal medicine - description: The branch of medicine that deals with the prevention, diagnosis, + description: + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. meaning: edam:topic_3416 edam:topic_3417: title: Ophthalmology - description: The branch of medicine that deals with disorders of the eye, + description: + The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. meaning: edam:topic_3417 edam:topic_3418: title: Paediatrics - description: The branch of medicine that deals with the medical care of infants, + description: + The branch of medicine that deals with the medical care of infants, children and adolescents. meaning: edam:topic_3418 edam:topic_3419: title: Psychiatry - description: The branch of medicine that deals with the management of mental + description: + The branch of medicine that deals with the management of mental illness, emotional disturbance and abnormal behaviour. meaning: edam:topic_3419 edam:topic_3420: title: Reproductive health - description: The health of the reproductive processes, functions and systems + description: + The health of the reproductive processes, functions and systems at all stages of life. meaning: edam:topic_3420 edam:topic_3421: title: Surgery - description: The use of operative, manual and instrumental techniques on a + description: + The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. meaning: edam:topic_3421 edam:topic_3422: title: Urology and nephrology - description: The branches of medicine and physiology focussing on the function + description: + The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. meaning: edam:topic_3422 edam:topic_3423: title: Complementary medicine - description: Medical therapies that fall beyond the scope of conventional + description: + Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. meaning: edam:topic_3423 edam:topic_3444: title: MRI - description: Techniques that uses magnetic fields and radiowaves to form images, + description: + Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. meaning: edam:topic_3444 edam:topic_3448: title: Neutron diffraction - description: The study of matter by studying the diffraction pattern from + description: + The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. meaning: edam:topic_3448 edam:topic_3452: title: Tomography - description: Imaging in sections (sectioning), through the use of a wave-generating + description: + Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). meaning: edam:topic_3452 edam:topic_3473: title: Data mining - description: The discovery of patterns in large data sets and the extraction + description: + The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. meaning: edam:topic_3473 edam:topic_3474: title: Machine learning - description: A topic concerning the application of artificial intelligence + description: + A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an output, rather than relying on explicitly encoded information only. meaning: edam:topic_3474 edam:topic_3489: title: Database management - description: The general handling of data stored in digital archives such + description: + The general handling of data stored in digital archives such as databases, databanks, web portals, and other data resources. meaning: edam:topic_3489 edam:topic_3500: title: Zoology - description: Animals, e.g. information on a specific animal genome including + description: + Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. meaning: edam:topic_3500 edam:topic_3510: title: Protein sites, features and motifs - description: The biology, archival, detection, prediction and analysis of + description: + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. meaning: edam:topic_3510 edam:topic_3511: title: Nucleic acid sites, features and motifs - description: The biology, archival, detection, prediction and analysis of + description: + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. meaning: edam:topic_3511 edam:topic_3512: title: Gene transcripts - description: Transcription of DNA into RNA and features of a messenger RNA + description: + Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. meaning: edam:topic_3512 edam:topic_3516: title: Genotyping experiment - description: Genotype experiment including case control, population, and family + description: + Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. meaning: edam:topic_3516 edam:topic_3517: @@ -1102,7 +1269,8 @@ enums: meaning: edam:topic_3517 edam:topic_3518: title: Microarray experiment - description: Microarray experiments including conditions, protocol, sample:data + description: + Microarray experiments including conditions, protocol, sample:data relationships etc. meaning: edam:topic_3518 edam:topic_3519: @@ -1115,20 +1283,23 @@ enums: meaning: edam:topic_3520 edam:topic_3523: title: RNAi experiment - description: Experiment in which the expression of a specific gene is post-transcriptionally + description: + Experiment in which the expression of a specific gene is post-transcriptionally knocked down or silenced by means of a small RNA (sRNA) causing the degradation of the gene transcript (mRNA), and thus preventing the production of the corresponding protein. meaning: edam:topic_3523 edam:topic_3524: title: Simulation experiment - description: Biological computational model experiments (simulation), for + description: + Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. meaning: edam:topic_3524 edam:topic_3534: title: Protein binding sites - description: Binding sites in proteins, including cleavage sites (for a proteolytic + description: + Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA @@ -1140,12 +1311,14 @@ enums: meaning: edam:topic_3538 edam:topic_3542: title: Protein secondary structure - description: Secondary structure (predicted or real) of a protein, including + description: + Secondary structure (predicted or real) of a protein, including super-secondary structure. meaning: edam:topic_3542 edam:topic_3569: title: Applied mathematics - description: The application of mathematics to specific problems in science, + description: + The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models. meaning: edam:topic_3569 edam:topic_3570: @@ -1154,7 +1327,8 @@ enums: meaning: edam:topic_3570 edam:topic_3571: title: Data governance - description: Data governance is the control of data entry and maintenance + description: + Data governance is the control of data entry and maintenance to ensure the data meets defined standards, qualities, or constraints. meaning: edam:topic_3571 edam:topic_3572: @@ -1171,29 +1345,34 @@ enums: meaning: edam:topic_3574 edam:topic_3575: title: Tropical medicine - description: Health problems that are prevalent in tropical and subtropical + description: + Health problems that are prevalent in tropical and subtropical regions. meaning: edam:topic_3575 edam:topic_3576: title: Medical biotechnology - description: Biotechnology applied to the medical sciences and the development + description: + Biotechnology applied to the medical sciences and the development of medicines. meaning: edam:topic_3576 edam:topic_3577: title: Personalised medicine - description: An approach to medicine whereby decisions, practices and are + description: + An approach to medicine whereby decisions, practices and are tailored to the individual patient based on their predicted response or risk of disease. meaning: edam:topic_3577 edam:topic_3656: title: Immunoprecipitation experiment - description: Experimental techniques to purify a protein-DNA crosslinked complex. + description: + Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq. meaning: edam:topic_3656 edam:topic_3673: title: Whole genome sequencing - description: Laboratory technique to sequence the complete DNA sequence of + description: + Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. meaning: edam:topic_3673 edam:topic_3674: @@ -1202,12 +1381,14 @@ enums: meaning: edam:topic_3674 edam:topic_3676: title: Exome sequencing - description: Laboratory technique to sequence all the protein-coding regions + description: + Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome. meaning: edam:topic_3676 edam:topic_3678: title: Experimental design and studies - description: The design of an experiment intended to test a hypothesis, and + description: + The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. meaning: edam:topic_3678 edam:topic_3679: @@ -1216,7 +1397,8 @@ enums: meaning: edam:topic_3679 edam:topic_3697: title: Microbial ecology - description: The ecology of microorganisms including their relationship with + description: + The ecology of microorganisms including their relationship with one another and their environment. meaning: edam:topic_3697 edam:topic_3794: @@ -1225,49 +1407,58 @@ enums: meaning: edam:topic_3794 edam:topic_3796: title: Population genomics - description: Large-scale study (typically comparison) of DNA sequences of + description: + Large-scale study (typically comparison) of DNA sequences of populations. meaning: edam:topic_3796 edam:topic_3810: title: Agricultural science - description: Multidisciplinary study, research and development within the + description: + Multidisciplinary study, research and development within the field of agriculture. meaning: edam:topic_3810 edam:topic_3837: title: Metagenomic sequencing - description: Approach which samples, in parallel, all genes in all organisms + description: + Approach which samples, in parallel, all genes in all organisms present in a given sample, e.g. to provide insight into biodiversity and function. meaning: edam:topic_3837 edam:topic_3855: title: Environmental sciences - description: Study of the environment, the interactions between its physical, + description: + Study of the environment, the interactions between its physical, chemical, and biological components and it's effect on life. Also how humans impact upon the environment, and how we can manage and utilise natural resources. meaning: edam:topic_3855 edam:topic_3892: title: Biomolecular simulation - description: The study and simulation of molecular conformations using a computational + description: + The study and simulation of molecular conformations using a computational model and computer simulations. meaning: edam:topic_3892 edam:topic_3895: title: Synthetic biology - description: The application of multi-disciplinary science and technology + description: + The application of multi-disciplinary science and technology for the construction of artificial biological systems for diverse applications. meaning: edam:topic_3895 edam:topic_3912: title: Genetic engineering - description: The application of biotechnology to directly manipulate an organism's + description: + The application of biotechnology to directly manipulate an organism's genes. meaning: edam:topic_3912 edam:topic_3922: title: Proteogenomics - description: A field of biological research focused on the discovery and identification + description: + A field of biological research focused on the discovery and identification of peptides, typically by comparing mass spectra against a protein database. meaning: edam:topic_3922 edam:topic_3923: title: Genome resequencing - description: Laboratory experiment to identify the differences between a specific + description: + Laboratory experiment to identify the differences between a specific genome (of an individual) and a reference genome (developed typically from many thousands of individuals). WGS re-sequencing is used as golden standard to detect variations compared to a given reference genome, including small @@ -1276,12 +1467,14 @@ enums: meaning: edam:topic_3923 edam:topic_3930: title: Immunogenetics - description: A biomedical field that bridges immunology and genetics, to study + description: + A biomedical field that bridges immunology and genetics, to study the genetic basis of the immune system. meaning: edam:topic_3930 edam:topic_3931: title: Chemometrics - description: Interdisciplinary science focused on extracting information from + description: + Interdisciplinary science focused on extracting information from chemical systems by data analytical approaches, for example multivariate statistics, applied mathematics, and computer science. meaning: edam:topic_3931 @@ -1291,38 +1484,45 @@ enums: meaning: edam:topic_3934 edam:topic_3939: title: Metabolic engineering - description: Biotechnology approach that seeks to optimize cellular genetic + description: + Biotechnology approach that seeks to optimize cellular genetic and regulatory processes in order to increase the cells' production of a certain substance. meaning: edam:topic_3939 edam:topic_3940: title: Chromosome conformation capture - description: Molecular biology methods used to analyze the spatial organization + description: + Molecular biology methods used to analyze the spatial organization of chromatin in a cell. meaning: edam:topic_3940 edam:topic_3941: title: Metatranscriptomics - description: The study of microbe gene expression within natural environments + description: + The study of microbe gene expression within natural environments (i.e. the metatranscriptome). meaning: edam:topic_3941 edam:topic_3943: title: Paleogenomics - description: The reconstruction and analysis of genomic information in extinct + description: + The reconstruction and analysis of genomic information in extinct species. meaning: edam:topic_3943 edam:topic_3944: title: Cladistics - description: The biological classification of organisms by categorizing them + description: + The biological classification of organisms by categorizing them in groups ("clades") based on their most recent common ancestor. meaning: edam:topic_3944 edam:topic_3945: title: Molecular evolution - description: The study of the process and mechanism of change of biomolecules + description: + The study of the process and mechanism of change of biomolecules such as DNA, RNA, and proteins across generations. meaning: edam:topic_3945 edam:topic_3948: title: Immunoinformatics - description: Immunoinformatics is the field of computational biology that + description: + Immunoinformatics is the field of computational biology that deals with the study of immunoloogical questions. Immunoinformatics is at the interface between immunology and computer science. It takes advantage of computational, statistical, mathematical approaches and enhances the @@ -1334,7 +1534,8 @@ enums: meaning: edam:topic_3954 edam:topic_3955: title: Fluxomics - description: Experimental approaches to determine the rates of metabolic reactions + description: + Experimental approaches to determine the rates of metabolic reactions - the metabolic fluxes - within a biological entity. meaning: edam:topic_3955 edam:topic_3957: @@ -1343,95 +1544,112 @@ enums: meaning: edam:topic_3957 edam:topic_3958: title: Copy number variation - description: A DNA structural variation, specifically a duplication or deletion + description: + A DNA structural variation, specifically a duplication or deletion event, resulting in sections of the genome to be repeated, or the number of repeats in the genome to vary between individuals. meaning: edam:topic_3958 edam:topic_3959: title: Cytogenetics - description: The branch of genetics concerned with the relationships between + description: + The branch of genetics concerned with the relationships between chromosomes and cellular behaviour, especially during mitosis and meiosis. meaning: edam:topic_3959 edam:topic_3966: title: Vaccinology - description: The design of vaccines to protect against a particular pathogen, + description: + The design of vaccines to protect against a particular pathogen, including antigens, delivery systems, and adjuvants to elicit a predictable immune response against specific epitopes. meaning: edam:topic_3966 edam:topic_3967: title: Immunomics - description: The study of immune system as a whole, its regulation and response + description: + The study of immune system as a whole, its regulation and response to pathogens using genome-wide approaches. meaning: edam:topic_3967 edam:topic_3974: title: Epistasis - description: 'Epistasis can be defined as the ability of the genotype at one + description: + "Epistasis can be defined as the ability of the genotype at one locus to supersede the phenotypic effect of a mutation at another locus. This interaction between genes can occur at different level: gene expression, - protein levels, etc...' + protein levels, etc..." meaning: edam:topic_3974 edam:topic_4010: title: Open science - description: Open science encompasses the practices of making scientific research + description: + Open science encompasses the practices of making scientific research transparent and participatory, and its outputs publicly accessible. meaning: edam:topic_4010 edam:topic_4011: title: Data rescue - description: Data rescue denotes digitalisation, formatting, archival, and + description: + Data rescue denotes digitalisation, formatting, archival, and publication of data that were not available in accessible or usable form. Examples are data from private archives, data inside publications, or in paper records stored privately or publicly. meaning: edam:topic_4011 edam:topic_4012: title: FAIR data - description: FAIR data is scientific data that meets the principles of being + description: + FAIR data is scientific data that meets the principles of being findable, accessible, interoperable, and reusable. meaning: edam:topic_4012 edam:topic_4013: title: Antimicrobial resistance - description: Microbial mechanisms for protecting microorganisms against antimicrobial + description: + Microbial mechanisms for protecting microorganisms against antimicrobial agents. meaning: edam:topic_4013 edam:topic_4014: title: Electroencephalography - description: The monitoring method for measuring electrical activity in the + description: + The monitoring method for measuring electrical activity in the brain. meaning: edam:topic_4014 edam:topic_4016: title: Electrocardiography - description: The monitoring method for measuring electrical activity in the + description: + The monitoring method for measuring electrical activity in the heart. meaning: edam:topic_4016 edam:topic_4017: title: Cryogenic electron microscopy - description: A method for studying biomolecules and other structures at very + description: + A method for studying biomolecules and other structures at very low (cryogenic) temperature using electron microscopy. meaning: edam:topic_4017 edam:topic_4019: title: Biosciences - description: Biosciences, or life sciences, include fields of study related + description: + Biosciences, or life sciences, include fields of study related to life, living beings, and biomolecules. meaning: edam:topic_4019 edam:topic_4020: title: Carbon cycle - description: The carbon cycle is the biogeochemical pathway of carbon moving + description: + The carbon cycle is the biogeochemical pathway of carbon moving through the different parts of the Earth (such as ocean, atmosphere, soil), or eventually another planet. meaning: edam:topic_4020 edam:topic_4021: title: Multiomics - description: Multiomics concerns integration of data from multiple omics (e.g. + description: + Multiomics concerns integration of data from multiple omics (e.g. transcriptomics, proteomics, epigenomics). meaning: edam:topic_4021 edam:topic_4027: title: Ribosome Profiling - description: With ribosome profiling, ribosome-protected mRNA fragments are + description: + With ribosome profiling, ribosome-protected mRNA fragments are analyzed with RNA-seq techniques leading to a genome-wide measurement of the translation landscape. meaning: edam:topic_4027 edam:topic_4028: title: Single-cell sequencing - description: Combined with NGS (Next Generation Sequencing) technologies, + description: + Combined with NGS (Next Generation Sequencing) technologies, single-cell sequencing allows the study of genetic information (DNA, RNA, epigenome...) at a single cell level. It is often used for differential analysis and gene expression profiling. @@ -1442,12 +1660,14 @@ enums: meaning: edam:topic_4029 edam:topic_4030: title: Microfluidics - description: Interdisplinary study of behavior, precise control, and manipulation + description: + Interdisplinary study of behavior, precise control, and manipulation of low (microlitre) volume fluids in constrained space. meaning: edam:topic_4030 edam:topic_4037: title: Genomic imprinting - description: Genomic imprinting is a gene regulation mechanism by which a + description: + Genomic imprinting is a gene regulation mechanism by which a subset of genes are expressed from one of the two parental chromosomes only. Imprinted genes are organized in clusters, their silencing/activation of the imprinted loci involves epigenetic marks (DNA methylation, etc) and @@ -1456,30 +1676,35 @@ enums: meaning: edam:topic_4037 edam:topic_4038: title: Metabarcoding - description: Metabarcoding is the barcoding of (environmental) DNA or RNA + description: + Metabarcoding is the barcoding of (environmental) DNA or RNA to identify multiple taxa from the same sample. meaning: edam:topic_4038 edam:topic_4044: title: Data protection - description: Data protection is a topic concerning data that should be protected + description: + Data protection is a topic concerning data that should be protected from disclosure, damage, or unauthorised access, due to its sensitive nature. meaning: edam:topic_4044 edam:topic_4045: title: Cybersecurity - description: Cybersecurity is a topic comprising the approaches and technologies + description: + Cybersecurity is a topic comprising the approaches and technologies that enable the protection of computer systems, networks and programs from digital attacks. It ensures the availability, integrity, and confidentiality of processed and stored information. meaning: edam:topic_4045 edam:topic_4046: title: Version control - description: Version control is a technology for consistent management, storing, + description: + Version control is a technology for consistent management, storing, and sharing of evolving versions of digital artefacts, such as computer programs, scripts, documents, data, or media files. meaning: edam:topic_4046 edam:topic_4047: title: Software management - description: Software management comprises the practices and principles of + description: + Software management comprises the practices and principles of taking care of software and software-based or software-like services, other than programming and maintenance. This includes for example taking care of the associated information and documentation, and the processes of contribution, @@ -1487,77 +1712,90 @@ enums: meaning: edam:topic_4047 edam:topic_4051: title: ChIP-exo - description: Chromatin immunoprecipitation-based exeperiment similar to ChIP-seq, + description: + Chromatin immunoprecipitation-based exeperiment similar to ChIP-seq, with an additional experimental step using an exonuclease to increase the resolution of protein binding site identification. meaning: edam:topic_4051 edam:topic_4052: title: Hi-C - description: High-throughput genomic and epigenomic technique that capture + description: + High-throughput genomic and epigenomic technique that capture chromatin conformation, allowing a genome-wide identification of chromatin interactions and structure. meaning: edam:topic_4052 edam:topic_4053: title: ATAC-seq - description: Assay for Transposase-Accessible Chromatin with high throughput + description: + Assay for Transposase-Accessible Chromatin with high throughput sequencing. This technique is designed for the genome-wide detection of open chromatin regions. meaning: edam:topic_4053 edam:topic_4054: title: miRNA silencing - description: Experiment in which the expression of a given gene is knocked + description: + Experiment in which the expression of a given gene is knocked down by means of a micro RNA (miRNA) causing the degradation of the gene transcript (mRNA). meaning: edam:topic_4054 edam:topic_4055: title: siRNA experiment - description: Experiment in which the expression of a given gene is knocked + description: + Experiment in which the expression of a given gene is knocked down by means of a small interfering RNA (siRNA) causing the degradation of the gene transcript (mRNA). meaning: edam:topic_4055 edam:topic_4056: title: Long-read sequencing - description: Long-read sequencing is a sequencing method that produces reads + description: + Long-read sequencing is a sequencing method that produces reads thousands to millions of base pairs long, allowing for better resolution of complex regions, structural variants, and full-length transcripts. meaning: edam:topic_4056 edam:topic_4057: title: Short-read sequencing - description: Short-read sequencing is a high-throughput sequencing method + description: + Short-read sequencing is a high-throughput sequencing method that generates millions of short nucleotide fragments, typically 50–300 base pairs in length. meaning: edam:topic_4057 edam:topic_4060: title: Metaproteomics - description: Metaproteomics is the profiling of proteins in a sample that + description: + Metaproteomics is the profiling of proteins in a sample that contains material from multiple species or strains of organisms. meaning: edam:topic_4060 edam:topic_4061: title: Bisulfite sequencing - description: Bisulfite sequencing is a sequencing technique used to determine + description: + Bisulfite sequencing is a sequencing technique used to determine DNA methylation patterns by treating DNA with bisulfite, which converts unmethylated cytosines to uracils while leaving methylated cytosines unchanged. meaning: edam:topic_4061 edam:topic_4062: title: Bulk RNA barcoding and sequencing - description: Bulk RNA barcoding and sequencing (BRB-seq) is a highly mutliplexed + description: + Bulk RNA barcoding and sequencing (BRB-seq) is a highly mutliplexed bulk RNA-Seq technique where each RNA sample gets a barcode, and many samples are sequenced together. meaning: edam:topic_4062 edam:topic_4063: title: DNase sequencing - description: DNase sequencing is a technique used to identify regions of open + description: + DNase sequencing is a technique used to identify regions of open chromatin by sequencing DNA fragments generated after treatment with DNase I, which preferentially cuts accessible DNA. meaning: edam:topic_4063 edam:topic_4064: title: MicroRNA sequencing - description: Specific sequencing of small RNAs using a variant of RNA-seq, + description: + Specific sequencing of small RNAs using a variant of RNA-seq, with an additional fragment size selection step. meaning: edam:topic_4064 edam:topic_4065: title: Exposomics - description: Exposomics is the systematic and comprehensive study of the exposome + description: + Exposomics is the systematic and comprehensive study of the exposome and the associated biological responses (exposure-phenotype interaction). Exposome is the totality of environmental exposures, that is, the cumulative (e.g. life-long) totality of contacts between external factors (e.g. chemical diff --git a/src/common_access_model/schema/enums/EnumDataSourceType.yaml b/src/common_access_model/schema/enums/EnumDataSourceType.yaml index 61aa503..913a28e 100644 --- a/src/common_access_model/schema/enums/EnumDataSourceType.yaml +++ b/src/common_access_model/schema/enums/EnumDataSourceType.yaml @@ -17,17 +17,17 @@ enums: title: Electronic Health Record description: Data obtained directly from an Electronic Health Record. aliases: - - medical_record + - medical_record CAMO:0000010: title: Survey description: Data obtained from a survey or questionnaire given to a participant or their representative. aliases: - - participant_or_caregiver_report + - participant_or_caregiver_report CAMO:0000011: title: Research Assessment description: Data obtained by research staff for the study. aliases: - - investigator_assessment + - investigator_assessment CAMO:0000012: title: Interview description: Data obtained by research staff interviewing participants, representatives, or others. diff --git a/src/common_access_model/schema/enums/EnumDataUseModifier.yaml b/src/common_access_model/schema/enums/EnumDataUseModifier.yaml index a05aa63..28ed3ba 100644 --- a/src/common_access_model/schema/enums/EnumDataUseModifier.yaml +++ b/src/common_access_model/schema/enums/EnumDataUseModifier.yaml @@ -15,109 +15,127 @@ enums: permissible_values: DUO:00000044: title: population origins or ancestry research prohibited - description: This data use modifier indicates use for purposes of population, + description: + This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited. meaning: DUO:00000044 DUO:0000012: title: research specific restrictions - description: This data use modifier indicates that use is limited to studies + description: + This data use modifier indicates that use is limited to studies of a certain research type. meaning: DUO:0000012 DUO:0000015: title: no general methods research - description: This data use modifier indicates that use does not allow methods + description: + This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms). meaning: DUO:0000015 DUO:0000016: title: genetic studies only - description: This data use modifier indicates that use is limited to genetic + description: + This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively) meaning: DUO:0000016 DUO:0000018: title: not for profit, non commercial use only - description: This data use modifier indicates that use of the data is limited + description: + This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. meaning: DUO:0000018 DUO:0000019: title: publication required - description: This data use modifier indicates that requestor agrees to make + description: + This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community. meaning: DUO:0000019 DUO:0000020: title: collaboration required - description: 'This could be coupled with a string describing the primary study + description: + "This could be coupled with a string describing the primary study investigator(s). This data use modifier indicates that the requestor must agree to collaboration - with the primary study investigator(s).' + with the primary study investigator(s)." meaning: DUO:0000020 DUO:0000021: title: ethics approval required - description: This data use modifier indicates that the requestor must provide + description: + This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. meaning: DUO:0000021 DUO:0000022: title: geographical restriction - description: 'This data use modifier indicates that use is limited to within + description: + "This data use modifier indicates that use is limited to within a specific geographic region. This should be coupled with an ontology term describing the geographical - location the restriction applies to.' + location the restriction applies to." meaning: DUO:0000022 DUO:0000024: title: publication moratorium - description: 'This data use modifier indicates that requestor agrees not to + description: + "This data use modifier indicates that requestor agrees not to publish results of studies until a specific date. - This should be coupled with a date specified as ISO8601' + This should be coupled with a date specified as ISO8601" meaning: DUO:0000024 DUO:0000025: title: time limit on use - description: 'This data use modifier indicates that use is approved for a + description: + "This data use modifier indicates that use is approved for a specific number of months. - This should be coupled with an integer value indicating the number of months.' + This should be coupled with an integer value indicating the number of months." meaning: DUO:0000025 DUO:0000026: title: user specific restriction - description: This data use modifier indicates that use is limited to use by + description: + This data use modifier indicates that use is limited to use by approved users. meaning: DUO:0000026 DUO:0000027: title: project specific restriction - description: This data use modifier indicates that use is limited to use within + description: + This data use modifier indicates that use is limited to use within an approved project. meaning: DUO:0000027 DUO:0000028: title: institution specific restriction - description: This data use modifier indicates that use is limited to use within + description: + This data use modifier indicates that use is limited to use within an approved institution. meaning: DUO:0000028 DUO:0000029: title: return to database or resource - description: This data use modifier indicates that the requestor must return + description: + This data use modifier indicates that the requestor must return derived/enriched data to the database/resource. meaning: DUO:0000029 DUO:0000043: title: clinical care use - description: 'Clinical Care is defined as Health care or services provided + description: + "Clinical Care is defined as Health care or services provided at home, in a healthcare facility or hospital. Data may be used for clinical decision making. This data use modifier indicates that use is allowed for clinical use and - care.' + care." meaning: DUO:0000043 DUO:0000045: title: not for profit organisation use only - description: This data use modifier indicates that use of the data is limited + description: + This data use modifier indicates that use of the data is limited to not-for-profit organizations. meaning: DUO:0000045 DUO:0000046: title: non-commercial use only - description: 'This data use modifier indicates that use of the data is limited + description: + "This data use modifier indicates that use of the data is limited to not-for-profit use. This indicates that data can be used by commercial organisations for research - purposes, but not commercial purposes.' + purposes, but not commercial purposes." meaning: DUO:0000046 diff --git a/src/common_access_model/schema/enums/EnumDataUsePermission.yaml b/src/common_access_model/schema/enums/EnumDataUsePermission.yaml index 39092c9..b9c3d96 100644 --- a/src/common_access_model/schema/enums/EnumDataUsePermission.yaml +++ b/src/common_access_model/schema/enums/EnumDataUsePermission.yaml @@ -15,17 +15,20 @@ enums: permissible_values: DUO:0000004: title: no restriction - description: This data use permission indicates there is no restriction on + description: + This data use permission indicates there is no restriction on use. meaning: DUO:0000004 DUO:0000006: title: health or medical or biomedical research - description: This data use permission indicates that use is allowed for health/medical/biomedical + description: + This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. meaning: DUO:0000006 DUO:0000007: title: disease specific research - description: "This data use permission indicates that use is allowed provided\ + description: + "This data use permission indicates that use is allowed provided\ \ it is related to the specified disease.\nThis term should be coupled with\ \ a term describing a disease from an ontology to specify the disease the\ \ restriction applies to. \n\nDUO recommends MONDO be used, to provide the\ @@ -36,15 +39,17 @@ enums: meaning: DUO:0000007 DUO:0000011: title: population origins or ancestry research only - description: This data use permission indicates that use of the data is limited + description: + This data use permission indicates that use of the data is limited to the study of population origins or ancestry. meaning: DUO:0000011 DUO:0000042: title: general research use - description: 'This data use permission indicates that use is allowed for general + description: + "This data use permission indicates that use is allowed for general research use for any research purpose. This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, - statistical methods and algorithms development, and social-sciences research.' + statistical methods and algorithms development, and social-sciences research." meaning: DUO:0000042 diff --git a/src/common_access_model/schema/enums/EnumEDAMDataTypes.yaml b/src/common_access_model/schema/enums/EnumEDAMDataTypes.yaml index ea494d8..3e31e1a 100644 --- a/src/common_access_model/schema/enums/EnumEDAMDataTypes.yaml +++ b/src/common_access_model/schema/enums/EnumEDAMDataTypes.yaml @@ -15,12 +15,14 @@ enums: permissible_values: edam:data_0582: title: Ontology - description: An ontology of biological or bioinformatics concepts and relations, + description: + An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. meaning: edam:data_0582 edam:data_0842: title: Identifier - description: A text token, number or something else which identifies an entity, + description: + A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). meaning: edam:data_0842 @@ -38,7 +40,8 @@ enums: meaning: edam:data_0846 edam:data_0847: title: QSAR descriptor - description: A QSAR quantitative descriptor (name-value pair) of chemical + description: + A QSAR quantitative descriptor (name-value pair) of chemical structure. meaning: edam:data_0847 edam:data_0849: @@ -47,38 +50,44 @@ enums: meaning: edam:data_0849 edam:data_0850: title: Sequence set - description: A collection of one or typically multiple molecular sequences + description: + A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. meaning: edam:data_0850 edam:data_0856: title: Sequence feature source - description: How the annotation of a sequence feature (for example in EMBL + description: + How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. meaning: edam:data_0856 edam:data_0857: title: Sequence search results - description: A report of sequence hits and associated data from searching + description: + A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. meaning: edam:data_0857 edam:data_0858: title: Sequence signature matches - description: Report on the location of matches ("hits") between sequences, + description: + Report on the location of matches ("hits") between sequences, sequence profiles, motifs (conserved or functional patterns) and other types of sequence signatures. meaning: edam:data_0858 edam:data_0860: title: Sequence signature data - description: Sequence signature data concerns specific or conserved pattern + description: + Sequence signature data concerns specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. meaning: edam:data_0860 edam:data_0862: title: Dotplot - description: A dotplot of sequence similarities identified from word-matching + description: + A dotplot of sequence similarities identified from word-matching or character comparison. meaning: edam:data_0862 edam:data_0863: @@ -91,12 +100,14 @@ enums: meaning: edam:data_0865 edam:data_0867: title: Sequence alignment report - description: An informative report of molecular sequence alignment-derived + description: + An informative report of molecular sequence alignment-derived data or metadata. meaning: edam:data_0867 edam:data_0870: title: Sequence distance matrix - description: A matrix of estimated evolutionary distance between molecular + description: + A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. meaning: edam:data_0870 edam:data_0871: @@ -105,33 +116,39 @@ enums: meaning: edam:data_0871 edam:data_0872: title: Phylogenetic tree - description: The raw data (not just an image) from which a phylogenetic tree + description: + The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. meaning: edam:data_0872 edam:data_0874: title: Comparison matrix - description: Matrix of integer or floating point numbers for amino acid or + description: + Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. meaning: edam:data_0874 edam:data_0878: title: Protein secondary structure alignment - description: Alignment of the (1D representations of) secondary structure + description: + Alignment of the (1D representations of) secondary structure of two or more proteins. meaning: edam:data_0878 edam:data_0880: title: RNA secondary structure - description: An informative report of secondary structure (predicted or real) + description: + An informative report of secondary structure (predicted or real) of an RNA molecule. meaning: edam:data_0880 edam:data_0881: title: RNA secondary structure alignment - description: Alignment of the (1D representations of) secondary structure + description: + Alignment of the (1D representations of) secondary structure of two or more RNA molecules. meaning: edam:data_0881 edam:data_0883: title: Structure - description: 3D coordinate and associated data for a macromolecular tertiary + description: + 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. meaning: edam:data_0883 edam:data_0886: @@ -140,22 +157,26 @@ enums: meaning: edam:data_0886 edam:data_0887: title: Structure alignment report - description: An informative report of molecular tertiary structure alignment-derived + description: + An informative report of molecular tertiary structure alignment-derived data. meaning: edam:data_0887 edam:data_0888: title: Structure similarity score - description: A value representing molecular structure similarity, measured + description: + A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. meaning: edam:data_0888 edam:data_0889: title: Structural profile - description: Some type of structural (3D) profile or template (representing + description: + Some type of structural (3D) profile or template (representing a structure or structure alignment). meaning: edam:data_0889 edam:data_0890: title: Structural (3D) profile alignment - description: A 3D profile-3D profile alignment (each profile representing + description: + A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). meaning: edam:data_0890 edam:data_0892: @@ -164,29 +185,34 @@ enums: meaning: edam:data_0892 edam:data_0893: title: Sequence-structure alignment - description: An alignment of molecular sequence to structure (from threading + description: + An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). meaning: edam:data_0893 edam:data_0896: title: Protein report - description: An informative human-readable report about one or more specific + description: + An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. meaning: edam:data_0896 edam:data_0897: title: Protein property - description: A report of primarily non-positional data describing intrinsic + description: + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. meaning: edam:data_0897 edam:data_0905: title: Protein interaction raw data - description: Protein-protein interaction data from for example yeast two-hybrid + description: + Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. meaning: edam:data_0905 edam:data_0906: title: Protein interaction data - description: Data concerning the interactions (predicted or known) within + description: + Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal @@ -194,32 +220,38 @@ enums: meaning: edam:data_0906 edam:data_0907: title: Protein family report - description: An informative report on a specific protein family or other classification + description: + An informative report on a specific protein family or other classification or group of protein sequences or structures. meaning: edam:data_0907 edam:data_0909: title: Vmax - description: The maximum initial velocity or rate of a reaction. It is the + description: + The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. meaning: edam:data_0909 edam:data_0910: title: Km - description: Km is the concentration (usually in Molar units) of substrate + description: + Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. meaning: edam:data_0910 edam:data_0912: title: Nucleic acid property - description: A report of primarily non-positional data describing intrinsic + description: + A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. meaning: edam:data_0912 edam:data_0914: title: Codon usage data - description: Data derived from analysis of codon usage (typically a codon + description: + Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. meaning: edam:data_0914 edam:data_0916: title: Gene report - description: A report on predicted or actual gene structure, regions which + description: + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. meaning: edam:data_0916 @@ -229,14 +261,16 @@ enums: meaning: edam:data_0919 edam:data_0920: title: Genotype/phenotype report - description: A human-readable collection of information about the set of genes + description: + A human-readable collection of information about the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. meaning: edam:data_0920 edam:data_0924: title: Sequence trace - description: Fluorescence trace data generated by an automated DNA sequencer, + description: + Fluorescence trace data generated by an automated DNA sequencer, which can be interpreted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. meaning: edam:data_0924 @@ -250,12 +284,14 @@ enums: meaning: edam:data_0926 edam:data_0927: title: Genetic linkage report - description: A human-readable collection of information about the linkage + description: + A human-readable collection of information about the linkage of alleles. meaning: edam:data_0927 edam:data_0928: title: Gene expression profile - description: Data quantifying the level of expression of (typically) multiple + description: + Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. meaning: edam:data_0928 edam:data_0937: @@ -268,7 +304,8 @@ enums: meaning: edam:data_0938 edam:data_0939: title: CD spectra - description: Protein secondary structure from protein coordinate or circular + description: + Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. meaning: edam:data_0939 edam:data_0940: @@ -285,19 +322,22 @@ enums: meaning: edam:data_0943 edam:data_0944: title: Peptide mass fingerprint - description: A set of peptide masses (peptide mass fingerprint) from mass + description: + A set of peptide masses (peptide mass fingerprint) from mass spectrometry. meaning: edam:data_0944 edam:data_0945: title: Peptide identification - description: Protein or peptide identifications with evidence supporting the + description: + Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer. meaning: edam:data_0945 edam:data_0949: title: Workflow metadata - description: Basic information, annotation or documentation concerning a workflow + description: + Basic information, annotation or documentation concerning a workflow (but not the workflow itself). meaning: edam:data_0949 edam:data_0950: @@ -306,12 +346,14 @@ enums: meaning: edam:data_0950 edam:data_0951: title: Statistical estimate score - description: A value representing estimated statistical significance of some + description: + A value representing estimated statistical significance of some observed data; typically sequence database hits. meaning: edam:data_0951 edam:data_0954: title: Database cross-mapping - description: A mapping of the accession numbers (or other database identifier) + description: + A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. meaning: edam:data_0954 edam:data_0955: @@ -320,32 +362,38 @@ enums: meaning: edam:data_0955 edam:data_0956: title: Data index report - description: A human-readable collection of information concerning an analysis + description: + A human-readable collection of information concerning an analysis of an index of biological data. meaning: edam:data_0956 edam:data_0957: title: Database metadata - description: Basic information on bioinformatics database(s) or other data + description: + Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. meaning: edam:data_0957 edam:data_0958: title: Tool metadata - description: Basic information about one or more bioinformatics applications + description: + Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. meaning: edam:data_0958 edam:data_0960: title: User metadata - description: Textual metadata on a software author or end-user, for example + description: + Textual metadata on a software author or end-user, for example a person or other software. meaning: edam:data_0960 edam:data_0962: title: Small molecule report - description: A human-readable collection of information about a specific chemical + description: + A human-readable collection of information about a specific chemical compound. meaning: edam:data_0962 edam:data_0963: title: Cell line report - description: A human-readable collection of information about a particular + description: + A human-readable collection of information about a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. @@ -364,17 +412,20 @@ enums: meaning: edam:data_0968 edam:data_0970: title: Citation - description: Bibliographic data that uniquely identifies a scientific article, + description: + Bibliographic data that uniquely identifies a scientific article, book or other published material. meaning: edam:data_0970 edam:data_0971: title: Article - description: A scientific text, typically a full text article from a scientific + description: + A scientific text, typically a full text article from a scientific journal. meaning: edam:data_0971 edam:data_0972: title: Text mining report - description: A human-readable collection of information resulting from text + description: + A human-readable collection of information resulting from text mining. meaning: edam:data_0972 edam:data_0976: @@ -383,7 +434,8 @@ enums: meaning: edam:data_0976 edam:data_0977: title: Tool identifier - description: An identifier of a bioinformatics tool, e.g. an application or + description: + An identifier of a bioinformatics tool, e.g. an application or web service. meaning: edam:data_0977 edam:data_0982: @@ -436,7 +488,8 @@ enums: meaning: edam:data_0996 edam:data_0997: title: Chemical name (ChEBI) - description: Unique name from Chemical Entities of Biological Interest (ChEBI) + description: + Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. meaning: edam:data_0997 edam:data_0998: @@ -445,7 +498,8 @@ enums: meaning: edam:data_0998 edam:data_0999: title: Chemical name (INN) - description: International Non-proprietary Name (INN or 'generic name') of + description: + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO). meaning: edam:data_0999 edam:data_1000: @@ -458,7 +512,8 @@ enums: meaning: edam:data_1001 edam:data_1002: title: CAS number - description: CAS registry number of a chemical compound; a unique numerical + description: + CAS registry number of a chemical compound; a unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. meaning: edam:data_1002 @@ -472,12 +527,14 @@ enums: meaning: edam:data_1004 edam:data_1005: title: HET group name - description: 3-letter code word for a ligand (HET group) from a PDB file, + description: + 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. meaning: edam:data_1005 edam:data_1006: title: Amino acid name - description: String of one or more ASCII characters representing an amino + description: + String of one or more ASCII characters representing an amino acid. meaning: edam:data_1006 edam:data_1007: @@ -494,7 +551,8 @@ enums: meaning: edam:data_1009 edam:data_1010: title: Enzyme identifier - description: Name or other identifier of an enzyme or record from a database + description: + Name or other identifier of an enzyme or record from a database of enzymes. meaning: edam:data_1010 edam:data_1011: @@ -511,12 +569,14 @@ enums: meaning: edam:data_1013 edam:data_1015: title: Sequence feature ID - description: A unique identifier of molecular sequence feature, for example + description: + A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. meaning: edam:data_1015 edam:data_1016: title: Sequence position - description: A position of one or more points (base or residue) in a sequence, + description: + A position of one or more points (base or residue) in a sequence, or part of such a specification. meaning: edam:data_1016 edam:data_1017: @@ -525,7 +585,8 @@ enums: meaning: edam:data_1017 edam:data_1020: title: Sequence feature key - description: The type of a sequence feature, typically a term or accession + description: + The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. meaning: edam:data_1020 @@ -535,22 +596,26 @@ enums: meaning: edam:data_1021 edam:data_1022: title: Sequence feature label - description: A name of a sequence feature, e.g. the name of a feature to be + description: + A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label. meaning: edam:data_1022 edam:data_1023: title: EMBOSS Uniform Feature Object - description: The name of a sequence feature-containing entity adhering to + description: + The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. meaning: edam:data_1023 edam:data_1025: title: Gene identifier - description: An identifier of a gene, such as a name/symbol or a unique identifier + description: + An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. meaning: edam:data_1025 edam:data_1026: title: Gene symbol - description: The short name of a gene; a single word that does not contain + description: + The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. meaning: edam:data_1026 edam:data_1027: @@ -567,7 +632,8 @@ enums: meaning: edam:data_1032 edam:data_1033: title: Ensembl gene ID - description: Unique identifier for a gene (or other feature) from the Ensembl + description: + Unique identifier for a gene (or other feature) from the Ensembl database. meaning: edam:data_1033 edam:data_1034: @@ -592,7 +658,8 @@ enums: meaning: edam:data_1038 edam:data_1039: title: SCOP domain identifier - description: Identifier of a protein domain (or other node) from the SCOP + description: + Identifier of a protein domain (or other node) from the SCOP database. meaning: edam:data_1039 edam:data_1040: @@ -601,12 +668,14 @@ enums: meaning: edam:data_1040 edam:data_1041: title: SCOP concise classification string (sccs) - description: A SCOP concise classification string (sccs) is a compact representation + description: + A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. meaning: edam:data_1041 edam:data_1042: title: SCOP sunid - description: Unique identifier (number) of an entry in the SCOP hierarchy, + description: + Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. meaning: edam:data_1042 edam:data_1043: @@ -623,12 +692,14 @@ enums: meaning: edam:data_1045 edam:data_1046: title: Strain name - description: The name of a strain of an organism variant, typically a plant, + description: + The name of a strain of an organism variant, typically a plant, virus or bacterium. meaning: edam:data_1046 edam:data_1047: title: URI - description: A string of characters that name or otherwise identify a resource + description: + A string of characters that name or otherwise identify a resource on the Internet. meaning: edam:data_1047 edam:data_1048: @@ -645,7 +716,8 @@ enums: meaning: edam:data_1050 edam:data_1051: title: Ontology name - description: Name of an ontology of biological or bioinformatics concepts + description: + Name of an ontology of biological or bioinformatics concepts and relations. meaning: edam:data_1051 edam:data_1052: @@ -658,7 +730,8 @@ enums: meaning: edam:data_1053 edam:data_1055: title: LSID - description: A Life Science Identifier (LSID) - a unique identifier of some + description: + A Life Science Identifier (LSID) - a unique identifier of some data. meaning: edam:data_1055 edam:data_1056: @@ -683,7 +756,8 @@ enums: meaning: edam:data_1061 edam:data_1063: title: Sequence identifier - description: An identifier of molecular sequence(s) or entries from a molecular + description: + An identifier of molecular sequence(s) or entries from a molecular sequence database. meaning: edam:data_1063 edam:data_1064: @@ -692,12 +766,14 @@ enums: meaning: edam:data_1064 edam:data_1066: title: Sequence alignment ID - description: Identifier of a molecular sequence alignment, for example a record + description: + Identifier of a molecular sequence alignment, for example a record from an alignment database. meaning: edam:data_1066 edam:data_1068: title: Phylogenetic tree ID - description: Identifier of a phylogenetic tree for example from a phylogenetic + description: + Identifier of a phylogenetic tree for example from a phylogenetic tree database. meaning: edam:data_1068 edam:data_1069: @@ -706,27 +782,32 @@ enums: meaning: edam:data_1069 edam:data_1070: title: Structure ID - description: A unique and persistent identifier of a molecular tertiary structure, + description: + A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. meaning: edam:data_1070 edam:data_1071: title: Structural (3D) profile ID - description: Identifier or name of a structural (3D) profile or template (representing + description: + Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). meaning: edam:data_1071 edam:data_1072: title: Structure alignment ID - description: Identifier of an entry from a database of tertiary structure + description: + Identifier of an entry from a database of tertiary structure alignments. meaning: edam:data_1072 edam:data_1073: title: Amino acid index ID - description: Identifier of an index of amino acid physicochemical and biochemical + description: + Identifier of an index of amino acid physicochemical and biochemical property data. meaning: edam:data_1073 edam:data_1074: title: Protein interaction ID - description: Identifier of a report of protein interactions from a protein + description: + Identifier of a report of protein interactions from a protein interaction database (typically). meaning: edam:data_1074 edam:data_1075: @@ -747,12 +828,14 @@ enums: meaning: edam:data_1078 edam:data_1079: title: Electron microscopy model ID - description: Identifier of an entry from a database of electron microscopy + description: + Identifier of an entry from a database of electron microscopy data. meaning: edam:data_1079 edam:data_1080: title: Gene expression report ID - description: Accession of a report of gene expression (e.g. a gene expression + description: + Accession of a report of gene expression (e.g. a gene expression profile) from a database. meaning: edam:data_1080 edam:data_1081: @@ -761,12 +844,14 @@ enums: meaning: edam:data_1081 edam:data_1082: title: Pathway or network identifier - description: Identifier of an entry from a database of biological pathways + description: + Identifier of an entry from a database of biological pathways or networks. meaning: edam:data_1082 edam:data_1083: title: Workflow ID - description: Identifier of a biological or biomedical workflow, typically + description: + Identifier of a biological or biomedical workflow, typically from a database of workflows. meaning: edam:data_1083 edam:data_1084: @@ -775,7 +860,8 @@ enums: meaning: edam:data_1084 edam:data_1085: title: Biological model ID - description: Identifier of a mathematical model, typically an entry from a + description: + Identifier of a mathematical model, typically an entry from a database. meaning: edam:data_1085 edam:data_1086: @@ -784,7 +870,8 @@ enums: meaning: edam:data_1086 edam:data_1087: title: Ontology concept ID - description: A unique (typically numerical) identifier of a concept in an + description: + A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. meaning: edam:data_1087 edam:data_1088: @@ -797,7 +884,8 @@ enums: meaning: edam:data_1089 edam:data_1091: title: WormBase name - description: Name of an object from the WormBase database, usually a human-readable + description: + Name of an object from the WormBase database, usually a human-readable name. meaning: edam:data_1091 edam:data_1092: @@ -806,12 +894,14 @@ enums: meaning: edam:data_1092 edam:data_1093: title: Sequence accession - description: A persistent, unique identifier of a molecular sequence database + description: + A persistent, unique identifier of a molecular sequence database entry. meaning: edam:data_1093 edam:data_1095: title: EMBOSS Uniform Sequence Address - description: The name of a sequence-based entity adhering to the standard + description: + The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. meaning: edam:data_1095 edam:data_1096: @@ -836,12 +926,14 @@ enums: meaning: edam:data_1102 edam:data_1103: title: EMBL/GenBank/DDBJ ID - description: Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ + description: + Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. meaning: edam:data_1103 edam:data_1104: title: Sequence cluster ID (UniGene) - description: A unique identifier of an entry (gene cluster) from the NCBI + description: + A unique identifier of an entry (gene cluster) from the NCBI UniGene database. meaning: edam:data_1104 edam:data_1105: @@ -862,7 +954,8 @@ enums: meaning: edam:data_1113 edam:data_1114: title: Sequence motif identifier - description: Identifier of a sequence motif, for example an entry from a motif + description: + Identifier of a sequence motif, for example an entry from a motif database. meaning: edam:data_1114 edam:data_1115: @@ -871,7 +964,8 @@ enums: meaning: edam:data_1115 edam:data_1116: title: ELM ID - description: Identifier of an entry from the ELMdb database of protein functional + description: + Identifier of an entry from the ELMdb database of protein functional sites. meaning: edam:data_1116 edam:data_1117: @@ -920,7 +1014,8 @@ enums: meaning: edam:data_1131 edam:data_1132: title: InterPro entry name - description: Name of an InterPro entry, usually indicating the type of protein + description: + Name of an InterPro entry, usually indicating the type of protein matches for that entry. meaning: edam:data_1132 edam:data_1133: @@ -953,7 +1048,8 @@ enums: meaning: edam:data_1139 edam:data_1140: title: Superfamily hidden Markov model number - description: Unique identifier (number) of a hidden Markov model from the + description: + Unique identifier (number) of a hidden Markov model from the Superfamily database. meaning: edam:data_1140 edam:data_1141: @@ -1006,7 +1102,8 @@ enums: meaning: edam:data_1153 edam:data_1154: title: KEGG object identifier - description: Unique identifier of an object from one of the KEGG databases + description: + Unique identifier of an object from one of the KEGG databases (excluding the GENES division). meaning: edam:data_1154 edam:data_1155: @@ -1015,7 +1112,8 @@ enums: meaning: edam:data_1155 edam:data_1157: title: Pathway ID (BioCyc) - description: Identifier of an pathway from the BioCyc biological pathways + description: + Identifier of an pathway from the BioCyc biological pathways database. meaning: edam:data_1157 edam:data_1158: @@ -1028,13 +1126,15 @@ enums: meaning: edam:data_1159 edam:data_1160: title: Pathway ID (CPDB) - description: Identifier of an entry from the CPDB (ConsensusPathDB) biological + description: + Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. meaning: edam:data_1160 edam:data_1161: title: Pathway ID (Panther) - description: Identifier of a biological pathway from the Panther Pathways + description: + Identifier of a biological pathway from the Panther Pathways database. meaning: edam:data_1161 edam:data_1162: @@ -1071,7 +1171,8 @@ enums: meaning: edam:data_1171 edam:data_1172: title: PubChem CID - description: Chemical structure specified in PubChem Compound Identification + description: + Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. meaning: edam:data_1172 edam:data_1173: @@ -1100,7 +1201,8 @@ enums: meaning: edam:data_1178 edam:data_1179: title: NCBI taxonomy ID - description: A stable unique identifier for each taxon (for a species, a family, + description: + A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. meaning: edam:data_1179 edam:data_1180: @@ -1189,34 +1291,40 @@ enums: meaning: edam:data_1205 edam:data_1233: title: Sequence set (protein) - description: Any collection of multiple protein sequences and associated metadata + description: + Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. meaning: edam:data_1233 edam:data_1234: title: Sequence set (nucleic acid) - description: Any collection of multiple nucleotide sequences and associated + description: + Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. meaning: edam:data_1234 edam:data_1235: title: Sequence cluster - description: A set of sequences that have been clustered or otherwise classified + description: + A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. meaning: edam:data_1235 edam:data_1238: title: Proteolytic digest - description: A protein sequence cleaved into peptide fragments (by enzymatic + description: + A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. meaning: edam:data_1238 edam:data_1239: title: Restriction digest - description: Restriction digest fragments from digesting a nucleotide sequence + description: + Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. meaning: edam:data_1239 edam:data_1240: title: PCR primers - description: Oligonucleotide primer(s) for PCR and DNA amplification, for + description: + Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. meaning: edam:data_1240 edam:data_1245: @@ -1229,23 +1337,27 @@ enums: meaning: edam:data_1246 edam:data_1249: title: Sequence length - description: The size (length) of a sequence, subsequence or region in a sequence, + description: + The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. meaning: edam:data_1249 edam:data_1254: title: Sequence property - description: An informative report about non-positional sequence features, + description: + An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. meaning: edam:data_1254 edam:data_1255: title: Sequence features - description: Annotation of positional features of molecular sequence(s), i.e. + description: + Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. meaning: edam:data_1255 edam:data_1259: title: Sequence complexity report - description: A report on sequence complexity, for example low-complexity or + description: + A report on sequence complexity, for example low-complexity or repeat regions in sequences. meaning: edam:data_1259 edam:data_1260: @@ -1254,12 +1366,14 @@ enums: meaning: edam:data_1260 edam:data_1261: title: Sequence composition report - description: A report (typically a table) on character or word composition + description: + A report (typically a table) on character or word composition / frequency of a molecular sequence(s). meaning: edam:data_1261 edam:data_1262: title: Peptide molecular weight hits - description: A report on peptide fragments of certain molecular weight(s) + description: + A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. meaning: edam:data_1262 edam:data_1263: @@ -1284,54 +1398,64 @@ enums: meaning: edam:data_1268 edam:data_1270: title: Feature table - description: Annotation of positional sequence features, organised into a + description: + Annotation of positional sequence features, organised into a standard feature table. meaning: edam:data_1270 edam:data_1274: title: Map - description: A map of (typically one) DNA sequence annotated with positional + description: + A map of (typically one) DNA sequence annotated with positional or non-positional features. meaning: edam:data_1274 edam:data_1276: title: Nucleic acid features - description: An informative report on intrinsic positional features of a nucleotide + description: + An informative report on intrinsic positional features of a nucleotide sequence, formatted to be machine-readable. meaning: edam:data_1276 edam:data_1277: title: Protein features - description: An informative report on intrinsic positional features of a protein + description: + An informative report on intrinsic positional features of a protein sequence. meaning: edam:data_1277 edam:data_1278: title: Genetic map - description: A map showing the relative positions of genetic markers in a + description: + A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. meaning: edam:data_1278 edam:data_1279: title: Sequence map - description: A map of genetic markers in a contiguous, assembled genomic sequence, + description: + A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. meaning: edam:data_1279 edam:data_1280: title: Physical map - description: A map of DNA (linear or circular) annotated with physical features + description: + A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. meaning: edam:data_1280 edam:data_1283: title: Cytogenetic map - description: A map showing banding patterns derived from direct observation + description: + A map showing banding patterns derived from direct observation of a stained chromosome. meaning: edam:data_1283 edam:data_1284: title: DNA transduction map - description: A gene map showing distances between loci based on relative cotransduction + description: + A gene map showing distances between loci based on relative cotransduction frequencies. meaning: edam:data_1284 edam:data_1285: title: Gene map - description: Sequence map of a single gene annotated with genetic features + description: + Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene. meaning: edam:data_1285 @@ -1345,7 +1469,8 @@ enums: meaning: edam:data_1288 edam:data_1289: title: Restriction map - description: Image of the restriction enzyme cleavage sites (restriction sites) + description: + Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. meaning: edam:data_1289 edam:data_1347: @@ -1358,44 +1483,52 @@ enums: meaning: edam:data_1352 edam:data_1353: title: Sequence motif - description: Any specific or conserved pattern (typically expressed as a regular + description: + Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. meaning: edam:data_1353 edam:data_1354: title: Sequence profile - description: Some type of statistical model representing a (typically multiple) + description: + Some type of statistical model representing a (typically multiple) sequence alignment. meaning: edam:data_1354 edam:data_1355: title: Protein signature - description: An informative report about a specific or conserved protein sequence + description: + An informative report about a specific or conserved protein sequence pattern. meaning: edam:data_1355 edam:data_1361: title: Position frequency matrix - description: A profile (typically representing a sequence alignment) that + description: + A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. meaning: edam:data_1361 edam:data_1362: title: Position weight matrix - description: A profile (typically representing a sequence alignment) that + description: + A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. meaning: edam:data_1362 edam:data_1363: title: Information content matrix - description: A profile (typically representing a sequence alignment) derived + description: + A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. meaning: edam:data_1363 edam:data_1364: title: Hidden Markov model - description: A statistical Markov model of a system which is assumed to be + description: + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences. meaning: edam:data_1364 edam:data_1365: title: Fingerprint - description: One or more fingerprints (sequence classifiers) as used in the + description: + One or more fingerprints (sequence classifiers) as used in the PRINTS database. meaning: edam:data_1365 edam:data_1381: @@ -1416,7 +1549,8 @@ enums: meaning: edam:data_1385 edam:data_1394: title: Alignment score or penalty - description: A simple floating point number defining the penalty for opening + description: + A simple floating point number defining the penalty for opening or extending a gap in an alignment. meaning: edam:data_1394 edam:data_1397: @@ -1433,56 +1567,66 @@ enums: meaning: edam:data_1399 edam:data_1401: title: Match reward score - description: The score for a 'match' used in various sequence database search + description: + The score for a 'match' used in various sequence database search applications with simple scoring schemes. meaning: edam:data_1401 edam:data_1402: title: Mismatch penalty score - description: The score (penalty) for a 'mismatch' used in various alignment + description: + The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. meaning: edam:data_1402 edam:data_1403: title: Drop off score - description: This is the threshold drop in score at which extension of word + description: + This is the threshold drop in score at which extension of word alignment is halted. meaning: edam:data_1403 edam:data_1410: title: Terminal gap opening penalty - description: A number defining the penalty for opening gaps at the termini + description: + A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. meaning: edam:data_1410 edam:data_1411: title: Terminal gap extension penalty - description: A number defining the penalty for extending gaps at the termini + description: + A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. meaning: edam:data_1411 edam:data_1412: title: Sequence identity - description: Sequence identity is the number (%) of matches (identical characters) + description: + Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. meaning: edam:data_1412 edam:data_1413: title: Sequence similarity - description: Sequence similarity is the similarity (expressed as a percentage) + description: + Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. meaning: edam:data_1413 edam:data_1426: title: Phylogenetic continuous quantitative data - description: Continuous quantitative data that may be read during phylogenetic + description: + Continuous quantitative data that may be read during phylogenetic tree calculation. meaning: edam:data_1426 edam:data_1427: title: Phylogenetic discrete data - description: Character data with discrete states that may be read during phylogenetic + description: + Character data with discrete states that may be read during phylogenetic tree calculation. meaning: edam:data_1427 edam:data_1428: title: Phylogenetic character cliques - description: One or more cliques of mutually compatible characters that are + description: + One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. meaning: edam:data_1428 @@ -1492,17 +1636,20 @@ enums: meaning: edam:data_1429 edam:data_1439: title: DNA substitution model - description: A model of DNA substitution that explains a DNA sequence alignment, + description: + A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. meaning: edam:data_1439 edam:data_1442: title: Phylogenetic tree distances - description: Distances, such as Branch Score distance, between two or more + description: + Distances, such as Branch Score distance, between two or more phylogenetic trees. meaning: edam:data_1442 edam:data_1444: title: Phylogenetic character contrasts - description: Independent contrasts for characters used in a phylogenetic tree, + description: + Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. meaning: edam:data_1444 @@ -1516,17 +1663,20 @@ enums: meaning: edam:data_1449 edam:data_1459: title: Nucleic acid structure - description: 3D coordinate and associated data for a nucleic acid tertiary + description: + 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. meaning: edam:data_1459 edam:data_1460: title: Protein structure - description: 3D coordinate and associated data for a protein tertiary (3D) + description: + 3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules. meaning: edam:data_1460 edam:data_1461: title: Protein-ligand complex - description: The structure of a protein in complex with a ligand, typically + description: + The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. meaning: edam:data_1461 @@ -1536,7 +1686,8 @@ enums: meaning: edam:data_1462 edam:data_1463: title: Small molecule structure - description: 3D coordinate and associated data for the (3D) structure of a + description: + 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. meaning: edam:data_1463 edam:data_1464: @@ -1549,27 +1700,32 @@ enums: meaning: edam:data_1465 edam:data_1466: title: tRNA structure - description: 3D coordinate and associated data for a tRNA tertiary (3D) structure, + description: + 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. meaning: edam:data_1466 edam:data_1467: title: Protein chain - description: 3D coordinate and associated data for the tertiary (3D) structure + description: + 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. meaning: edam:data_1467 edam:data_1468: title: Protein domain - description: 3D coordinate and associated data for the tertiary (3D) structure + description: + 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. meaning: edam:data_1468 edam:data_1470: title: C-alpha trace - description: 3D coordinate and associated data for a protein tertiary (3D) + description: + 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). meaning: edam:data_1470 edam:data_1479: title: Structure alignment (pair) - description: Alignment (superimposition) of exactly two molecular tertiary + description: + Alignment (superimposition) of exactly two molecular tertiary (3D) structures. meaning: edam:data_1479 edam:data_1481: @@ -1586,12 +1742,14 @@ enums: meaning: edam:data_1493 edam:data_1494: title: Structural transformation matrix - description: Matrix to transform (rotate/translate) 3D coordinates, typically + description: + Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. meaning: edam:data_1494 edam:data_1497: title: Root-mean-square deviation - description: Root-mean-square deviation (RMSD) is calculated to measure the + description: + Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. meaning: edam:data_1497 edam:data_1498: @@ -1600,17 +1758,20 @@ enums: meaning: edam:data_1498 edam:data_1499: title: 3D-1D scoring matrix - description: A matrix of 3D-1D scores reflecting the probability of amino + description: + A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. meaning: edam:data_1499 edam:data_1501: title: Amino acid index - description: A table of 20 numerical values which quantify a property (e.g. + description: + A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. meaning: edam:data_1501 edam:data_1502: title: Amino acid index (chemical classes) - description: Chemical classification (small, aliphatic, aromatic, polar, charged + description: + Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. meaning: edam:data_1502 edam:data_1503: @@ -1627,7 +1788,8 @@ enums: meaning: edam:data_1506 edam:data_1507: title: Amino acid index (White-Wimley data) - description: Experimental free energy values for the water-interface and water-octanol + description: + Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. meaning: edam:data_1507 edam:data_1508: @@ -1636,7 +1798,8 @@ enums: meaning: edam:data_1508 edam:data_1519: title: Peptide molecular weights - description: List of molecular weight(s) of one or more proteins or peptides, + description: + List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. meaning: edam:data_1519 edam:data_1520: @@ -1649,17 +1812,20 @@ enums: meaning: edam:data_1521 edam:data_1522: title: Protein sequence hydropathy plot - description: A protein sequence with annotation on hydrophobic or hydrophilic + description: + A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. meaning: edam:data_1522 edam:data_1523: title: Protein charge plot - description: A plot of the mean charge of the amino acids within a window + description: + A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. meaning: edam:data_1523 edam:data_1524: title: Protein solubility - description: The solubility or atomic solvation energy of a protein sequence + description: + The solubility or atomic solvation energy of a protein sequence or structure. meaning: edam:data_1524 edam:data_1525: @@ -1668,7 +1834,8 @@ enums: meaning: edam:data_1525 edam:data_1526: title: Protein globularity - description: Data on the stability, intrinsic disorder or globularity of a + description: + Data on the stability, intrinsic disorder or globularity of a protein sequence. meaning: edam:data_1526 edam:data_1527: @@ -1701,7 +1868,8 @@ enums: meaning: edam:data_1534 edam:data_1537: title: Protein structure report - description: A human-readable collection of information about one or more + description: + A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains. meaning: edam:data_1537 edam:data_1539: @@ -1710,7 +1878,8 @@ enums: meaning: edam:data_1539 edam:data_1542: title: Protein solvent accessibility - description: Data on the solvent accessible or buried surface area of a protein + description: + Data on the solvent accessible or buried surface area of a protein structure. meaning: edam:data_1542 edam:data_1544: @@ -1719,12 +1888,14 @@ enums: meaning: edam:data_1544 edam:data_1545: title: Protein dipole moment - description: Data on the net charge distribution (dipole moment) of a protein + description: + Data on the net charge distribution (dipole moment) of a protein structure. meaning: edam:data_1545 edam:data_1546: title: Protein distance matrix - description: A matrix of distances between amino acid residues (for example + description: + A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. meaning: edam:data_1546 edam:data_1547: @@ -1733,7 +1904,8 @@ enums: meaning: edam:data_1547 edam:data_1548: title: Protein residue 3D cluster - description: Report on clusters of contacting residues in protein structures + description: + Report on clusters of contacting residues in protein structures such as a key structural residue network. meaning: edam:data_1548 edam:data_1549: @@ -1746,17 +1918,20 @@ enums: meaning: edam:data_1566 edam:data_1583: title: Nucleic acid melting profile - description: Data on the dissociation characteristics of a double-stranded + description: + Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. meaning: edam:data_1583 edam:data_1584: title: Nucleic acid enthalpy - description: Enthalpy of hybridised or double stranded nucleic acid (DNA or + description: + Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). meaning: edam:data_1584 edam:data_1585: title: Nucleic acid entropy - description: Entropy of hybridised or double stranded nucleic acid (DNA or + description: + Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). meaning: edam:data_1585 edam:data_1588: @@ -1777,13 +1952,15 @@ enums: meaning: edam:data_1595 edam:data_1596: title: Nucleic acid folding report - description: A human-readable collection of information about RNA/DNA folding, + description: + A human-readable collection of information about RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. meaning: edam:data_1596 edam:data_1597: title: Codon usage table - description: Table of codon usage data calculated from one or more nucleic + description: + Table of codon usage data calculated from one or more nucleic acid sequences. meaning: edam:data_1597 edam:data_1598: @@ -1792,17 +1969,20 @@ enums: meaning: edam:data_1598 edam:data_1600: title: Codon usage bias plot - description: A plot of the synonymous codon usage calculated for windows over + description: + A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. meaning: edam:data_1600 edam:data_1602: title: Codon usage fraction difference - description: The differences in codon usage fractions between two codon usage + description: + The differences in codon usage fractions between two codon usage tables. meaning: edam:data_1602 edam:data_1621: title: Pharmacogenomic test report - description: A human-readable collection of information about the influence + description: + A human-readable collection of information about the influence of genotype on drug response. meaning: edam:data_1621 edam:data_1622: @@ -1811,24 +1991,28 @@ enums: meaning: edam:data_1622 edam:data_1636: title: Heat map - description: A graphical 2D tabular representation of expression data, typically + description: + A graphical 2D tabular representation of expression data, typically derived from an omics experiment. A heat map is a table where rows and columns correspond to different features and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that context. meaning: edam:data_1636 edam:data_1667: title: E-value - description: A simple floating point number defining the lower or upper limit + description: + A simple floating point number defining the lower or upper limit of an expectation value (E-value). meaning: edam:data_1667 edam:data_1668: title: Z-value - description: The z-value is the number of standard deviations a data value + description: + The z-value is the number of standard deviations a data value is above or below a mean value. meaning: edam:data_1668 edam:data_1669: title: P-value - description: The P-value is the probability of obtaining by random chance + description: + The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. meaning: edam:data_1669 @@ -1854,7 +2038,8 @@ enums: meaning: edam:data_1696 edam:data_1707: title: Phylogenetic tree image - description: An image (for viewing or printing) of a phylogenetic tree including + description: + An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. meaning: edam:data_1707 @@ -1872,7 +2057,8 @@ enums: meaning: edam:data_1710 edam:data_1711: title: Sequence alignment image - description: Image of two or more aligned molecular sequences possibly annotated + description: + Image of two or more aligned molecular sequences possibly annotated with alignment features. meaning: edam:data_1711 edam:data_1712: @@ -1881,7 +2067,8 @@ enums: meaning: edam:data_1712 edam:data_1713: title: Fate map - description: A fate map is a plan of early stage of an embryo such as a blastula, + description: + A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. meaning: edam:data_1713 edam:data_1714: @@ -1902,7 +2089,8 @@ enums: meaning: edam:data_1743 edam:data_1748: title: PDB atom name - description: Identifier (a string) of a specific atom from a PDB file for + description: + Identifier (a string) of a specific atom from a PDB file for a molecular structure. meaning: edam:data_1748 edam:data_1755: @@ -1931,7 +2119,8 @@ enums: meaning: edam:data_1771 edam:data_1772: title: Score - description: A numerical value, that is some type of scored value arising + description: + A numerical value, that is some type of scored value arising for example from a prediction method. meaning: edam:data_1772 edam:data_1794: @@ -1952,7 +2141,8 @@ enums: meaning: edam:data_1802 edam:data_1803: title: Gene ID (Virginia microbial) - description: Gene identifier from Virginia Bioinformatics Institute microbial + description: + Gene identifier from Virginia Bioinformatics Institute microbial database. meaning: edam:data_1803 edam:data_1804: @@ -1965,7 +2155,8 @@ enums: meaning: edam:data_1805 edam:data_1807: title: ORF name - description: The name of an open reading frame attributed by a sequencing + description: + The name of an open reading frame attributed by a sequencing project. meaning: edam:data_1807 edam:data_1855: @@ -1974,32 +2165,38 @@ enums: meaning: edam:data_1855 edam:data_1856: title: PDB insertion code - description: An insertion code (part of the residue number) for an amino acid + description: + An insertion code (part of the residue number) for an amino acid residue from a PDB file. meaning: edam:data_1856 edam:data_1857: title: Atomic occupancy - description: The fraction of an atom type present at a site in a molecular + description: + The fraction of an atom type present at a site in a molecular structure. meaning: edam:data_1857 edam:data_1858: title: Isotropic B factor - description: Isotropic B factor (atomic displacement parameter) for an atom + description: + Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. meaning: edam:data_1858 edam:data_1859: title: Deletion map - description: A cytogenetic map showing chromosome banding patterns in mutant + description: + A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. meaning: edam:data_1859 edam:data_1860: title: QTL map - description: A genetic map which shows the approximate location of quantitative + description: + A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. meaning: edam:data_1860 edam:data_1863: title: Haplotype map - description: A map of haplotypes in a genome or other sequence, describing + description: + A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. meaning: edam:data_1863 edam:data_1867: @@ -2008,7 +2205,8 @@ enums: meaning: edam:data_1867 edam:data_1868: title: Taxon - description: The name of a group of organisms belonging to the same taxonomic + description: + The name of a group of organisms belonging to the same taxonomic rank. meaning: edam:data_1868 edam:data_1869: @@ -2021,7 +2219,8 @@ enums: meaning: edam:data_1870 edam:data_1872: title: Taxonomic classification - description: The full name for a group of organisms, reflecting their biological + description: + The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. meaning: edam:data_1872 edam:data_1873: @@ -2046,7 +2245,8 @@ enums: meaning: edam:data_1882 edam:data_1883: title: Annotated URI - description: A URI along with annotation describing the data found at the + description: + A URI along with annotation describing the data found at the address. meaning: edam:data_1883 edam:data_1885: @@ -2063,14 +2263,16 @@ enums: meaning: edam:data_1891 edam:data_1893: title: Locus ID - description: A unique name or other identifier of a genetic locus, typically + description: + A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. meaning: edam:data_1893 edam:data_1895: title: Locus ID (AGI) - description: Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR + description: + Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases). meaning: edam:data_1895 edam:data_1896: @@ -2079,7 +2281,8 @@ enums: meaning: edam:data_1896 edam:data_1897: title: Locus ID (MGG) - description: Identifier for loci from Magnaporthe grisea Database at the Broad + description: + Identifier for loci from Magnaporthe grisea Database at the Broad Institute. meaning: edam:data_1897 edam:data_1898: @@ -2088,7 +2291,8 @@ enums: meaning: edam:data_1898 edam:data_1899: title: Locus ID (CMR) - description: Locus identifier for Comprehensive Microbial Resource at the + description: + Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. meaning: edam:data_1899 edam:data_1900: @@ -2125,7 +2329,8 @@ enums: meaning: edam:data_1908 edam:data_1916: title: Alignment - description: An alignment of molecular sequences, structures or profiles derived + description: + An alignment of molecular sequences, structures or profiles derived from them. meaning: edam:data_1916 edam:data_1917: @@ -2134,22 +2339,26 @@ enums: meaning: edam:data_1917 edam:data_2007: title: UniProt keyword - description: A word or phrase that can appear in the keywords field (KW line) + description: + A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. meaning: edam:data_2007 edam:data_2012: title: Sequence coordinates - description: A position in a map (for example a genetic map), either a single + description: + A position in a map (for example a genetic map), either a single position (point) or a region / interval. meaning: edam:data_2012 edam:data_2016: title: Amino acid property - description: Data concerning the intrinsic physical (e.g. structural) or chemical + description: + Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. meaning: edam:data_2016 edam:data_2019: title: Map data - description: Data describing a molecular map (genetic or physical) or a set + description: + Data describing a molecular map (genetic or physical) or a set of such maps, including various attributes of, data extracted from or derived from the analysis of them, but excluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped. @@ -2160,20 +2369,23 @@ enums: meaning: edam:data_2024 edam:data_2025: title: Michaelis Menten plot - description: A plot giving an approximation of the kinetics of an enzyme-catalysed + description: + A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent. meaning: edam:data_2025 edam:data_2026: title: Hanes Woolf plot - description: A plot based on the Michaelis Menten equation of enzyme kinetics + description: + A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). meaning: edam:data_2026 edam:data_2042: title: Evidence - description: Typically a human-readable summary of body of facts or information + description: + Typically a human-readable summary of body of facts or information indicating why a statement is true or valid. This may include a computational prediction, laboratory experiment, literature reference etc. meaning: edam:data_2042 @@ -2183,7 +2395,8 @@ enums: meaning: edam:data_2044 edam:data_2048: title: Report - description: A human-readable collection of information including annotation + description: + A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct @@ -2211,12 +2424,14 @@ enums: meaning: edam:data_2082 edam:data_2084: title: Nucleic acid report - description: A human-readable collection of information about one or more + description: + A human-readable collection of information about one or more specific nucleic acid molecules. meaning: edam:data_2084 edam:data_2085: title: Structure report - description: A human-readable collection of information about one or more + description: + A human-readable collection of information about one or more molecular tertiary (3D) structures. It might include annotation on the structure, a computer-generated report of analysis of structural data, and metadata (data about primary data) or any other free (essentially unformatted) text, @@ -2224,22 +2439,26 @@ enums: meaning: edam:data_2085 edam:data_2087: title: Molecular property - description: A report on the physical (e.g. structural) or chemical properties + description: + A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. meaning: edam:data_2087 edam:data_2088: title: DNA base structural data - description: Structural data for DNA base pairs or runs of bases, such as + description: + Structural data for DNA base pairs or runs of bases, such as energy or angle data. meaning: edam:data_2088 edam:data_2091: title: Accession - description: A persistent (stable) and unique identifier, typically identifying + description: + A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. meaning: edam:data_2091 edam:data_2093: title: Data reference - description: Reference to a dataset (or a cross-reference between two datasets), + description: + Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. meaning: edam:data_2093 edam:data_2098: @@ -2248,17 +2467,20 @@ enums: meaning: edam:data_2098 edam:data_2099: title: Name - description: A name of a thing, which need not necessarily uniquely identify + description: + A name of a thing, which need not necessarily uniquely identify it. meaning: edam:data_2099 edam:data_2101: title: Account authentication - description: Authentication data usually used to log in into an account on + description: + Authentication data usually used to log in into an account on an information system such as a web application or a database. meaning: edam:data_2101 edam:data_2102: title: KEGG organism code - description: A three-letter code used in the KEGG databases to uniquely identify + description: + A three-letter code used in the KEGG databases to uniquely identify organisms. meaning: edam:data_2102 edam:data_2104: @@ -2271,7 +2493,8 @@ enums: meaning: edam:data_2105 edam:data_2106: title: Reaction ID (BioCyc) - description: Identifier of a biological reaction from the BioCyc reactions + description: + Identifier of a biological reaction from the BioCyc reactions database. meaning: edam:data_2106 edam:data_2107: @@ -2284,7 +2507,8 @@ enums: meaning: edam:data_2108 edam:data_2109: title: Identifier (hybrid) - description: An identifier that is reused for data objects of fundamentally + description: + An identifier that is reused for data objects of fundamentally different types (typically served from a single database). meaning: edam:data_2109 edam:data_2110: @@ -2313,7 +2537,8 @@ enums: meaning: edam:data_2117 edam:data_2118: title: Person identifier - description: An identifier of a software end-user on a website or a database + description: + An identifier of a software end-user on a website or a database (typically a person or an entity). meaning: edam:data_2118 edam:data_2119: @@ -2330,7 +2555,8 @@ enums: meaning: edam:data_2128 edam:data_2129: title: File format name - description: Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and + description: + Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. meaning: edam:data_2129 edam:data_2131: @@ -2347,7 +2573,8 @@ enums: meaning: edam:data_2137 edam:data_2139: title: Nucleic acid melting temperature - description: A temperature concerning nucleic acid denaturation, typically + description: + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. meaning: edam:data_2139 @@ -2361,22 +2588,26 @@ enums: meaning: edam:data_2154 edam:data_2160: title: Fickett testcode plot - description: A plot of Fickett testcode statistic (identifying protein coding + description: + A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. meaning: edam:data_2160 edam:data_2161: title: Sequence similarity plot - description: A plot of sequence similarities identified from word-matching + description: + A plot of sequence similarities identified from word-matching or character comparison. meaning: edam:data_2161 edam:data_2162: title: Helical wheel - description: An image of peptide sequence sequence looking down the axis of + description: + An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. meaning: edam:data_2162 edam:data_2163: title: Helical net - description: An image of peptide sequence sequence in a simple 3,4,3,4 repeating + description: + An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. meaning: edam:data_2163 @@ -2386,7 +2617,8 @@ enums: meaning: edam:data_2165 edam:data_2166: title: Sequence composition plot - description: A plot of character or word composition / frequency of a molecular + description: + A plot of character or word composition / frequency of a molecular sequence. meaning: edam:data_2166 edam:data_2167: @@ -2395,7 +2627,8 @@ enums: meaning: edam:data_2167 edam:data_2168: title: Sequence trace image - description: Image of a sequence trace (nucleotide sequence versus probabilities + description: + Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). meaning: edam:data_2168 edam:data_2174: @@ -2404,7 +2637,8 @@ enums: meaning: edam:data_2174 edam:data_2190: title: Sequence checksum - description: A fixed-size datum calculated (by using a hash function) for + description: + A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. meaning: edam:data_2190 edam:data_2193: @@ -2465,12 +2699,14 @@ enums: meaning: edam:data_2293 edam:data_2294: title: Sequence variation ID - description: An identifier of an entry from a database of molecular sequence + description: + An identifier of an entry from a database of molecular sequence variation. meaning: edam:data_2294 edam:data_2295: title: Gene ID - description: A unique (and typically persistent) identifier of a gene in a + description: + A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. meaning: edam:data_2295 edam:data_2297: @@ -2479,12 +2715,14 @@ enums: meaning: edam:data_2297 edam:data_2298: title: Gene ID (HGNC) - description: Identifier for a gene approved by the HUGO Gene Nomenclature + description: + Identifier for a gene approved by the HUGO Gene Nomenclature Committee. meaning: edam:data_2298 edam:data_2299: title: Gene name - description: The name of a gene, (typically) assigned by a person and/or according + description: + The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. @@ -2495,28 +2733,33 @@ enums: meaning: edam:data_2301 edam:data_2302: title: STRING ID - description: Unique identifier of an entry from the STRING database of protein-protein + description: + Unique identifier of an entry from the STRING database of protein-protein interactions. meaning: edam:data_2302 edam:data_2309: title: Reaction ID (SABIO-RK) - description: Identifier of a biological reaction from the SABIO-RK reactions + description: + Identifier of a biological reaction from the SABIO-RK reactions database. meaning: edam:data_2309 edam:data_2313: title: Carbohydrate report - description: A human-readable collection of information about one or more + description: + A human-readable collection of information about one or more specific carbohydrate 3D structure(s). meaning: edam:data_2313 edam:data_2314: title: GI number - description: A series of digits that are assigned consecutively to each sequence + description: + A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. meaning: edam:data_2314 edam:data_2315: title: NCBI version - description: An identifier assigned to sequence records processed by NCBI, + description: + An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. meaning: edam:data_2315 @@ -2558,12 +2801,14 @@ enums: meaning: edam:data_2327 edam:data_2335: title: Bit score - description: A score derived from the alignment of two sequences, which is + description: + A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system. meaning: edam:data_2335 edam:data_2337: title: Resource metadata - description: Data concerning or describing some core computational resource, + description: + Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. meaning: edam:data_2337 @@ -2617,32 +2862,38 @@ enums: meaning: edam:data_2353 edam:data_2354: title: RNA family report - description: A human-readable collection of information about a specific RNA + description: + A human-readable collection of information about a specific RNA family or other group of classified RNA sequences. meaning: edam:data_2354 edam:data_2355: title: RNA family identifier - description: Identifier of an RNA family, typically an entry from a RNA sequence + description: + Identifier of an RNA family, typically an entry from a RNA sequence classification database. meaning: edam:data_2355 edam:data_2356: title: RFAM accession - description: Stable accession number of an entry (RNA family) from the RFAM + description: + Stable accession number of an entry (RNA family) from the RFAM database. meaning: edam:data_2356 edam:data_2362: title: Sequence accession (hybrid) - description: Accession number of a nucleotide or protein sequence database + description: + Accession number of a nucleotide or protein sequence database entry. meaning: edam:data_2362 edam:data_2365: title: Pathway or network accession - description: A persistent, unique identifier of a biological pathway or network + description: + A persistent, unique identifier of a biological pathway or network (typically a database entry). meaning: edam:data_2365 edam:data_2366: title: Secondary structure alignment - description: Alignment of the (1D representations of) secondary structure + description: + Alignment of the (1D representations of) secondary structure of two or more molecules. meaning: edam:data_2366 edam:data_2367: @@ -2667,22 +2918,26 @@ enums: meaning: edam:data_2371 edam:data_2373: title: Spot ID - description: Unique identifier of a spot from a two-dimensional (protein) + description: + Unique identifier of a spot from a two-dimensional (protein) gel. meaning: edam:data_2373 edam:data_2374: title: Spot serial number - description: Unique identifier of a spot from a two-dimensional (protein) + description: + Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. meaning: edam:data_2374 edam:data_2375: title: Spot ID (HSC-2DPAGE) - description: Unique identifier of a spot from a two-dimensional (protein) + description: + Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. meaning: edam:data_2375 edam:data_2379: title: Strain identifier - description: Identifier of a strain of an organism variant, typically a plant, + description: + Identifier of a strain of an organism variant, typically a plant, virus or bacterium. meaning: edam:data_2379 edam:data_2380: @@ -2691,7 +2946,8 @@ enums: meaning: edam:data_2380 edam:data_2382: title: Genotype experiment ID - description: Identifier of an entry from a database of genotype experiment + description: + Identifier of an entry from a database of genotype experiment metadata. meaning: edam:data_2382 edam:data_2383: @@ -2700,7 +2956,8 @@ enums: meaning: edam:data_2383 edam:data_2384: title: IPI protein ID - description: Identifier of a protein entry catalogued in the International + description: + Identifier of a protein entry catalogued in the International Protein Index (IPI) database. meaning: edam:data_2384 edam:data_2385: @@ -2745,13 +3002,15 @@ enums: meaning: edam:data_2398 edam:data_2523: title: Phylogenetic data - description: Data concerning phylogeny, typically of molecular sequences, + description: + Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. meaning: edam:data_2523 edam:data_2526: title: Text data - description: Data concerning, extracted from, or derived from the analysis + description: + Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. meaning: edam:data_2526 @@ -2761,18 +3020,21 @@ enums: meaning: edam:data_2530 edam:data_2531: title: Protocol - description: A human-readable collection of information about about how a + description: + A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis. meaning: edam:data_2531 edam:data_2534: title: Sequence attribute - description: An attribute of a molecular sequence, possibly in reference to + description: + An attribute of a molecular sequence, possibly in reference to some other sequence. meaning: edam:data_2534 edam:data_2535: title: Sequence tag profile - description: Output from a serial analysis of gene expression (SAGE), massively + description: + Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. @@ -2815,12 +3077,14 @@ enums: meaning: edam:data_2580 edam:data_2582: title: GO concept ID (biological process) - description: An identifier of a 'biological process' concept from the the + description: + An identifier of a 'biological process' concept from the the Gene Ontology. meaning: edam:data_2582 edam:data_2583: title: GO concept ID (molecular function) - description: An identifier of a 'molecular function' concept from the the + description: + An identifier of a 'molecular function' concept from the the Gene Ontology. meaning: edam:data_2583 edam:data_2586: @@ -2833,17 +3097,20 @@ enums: meaning: edam:data_2587 edam:data_2588: title: BlotBase blot ID - description: Unique identifier of a blot from a Northern Blot from the BlotBase + description: + Unique identifier of a blot from a Northern Blot from the BlotBase database. meaning: edam:data_2588 edam:data_2589: title: Hierarchy - description: Raw data on a biological hierarchy, describing the hierarchy + description: + Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. meaning: edam:data_2589 edam:data_2591: - title: Brite hierarchy ID - description: Identifier of an entry from the Brite database of biological + title: Bright hierarchy ID + description: + Identifier of an entry from the Bright database of biological hierarchies. meaning: edam:data_2591 edam:data_2593: @@ -2852,12 +3119,14 @@ enums: meaning: edam:data_2593 edam:data_2594: title: UniGene taxon - description: The name of a taxon using the controlled vocabulary of the UniGene + description: + The name of a taxon using the controlled vocabulary of the UniGene database. meaning: edam:data_2594 edam:data_2595: title: UTRdb taxon - description: The name of a taxon using the controlled vocabulary of the UTRdb + description: + The name of a taxon using the controlled vocabulary of the UTRdb database. meaning: edam:data_2595 edam:data_2596: @@ -2866,17 +3135,20 @@ enums: meaning: edam:data_2596 edam:data_2597: title: CABRI catalogue name - description: The name of a catalogue of biological resources from the CABRI + description: + The name of a catalogue of biological resources from the CABRI database. meaning: edam:data_2597 edam:data_2600: title: Pathway or network - description: Primary data about a specific biological pathway or network (the + description: + Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). meaning: edam:data_2600 edam:data_2603: title: Expression data - description: Image, hybridisation or some other data arising from a study + description: + Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification. meaning: edam:data_2603 edam:data_2605: @@ -2885,7 +3157,8 @@ enums: meaning: edam:data_2605 edam:data_2606: title: RFAM name - description: Name (not necessarily stable) an entry (RNA family) from the + description: + Name (not necessarily stable) an entry (RNA family) from the RFAM database. meaning: edam:data_2606 edam:data_2608: @@ -2898,12 +3171,14 @@ enums: meaning: edam:data_2609 edam:data_2610: title: Ensembl ID - description: Identifier of an entry (exon, gene, transcript or protein) from + description: + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. meaning: edam:data_2610 edam:data_2611: title: ICD identifier - description: An identifier of a disease from the International Classification + description: + An identifier of a disease from the International Classification of Diseases (ICD) database. meaning: edam:data_2611 edam:data_2612: @@ -2912,27 +3187,32 @@ enums: meaning: edam:data_2612 edam:data_2613: title: KEGG Glycan ID - description: Unique identifier of a glycan ligand from the KEGG GLYCAN database + description: + Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). meaning: edam:data_2613 edam:data_2614: title: TCDB ID - description: A unique identifier of a family from the transport classification + description: + A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. meaning: edam:data_2614 edam:data_2615: title: MINT ID - description: Unique identifier of an entry from the MINT database of protein-protein + description: + Unique identifier of an entry from the MINT database of protein-protein interactions. meaning: edam:data_2615 edam:data_2616: title: DIP ID - description: Unique identifier of an entry from the DIP database of protein-protein + description: + Unique identifier of an entry from the DIP database of protein-protein interactions. meaning: edam:data_2616 edam:data_2617: title: Signaling Gateway protein ID - description: Unique identifier of a protein listed in the UCSD-Nature Signaling + description: + Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. meaning: edam:data_2617 edam:data_2618: @@ -2941,7 +3221,8 @@ enums: meaning: edam:data_2618 edam:data_2619: title: RESID ID - description: Identifier of a protein modification catalogued in the RESID + description: + Identifier of a protein modification catalogued in the RESID database. meaning: edam:data_2619 edam:data_2620: @@ -2954,7 +3235,8 @@ enums: meaning: edam:data_2621 edam:data_2622: title: Compound ID (HMDB) - description: Identifier of a small molecule metabolite from the Human Metabolome + description: + Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). meaning: edam:data_2622 edam:data_2625: @@ -2983,7 +3265,8 @@ enums: meaning: edam:data_2631 edam:data_2632: title: SGD ID - description: Identifier of an entry from the Saccharomyces genome database + description: + Identifier of an entry from the Saccharomyces genome database (SGD). meaning: edam:data_2632 edam:data_2633: @@ -2992,7 +3275,8 @@ enums: meaning: edam:data_2633 edam:data_2634: title: ISBN - description: The International Standard Book Number (ISBN) is for identifying + description: + The International Standard Book Number (ISBN) is for identifying printed books. meaning: edam:data_2634 edam:data_2635: @@ -3005,7 +3289,8 @@ enums: meaning: edam:data_2636 edam:data_2637: title: cPath ID - description: A unique identifier for pathways, reactions, complexes and small + description: + A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. meaning: edam:data_2637 edam:data_2638: @@ -3026,7 +3311,8 @@ enums: meaning: edam:data_2642 edam:data_2643: title: Gene ID (ZFIN) - description: Identifier for a gene from the Zebrafish information network + description: + Identifier for a gene from the Zebrafish information network genome (ZFIN) database. meaning: edam:data_2643 edam:data_2644: @@ -3043,32 +3329,38 @@ enums: meaning: edam:data_2646 edam:data_2647: title: LGICdb identifier - description: Unique identifier of an entry from the Ligand-gated ion channel + description: + Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. meaning: edam:data_2647 edam:data_2648: title: Reaction kinetics ID (SABIO-RK) - description: Identifier of a biological reaction (kinetics entry) from the + description: + Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. meaning: edam:data_2648 edam:data_2649: title: PharmGKB ID - description: Identifier of an entry from the pharmacogenetics and pharmacogenomics + description: + Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). meaning: edam:data_2649 edam:data_2650: title: Pathway ID (PharmGKB) - description: Identifier of a pathway from the pharmacogenetics and pharmacogenomics + description: + Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). meaning: edam:data_2650 edam:data_2651: title: Disease ID (PharmGKB) - description: Identifier of a disease from the pharmacogenetics and pharmacogenomics + description: + Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). meaning: edam:data_2651 edam:data_2652: title: Drug ID (PharmGKB) - description: Identifier of a drug from the pharmacogenetics and pharmacogenomics + description: + Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). meaning: edam:data_2652 edam:data_2653: @@ -3077,7 +3369,8 @@ enums: meaning: edam:data_2653 edam:data_2654: title: Target ID (TTD) - description: Identifier of a target protein from the Therapeutic Target Database + description: + Identifier of a target protein from the Therapeutic Target Database (TTD). meaning: edam:data_2654 edam:data_2655: @@ -3098,17 +3391,20 @@ enums: meaning: edam:data_2658 edam:data_2659: title: Pathway ID (SMPDB) - description: Identifier of a pathway from the Small Molecule Pathway Database + description: + Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). meaning: edam:data_2659 edam:data_2660: title: BioNumbers ID - description: Identifier of an entry from the BioNumbers database of key numbers + description: + Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. meaning: edam:data_2660 edam:data_2662: title: T3DB ID - description: Unique identifier of a toxin from the Toxin and Toxin Target + description: + Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. meaning: edam:data_2662 edam:data_2663: @@ -3133,7 +3429,8 @@ enums: meaning: edam:data_2667 edam:data_2668: title: iRefIndex ID - description: Unique identifier of an entry from the iRefIndex database of + description: + Unique identifier of an entry from the iRefIndex database of protein-protein interactions. meaning: edam:data_2668 edam:data_2669: @@ -3142,12 +3439,14 @@ enums: meaning: edam:data_2669 edam:data_2670: title: Pathway ID (DQCS) - description: Identifier of a signaling pathway from the Database of Quantitative + description: + Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). meaning: edam:data_2670 edam:data_2700: title: CATH identifier - description: Identifier of a protein domain (or other node) from the CATH + description: + Identifier of a protein domain (or other node) from the CATH database. meaning: edam:data_2700 edam:data_2701: @@ -3160,12 +3459,14 @@ enums: meaning: edam:data_2702 edam:data_2704: title: Clone ID (IMAGE) - description: A unique identifier assigned by the I.M.A.G.E. consortium to + description: + A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). meaning: edam:data_2704 edam:data_2705: title: GO concept ID (cellular component) - description: An identifier of a 'cellular component' concept from the Gene + description: + An identifier of a 'cellular component' concept from the Gene Ontology. meaning: edam:data_2705 edam:data_2706: @@ -3178,12 +3479,14 @@ enums: meaning: edam:data_2709 edam:data_2710: title: CleanEx dataset code - description: An identifier of (typically a list of) gene expression experiments + description: + An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. meaning: edam:data_2710 edam:data_2711: title: Genome report - description: A human-readable collection of information concerning a genome + description: + A human-readable collection of information concerning a genome as a whole. meaning: edam:data_2711 edam:data_2713: @@ -3192,7 +3495,8 @@ enums: meaning: edam:data_2713 edam:data_2714: title: CDD PSSM-ID - description: Unique identifier of a position-specific scoring matrix from + description: + Unique identifier of a position-specific scoring matrix from the CDD database. meaning: edam:data_2714 edam:data_2715: @@ -3233,7 +3537,8 @@ enums: meaning: edam:data_2725 edam:data_2727: title: Promoter ID - description: An identifier of a promoter of a gene that is catalogued in a + description: + An identifier of a promoter of a gene that is catalogued in a database. meaning: edam:data_2727 edam:data_2728: @@ -3250,7 +3555,8 @@ enums: meaning: edam:data_2730 edam:data_2731: title: Protein family ID (GeneFarm) - description: Accession number of an entry (protein family) from the GeneFarm + description: + Accession number of an entry (protein family) from the GeneFarm database. meaning: edam:data_2731 edam:data_2732: @@ -3291,7 +3597,8 @@ enums: meaning: edam:data_2745 edam:data_2746: title: MonosaccharideDB ID - description: Unique identifier of a monosaccharide from the MonosaccharideDB + description: + Unique identifier of a monosaccharide from the MonosaccharideDB database. meaning: edam:data_2746 edam:data_2749: @@ -3300,12 +3607,14 @@ enums: meaning: edam:data_2749 edam:data_2752: title: GlycoMap ID - description: Identifier of an entry from the GlycoMapsDB (Glycosciences.de) + description: + Identifier of an entry from the GlycoMapsDB (Glycosciences.de) database. meaning: edam:data_2752 edam:data_2753: title: Carbohydrate conformational map - description: A conformational energy map of the glycosidic linkages in a carbohydrate + description: + A conformational energy map of the glycosidic linkages in a carbohydrate molecule. meaning: edam:data_2753 edam:data_2755: @@ -3314,7 +3623,8 @@ enums: meaning: edam:data_2755 edam:data_2756: title: TCID - description: Identifier of a membrane transport proteins from the transport + description: + Identifier of a membrane transport proteins from the transport classification database (TCDB). meaning: edam:data_2756 edam:data_2757: @@ -3331,12 +3641,14 @@ enums: meaning: edam:data_2759 edam:data_2761: title: UTRSite ID - description: Identifier of an entry from the UTRSite database of regulatory + description: + Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. meaning: edam:data_2761 edam:data_2762: title: Sequence signature report - description: An informative report about a specific or conserved pattern in + description: + An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. meaning: edam:data_2762 @@ -3366,12 +3678,14 @@ enums: meaning: edam:data_2772 edam:data_2773: title: IMGT/HLA ID - description: Identifier of a human major histocompatibility complex (HLA) + description: + Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. meaning: edam:data_2773 edam:data_2774: title: Gene ID (JCVI) - description: A unique identifier of gene assigned by the J. Craig Venter Institute + description: + A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). meaning: edam:data_2774 edam:data_2775: @@ -3416,7 +3730,8 @@ enums: meaning: edam:data_2784 edam:data_2785: title: Virus identifier - description: An accession of annotation on a (group of) viruses (catalogued + description: + An accession of annotation on a (group of) viruses (catalogued in a database). meaning: edam:data_2785 edam:data_2786: @@ -3441,12 +3756,14 @@ enums: meaning: edam:data_2791 edam:data_2792: title: Protein ID (PeroxiBase) - description: Unique identifier for a peroxidase protein from the PeroxiBase + description: + Unique identifier for a peroxidase protein from the PeroxiBase database. meaning: edam:data_2792 edam:data_2793: title: SISYPHUS ID - description: Identifier of an entry from the SISYPHUS database of tertiary + description: + Identifier of an entry from the SISYPHUS database of tertiary structure alignments. meaning: edam:data_2793 edam:data_2794: @@ -3463,7 +3780,8 @@ enums: meaning: edam:data_2796 edam:data_2797: title: Protein ID (LGICdb) - description: Unique identifier for a ligand-gated ion channel protein from + description: + Unique identifier for a ligand-gated ion channel protein from the LGICdb database. meaning: edam:data_2797 edam:data_2798: @@ -3484,12 +3802,14 @@ enums: meaning: edam:data_2802 edam:data_2803: title: Clone ID (RefSeq) - description: A unique identifier of a cDNA molecule catalogued in the RefSeq + description: + A unique identifier of a cDNA molecule catalogued in the RefSeq database. meaning: edam:data_2803 edam:data_2804: title: Protein ID (ConoServer) - description: Unique identifier for a cone snail toxin protein from the ConoServer + description: + Unique identifier for a cone snail toxin protein from the ConoServer database. meaning: edam:data_2804 edam:data_2805: @@ -3522,29 +3842,34 @@ enums: meaning: edam:data_2850 edam:data_2851: title: Drug structure - description: 3D coordinate and associated data for the (3D) structure of a + description: + 3D coordinate and associated data for the (3D) structure of a drug. meaning: edam:data_2851 edam:data_2852: title: Toxin structure - description: 3D coordinate and associated data for the (3D) structure of a + description: + 3D coordinate and associated data for the (3D) structure of a toxin. meaning: edam:data_2852 edam:data_2854: title: Position-specific scoring matrix - description: A simple matrix of numbers, where each value (or column of values) + description: + A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. meaning: edam:data_2854 edam:data_2855: title: Distance matrix - description: A matrix of distances between molecular entities, where a value + description: + A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. meaning: edam:data_2855 edam:data_2856: title: Structural distance matrix - description: Distances (values representing similarity) between a group of + description: + Distances (values representing similarity) between a group of molecular structures. meaning: edam:data_2856 edam:data_2858: @@ -3553,44 +3878,52 @@ enums: meaning: edam:data_2858 edam:data_2865: title: Codon usage bias - description: A numerical measure of differences in the frequency of occurrence + description: + A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. meaning: edam:data_2865 edam:data_2870: title: Radiation hybrid map - description: A map showing distance between genetic markers estimated by radiation-induced + description: + A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. meaning: edam:data_2870 edam:data_2872: title: ID list - description: A simple list of data identifiers (such as database accessions), + description: + A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. meaning: edam:data_2872 edam:data_2873: title: Phylogenetic gene frequencies data - description: Gene frequencies data that may be read during phylogenetic tree + description: + Gene frequencies data that may be read during phylogenetic tree calculation. meaning: edam:data_2873 edam:data_2877: title: Protein complex - description: 3D coordinate and associated data for a multi-protein complex; + description: + 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. meaning: edam:data_2877 edam:data_2878: title: Protein structural motif - description: 3D coordinate and associated data for a protein (3D) structural + description: + 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. meaning: edam:data_2878 edam:data_2879: title: Lipid report - description: A human-readable collection of information about one or more + description: + A human-readable collection of information about one or more specific lipid 3D structure(s). meaning: edam:data_2879 edam:data_2884: title: Plot - description: Biological data that has been plotted as a graph of some type, + description: + Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph. meaning: edam:data_2884 edam:data_2886: @@ -3603,7 +3936,8 @@ enums: meaning: edam:data_2887 edam:data_2891: title: Biological model accession - description: Accession of a mathematical model, typically an entry from a + description: + Accession of a mathematical model, typically an entry from a database. meaning: edam:data_2891 edam:data_2892: @@ -3644,7 +3978,8 @@ enums: meaning: edam:data_2900 edam:data_2901: title: Molecule accession - description: Molecule accession is any persistent, unique identifier of a + description: + Molecule accession is any persistent, unique identifier of a specific molecule (catalogued in a database). meaning: edam:data_2901 edam:data_2902: @@ -3657,7 +3992,8 @@ enums: meaning: edam:data_2903 edam:data_2904: title: Map accession - description: An accession of a map of a molecular sequence (deposited in a + description: + An accession of a map of a molecular sequence (deposited in a database). meaning: edam:data_2904 edam:data_2905: @@ -3674,7 +4010,8 @@ enums: meaning: edam:data_2907 edam:data_2908: title: Organism accession - description: An accession of annotation on a (group of) organisms (catalogued + description: + An accession of annotation on a (group of) organisms (catalogued in a database). meaning: edam:data_2908 edam:data_2909: @@ -3687,12 +4024,14 @@ enums: meaning: edam:data_2910 edam:data_2911: title: Transcription factor accession - description: Accession of an entry from a database of transcription factors + description: + Accession of an entry from a database of transcription factors or binding sites. meaning: edam:data_2911 edam:data_2912: title: Strain accession - description: Accession number of a strain of an organism variant, typically + description: + Accession number of a strain of an organism variant, typically a plant, virus or bacterium. meaning: edam:data_2912 edam:data_2914: @@ -3713,28 +4052,33 @@ enums: meaning: edam:data_2917 edam:data_2955: title: Sequence report - description: An informative report of information about molecular sequence(s), + description: + An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. meaning: edam:data_2955 edam:data_2956: title: Protein secondary structure - description: Data concerning the properties or features of one or more protein + description: + Data concerning the properties or features of one or more protein secondary structures. meaning: edam:data_2956 edam:data_2957: title: Hopp and Woods plot - description: A Hopp and Woods plot of predicted antigenicity of a peptide + description: + A Hopp and Woods plot of predicted antigenicity of a peptide or protein. meaning: edam:data_2957 edam:data_2968: title: Image - description: Data (typically biological or biomedical) that has been rendered + description: + Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen. meaning: edam:data_2968 edam:data_2969: title: Sequence image - description: Image of a molecular sequence, possibly with sequence features + description: + Image of a molecular sequence, possibly with sequence features or properties shown. meaning: edam:data_2969 edam:data_2970: @@ -3747,12 +4091,14 @@ enums: meaning: edam:data_2976 edam:data_2977: title: Nucleic acid sequence - description: One or more nucleic acid sequences, possibly with associated + description: + One or more nucleic acid sequences, possibly with associated annotation. meaning: edam:data_2977 edam:data_2978: title: Reaction data - description: Data concerning a biochemical reaction, typically data and more + description: + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. meaning: edam:data_2978 edam:data_2979: @@ -3761,7 +4107,8 @@ enums: meaning: edam:data_2979 edam:data_2984: title: Pathway or network report - description: An informative report concerning or derived from the analysis + description: + An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. meaning: edam:data_2984 edam:data_2985: @@ -3770,7 +4117,8 @@ enums: meaning: edam:data_2985 edam:data_2991: title: Protein geometry data - description: Geometry data for a protein structure, for example bond lengths, + description: + Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. meaning: edam:data_2991 edam:data_2992: @@ -3779,12 +4127,14 @@ enums: meaning: edam:data_2992 edam:data_2994: title: Phylogenetic character weights - description: Weights for sequence positions or characters in phylogenetic + description: + Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. meaning: edam:data_2994 edam:data_3002: title: Annotation track - description: Annotation of one particular positional feature on a biomolecular + description: + Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. meaning: edam:data_3002 @@ -3798,17 +4148,20 @@ enums: meaning: edam:data_3022 edam:data_3025: title: Ontology concept identifier - description: Identifier of a concept in an ontology of biological or bioinformatics + description: + Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. meaning: edam:data_3025 edam:data_3028: title: Taxonomy - description: Data concerning the classification, identification and naming + description: + Data concerning the classification, identification and naming of organisms. meaning: edam:data_3028 edam:data_3029: title: Protein ID (EMBL/GenBank/DDBJ) - description: EMBL/GENBANK/DDBJ coding feature protein identifier, issued by + description: + EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. meaning: edam:data_3029 edam:data_3034: @@ -3817,54 +4170,64 @@ enums: meaning: edam:data_3034 edam:data_3035: title: Structure identifier - description: An identifier of a molecular tertiary structure, typically an + description: + An identifier of a molecular tertiary structure, typically an entry from a structure database. meaning: edam:data_3035 edam:data_3036: title: Matrix identifier - description: An identifier of an array of numerical values, such as a comparison + description: + An identifier of an array of numerical values, such as a comparison matrix. meaning: edam:data_3036 edam:data_3103: title: ATC code - description: Unique identifier of a drug conforming to the Anatomical Therapeutic + description: + Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). meaning: edam:data_3103 edam:data_3104: title: UNII - description: A unique, unambiguous, alphanumeric identifier of a chemical + description: + A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). meaning: edam:data_3104 edam:data_3106: title: System metadata - description: Metadata concerning the software, hardware or other aspects of + description: + Metadata concerning the software, hardware or other aspects of a computer system. meaning: edam:data_3106 edam:data_3108: title: Experimental measurement - description: Raw data such as measurements or other results from laboratory + description: + Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. meaning: edam:data_3108 edam:data_3110: title: Raw microarray data - description: Raw data (typically MIAME-compliant) for hybridisations from + description: + Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. meaning: edam:data_3110 edam:data_3111: title: Processed microarray data - description: Data generated from processing and analysis of probe set data + description: + Data generated from processing and analysis of probe set data from a microarray experiment. meaning: edam:data_3111 edam:data_3112: title: Gene expression matrix - description: The final processed (normalised) data for a set of hybridisations + description: + The final processed (normalised) data for a set of hybridisations in a microarray experiment. meaning: edam:data_3112 edam:data_3113: title: Sample annotation - description: Annotation on a biological sample, for example experimental factors + description: + Annotation on a biological sample, for example experimental factors and their values. meaning: edam:data_3113 edam:data_3115: @@ -3873,24 +4236,28 @@ enums: meaning: edam:data_3115 edam:data_3117: title: Microarray hybridisation data - description: Data concerning the hybridisations measured during a microarray + description: + Data concerning the hybridisations measured during a microarray experiment. meaning: edam:data_3117 edam:data_3128: title: Nucleic acid structure report - description: A human-readable collection of information about regions within + description: + A human-readable collection of information about regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. meaning: edam:data_3128 edam:data_3134: title: Gene transcript report - description: An informative report on features of a messenger RNA (mRNA) molecules + description: + An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. meaning: edam:data_3134 edam:data_3148: title: Gene family report - description: A human-readable collection of information about a particular + description: + A human-readable collection of information about a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure. @@ -3941,7 +4308,8 @@ enums: meaning: edam:data_3271 edam:data_3272: title: Species tree - description: A phylogenetic tree that reflects phylogeny of the taxa from + description: + A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. meaning: edam:data_3272 edam:data_3273: @@ -3958,12 +4326,14 @@ enums: meaning: edam:data_3275 edam:data_3354: title: Transition matrix - description: A HMM transition matrix contains the probabilities of switching + description: + A HMM transition matrix contains the probabilities of switching from one HMM state to another. meaning: edam:data_3354 edam:data_3355: title: Emission matrix - description: A HMM emission matrix holds the probabilities of choosing the + description: + A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. meaning: edam:data_3355 edam:data_3358: @@ -3972,17 +4342,20 @@ enums: meaning: edam:data_3358 edam:data_3424: title: Raw image - description: Raw biological or biomedical image generated by some experimental + description: + Raw biological or biomedical image generated by some experimental technique. meaning: edam:data_3424 edam:data_3425: title: Carbohydrate property - description: Data concerning the intrinsic physical (e.g. structural) or chemical + description: + Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. meaning: edam:data_3425 edam:data_3442: title: MRI image - description: An imaging technique that uses magnetic fields and radiowaves + description: + An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. meaning: edam:data_3442 @@ -3992,7 +4365,8 @@ enums: meaning: edam:data_3449 edam:data_3451: title: Rate of association - description: Rate of association of a protein with another protein or some + description: + Rate of association of a protein with another protein or some other molecule. meaning: edam:data_3451 edam:data_3479: @@ -4001,17 +4375,20 @@ enums: meaning: edam:data_3479 edam:data_3483: title: Spectrum - description: The spectrum of frequencies of electromagnetic radiation emitted + description: + The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. meaning: edam:data_3483 edam:data_3488: title: NMR spectrum - description: Spectral information for a molecule from a nuclear magnetic resonance + description: + Spectral information for a molecule from a nuclear magnetic resonance experiment. meaning: edam:data_3488 edam:data_3492: title: Nucleic acid signature - description: An informative report about a specific or conserved nucleic acid + description: + An informative report about a specific or conserved nucleic acid sequence pattern. meaning: edam:data_3492 edam:data_3494: @@ -4024,16 +4401,18 @@ enums: meaning: edam:data_3495 edam:data_3498: title: Sequence variations - description: Data on gene sequence variations resulting large-scale genotyping + description: + Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. meaning: edam:data_3498 edam:data_3505: title: Bibliography - description: A list of publications such as scientic papers or books. + description: A list of publications such as scientific papers or books. meaning: edam:data_3505 edam:data_3509: title: Ontology mapping - description: A mapping of supplied textual terms or phrases to ontology concepts + description: + A mapping of supplied textual terms or phrases to ontology concepts (URIs). meaning: edam:data_3509 edam:data_3546: @@ -4042,7 +4421,8 @@ enums: meaning: edam:data_3546 edam:data_3558: title: Clinical trial report - description: A human-readable collection of information concerning a clinical + description: + A human-readable collection of information concerning a clinical trial. meaning: edam:data_3558 edam:data_3567: @@ -4063,7 +4443,8 @@ enums: meaning: edam:data_3668 edam:data_3669: title: Learning material - description: Learning material is a document or another digital object that + description: + Learning material is a document or another digital object that is designed for learning (educational, training) purposes. meaning: edam:data_3669 edam:data_3670: @@ -4072,7 +4453,8 @@ enums: meaning: edam:data_3670 edam:data_3671: title: Text - description: Any free or plain text, typically for human consumption and in + description: + Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query. meaning: edam:data_3671 edam:data_3707: @@ -4081,7 +4463,8 @@ enums: meaning: edam:data_3707 edam:data_3716: title: Biosafety report - description: A human-readable collection of information concerning biosafety + description: + A human-readable collection of information concerning biosafety data. meaning: edam:data_3716 edam:data_3717: @@ -4090,32 +4473,38 @@ enums: meaning: edam:data_3717 edam:data_3718: title: Pathogenicity report - description: Information about the ability of an organism to cause disease + description: + Information about the ability of an organism to cause disease in a corresponding host. meaning: edam:data_3718 edam:data_3719: title: Biosafety classification - description: Information about the biosafety classification of an organism + description: + Information about the biosafety classification of an organism according to corresponding law. meaning: edam:data_3719 edam:data_3720: title: Geographic location - description: A report about localisation of the isolaton of biological material + description: + A report about localisation of the isolaton of biological material e.g. country or coordinates. meaning: edam:data_3720 edam:data_3721: title: Isolation source - description: A report about any kind of isolation source of biological material + description: + A report about any kind of isolation source of biological material e.g. blood, water, soil. meaning: edam:data_3721 edam:data_3722: title: Physiology parameter - description: Experimentally determined parameter of the physiology of an organism, + description: + Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum. meaning: edam:data_3722 edam:data_3723: title: Morphology parameter - description: Experimentally determined parameter of the morphology of an organism, + description: + Experimentally determined parameter of the morphology of an organism, e.g. size & shape. meaning: edam:data_3723 edam:data_3724: @@ -4124,7 +4513,8 @@ enums: meaning: edam:data_3724 edam:data_3732: title: Sequencing metadata name - description: Data concerning a sequencing experiment, that may be specified + description: + Data concerning a sequencing experiment, that may be specified as an input to some tool. meaning: edam:data_3732 edam:data_3733: @@ -4133,18 +4523,21 @@ enums: meaning: edam:data_3733 edam:data_3734: title: Lane identifier - description: An identifier of a lane within a flow cell of a sequencing machine, + description: + An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced. meaning: edam:data_3734 edam:data_3735: title: Run number - description: A number corresponding to the number of an analysis performed + description: + A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. meaning: edam:data_3735 edam:data_3736: title: Ecological data - description: Data concerning ecology; for example measurements and reports + description: + Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment. meaning: edam:data_3736 edam:data_3737: @@ -4161,35 +4554,41 @@ enums: meaning: edam:data_3739 edam:data_3743: title: Ordination plot - description: A plot in which community data (e.g. species abundance data) + description: + A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart. meaning: edam:data_3743 edam:data_3753: title: Over-representation data - description: A ranked list of categories (usually ontology concepts), each + description: + A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data. meaning: edam:data_3753 edam:data_3754: title: GO-term enrichment data - description: A ranked list of Gene Ontology concepts, each associated with + description: + A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins. meaning: edam:data_3754 edam:data_3756: title: Localisation score - description: Score for localization of one or more post-translational modifications + description: + Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. meaning: edam:data_3756 edam:data_3757: title: Unimod ID - description: Identifier of a protein modification catalogued in the Unimod + description: + Identifier of a protein modification catalogued in the Unimod database. meaning: edam:data_3757 edam:data_3759: title: ProteomeXchange ID - description: Identifier for mass spectrometry proteomics data in the proteomexchange.org + description: + Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. meaning: edam:data_3759 edam:data_3768: @@ -4202,12 +4601,14 @@ enums: meaning: edam:data_3769 edam:data_3779: title: Annotated text - description: A text (such as a scientific article), annotated with notes, + description: + A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations. meaning: edam:data_3779 edam:data_3786: title: Query script - description: A structured query, in form of a script, that defines a database + description: + A structured query, in form of a script, that defines a database search task. meaning: edam:data_3786 edam:data_3805: @@ -4216,7 +4617,8 @@ enums: meaning: edam:data_3805 edam:data_3806: title: 3D EM Mask - description: Annotation on a structural 3D EM Map from electron microscopy. + description: + Annotation on a structural 3D EM Map from electron microscopy. This might include one or several locations in the map of the known features of a particular macromolecule. meaning: edam:data_3806 @@ -4226,62 +4628,73 @@ enums: meaning: edam:data_3807 edam:data_3808: title: EM Micrograph - description: Raw acquisition from electron microscopy or average of an aligned + description: + Raw acquisition from electron microscopy or average of an aligned DDD movie. meaning: edam:data_3808 edam:data_3842: title: Molecular simulation data - description: Data coming from molecular simulations, computer "experiments" + description: + Data coming from molecular simulations, computer "experiments" on model molecules. meaning: edam:data_3842 edam:data_3856: title: RNA central ID - description: Identifier of an entry from the RNA central database of annotated + description: + Identifier of an entry from the RNA central database of annotated human miRNAs. meaning: edam:data_3856 edam:data_3861: title: Electronic health record - description: A human-readable systematic collection of patient (or population) + description: + A human-readable systematic collection of patient (or population) health information in a digital format. meaning: edam:data_3861 edam:data_3869: title: Simulation - description: 'Data coming from molecular simulations, computer "experiments" + description: + 'Data coming from molecular simulations, computer "experiments" on model molecules. Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).' meaning: edam:data_3869 edam:data_3870: title: Trajectory data - description: 'Dynamic information of a structure molecular system coming from + description: + "Dynamic information of a structure molecular system coming from a molecular simulation: XYZ 3D coordinates (sometimes with their associated - velocities) for every atom along time.' + velocities) for every atom along time." meaning: edam:data_3870 edam:data_3871: title: Forcefield parameters - description: 'Force field parameters: charges, masses, radii, bond lengths, + description: + "Force field parameters: charges, masses, radii, bond lengths, bond dihedrals, etc. define the structural molecular system, and are essential - for the proper description and simulation of a molecular system.' + for the proper description and simulation of a molecular system." meaning: edam:data_3871 edam:data_3872: title: Topology data - description: 'Static information of a structure molecular system that is needed + description: + "Static information of a structure molecular system that is needed for a molecular simulation: the list of atoms, their non-bonded parameters for Van der Waals and electrostatic interactions, and the complete connectivity - in terms of bonds, angles and dihedrals.' + in terms of bonds, angles and dihedrals." meaning: edam:data_3872 edam:data_3905: title: Histogram - description: Visualization of distribution of quantitative data, e.g. expression + description: + Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots. meaning: edam:data_3905 edam:data_3914: title: Quality control report - description: Report of the quality control review that was made of factors + description: + Report of the quality control review that was made of factors involved in a procedure. meaning: edam:data_3914 edam:data_3917: title: Count matrix - description: A table of unnormalized values representing summarised read counts + description: + A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak). meaning: edam:data_3917 edam:data_3924: @@ -4290,14 +4703,16 @@ enums: meaning: edam:data_3924 edam:data_3932: title: Q-value - description: 'A score derived from the P-value to ensure correction for multiple + description: + "A score derived from the P-value to ensure correction for multiple tests. The Q-value provides an estimate of the positive False Discovery Rate (pFDR), i.e. the rate of false positives among all the cases reported - positive: pFDR = FP / (FP + TP).' + positive: pFDR = FP / (FP + TP)." meaning: edam:data_3932 edam:data_3949: title: Profile HMM - description: A profile HMM is a variant of a Hidden Markov model that is derived + description: + A profile HMM is a variant of a Hidden Markov model that is derived specifically from a set of (aligned) biological sequences. Profile HMMs provide the basis for a position-specific scoring system, which can be used to align sequences and search databases for related sequences. @@ -4308,25 +4723,29 @@ enums: meaning: edam:data_3952 edam:data_3953: title: Pathway overrepresentation data - description: A ranked list of pathways, each associated with z-score, p-value + description: + A ranked list of pathways, each associated with z-score, p-value or similar, concerning or derived from the analysis of e.g. a set of genes or proteins. meaning: edam:data_3953 edam:data_4022: title: ORCID Identifier - description: Identifier of a researcher registered with the ORCID database. + description: + Identifier of a researcher registered with the ORCID database. Used to identify author IDs. meaning: edam:data_4022 edam:data_4040: title: Data management plan - description: Data management plan is a document describing the data management + description: + Data management plan is a document describing the data management of a project or an organisation, including acquisition, reuse, structure, processing, storage, documentation, sharing, and preservation of data. This may include budgeting for these operations. meaning: edam:data_4040 edam:data_4075: title: RefMet ID - description: RefMet ID is the unique, persistent identifier used by the RefMet + description: + RefMet ID is the unique, persistent identifier used by the RefMet database (A Reference list of Metabolite names), a standardised reference nomenclature for metabolites. meaning: edam:data_4075 diff --git a/src/common_access_model/schema/enums/EnumEDAMFormats.yaml b/src/common_access_model/schema/enums/EnumEDAMFormats.yaml index ad026cd..945a734 100644 --- a/src/common_access_model/schema/enums/EnumEDAMFormats.yaml +++ b/src/common_access_model/schema/enums/EnumEDAMFormats.yaml @@ -15,43 +15,51 @@ enums: permissible_values: edam:format_1196: title: SMILES - description: Chemical structure specified in Simplified Molecular Input Line + description: + Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. meaning: edam:format_1196 edam:format_1197: title: InChI - description: Chemical structure specified in IUPAC International Chemical + description: + Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. meaning: edam:format_1197 edam:format_1198: title: mf - description: Chemical structure specified by Molecular Formula (MF), including + description: + Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. meaning: edam:format_1198 edam:format_1199: title: InChIKey - description: The InChIKey (hashed InChI) is a fixed length (25 character) + description: + The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. meaning: edam:format_1199 edam:format_1200: title: smarts - description: SMILES ARbitrary Target Specification (SMARTS) format for chemical + description: + SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. meaning: edam:format_1200 edam:format_1206: title: unambiguous pure - description: Alphabet for a molecular sequence with possible unknown positions + description: + Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. meaning: edam:format_1206 edam:format_1207: title: nucleotide - description: Alphabet for a nucleotide sequence with possible ambiguity, unknown + description: + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. meaning: edam:format_1207 edam:format_1208: title: protein - description: Alphabet for a protein sequence with possible ambiguity, unknown + description: + Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. meaning: edam:format_1208 edam:format_1209: @@ -60,93 +68,111 @@ enums: meaning: edam:format_1209 edam:format_1210: title: pure nucleotide - description: Alphabet for a nucleotide sequence with possible ambiguity and + description: + Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. meaning: edam:format_1210 edam:format_1211: title: unambiguous pure nucleotide - description: Alphabet for a nucleotide sequence (characters ACGTU only) with + description: + Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . meaning: edam:format_1211 edam:format_1212: title: dna - description: Alphabet for a DNA sequence with possible ambiguity, unknown + description: + Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. meaning: edam:format_1212 edam:format_1213: title: rna - description: Alphabet for an RNA sequence with possible ambiguity, unknown + description: + Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. meaning: edam:format_1213 edam:format_1214: title: unambiguous pure dna - description: Alphabet for a DNA sequence (characters ACGT only) with possible + description: + Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. meaning: edam:format_1214 edam:format_1215: title: pure dna - description: Alphabet for a DNA sequence with possible ambiguity and unknown + description: + Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. meaning: edam:format_1215 edam:format_1216: title: unambiguous pure rna sequence - description: Alphabet for an RNA sequence (characters ACGU only) with possible + description: + Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. meaning: edam:format_1216 edam:format_1217: title: pure rna - description: Alphabet for an RNA sequence with possible ambiguity and unknown + description: + Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. meaning: edam:format_1217 edam:format_1218: title: unambiguous pure protein - description: Alphabet for any protein sequence with possible unknown positions + description: + Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. meaning: edam:format_1218 edam:format_1219: title: pure protein - description: Alphabet for any protein sequence with possible ambiguity and + description: + Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. meaning: edam:format_1219 edam:format_1248: title: EMBL feature location - description: Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank + description: + Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. meaning: edam:format_1248 edam:format_1295: title: quicktandem - description: Report format for tandem repeats in a nucleotide sequence (format + description: + Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). meaning: edam:format_1295 edam:format_1296: title: Sanger inverted repeats - description: Report format for inverted repeats in a nucleotide sequence (format + description: + Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). meaning: edam:format_1296 edam:format_1297: title: EMBOSS repeat - description: Report format for tandem repeats in a sequence (an EMBOSS report + description: + Report format for tandem repeats in a sequence (an EMBOSS report format). meaning: edam:format_1297 edam:format_1316: title: est2genome format - description: Format of a report on exon-intron structure generated by EMBOSS + description: + Format of a report on exon-intron structure generated by EMBOSS est2genome. meaning: edam:format_1316 edam:format_1318: title: restrict format - description: Report format for restriction enzyme recognition sites used by + description: + Report format for restriction enzyme recognition sites used by EMBOSS restrict program. meaning: edam:format_1318 edam:format_1319: title: restover format - description: Report format for restriction enzyme recognition sites used by + description: + Report format for restriction enzyme recognition sites used by EMBOSS restover program. meaning: edam:format_1319 edam:format_1320: title: REBASE restriction sites - description: Report format for restriction enzyme recognition sites used by + description: + Report format for restriction enzyme recognition sites used by REBASE database. meaning: edam:format_1320 edam:format_1332: @@ -155,27 +181,32 @@ enums: meaning: edam:format_1332 edam:format_1333: title: BLAST results - description: Format of results of a sequence database search using some variant + description: + Format of results of a sequence database search using some variant of BLAST. meaning: edam:format_1333 edam:format_1334: title: mspcrunch - description: Format of results of a sequence database search using some variant + description: + Format of results of a sequence database search using some variant of MSPCrunch. meaning: edam:format_1334 edam:format_1335: title: Smith-Waterman format - description: Format of results of a sequence database search using some variant + description: + Format of results of a sequence database search using some variant of Smith Waterman. meaning: edam:format_1335 edam:format_1336: title: dhf - description: Format of EMBASSY domain hits file (DHF) of hits (sequences) + description: + Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. meaning: edam:format_1336 edam:format_1337: title: lhf - description: Format of EMBASSY ligand hits file (LHF) of database hits (sequences) + description: + Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. meaning: edam:format_1337 edam:format_1341: @@ -184,12 +215,14 @@ enums: meaning: edam:format_1341 edam:format_1342: title: InterPro protein view report format - description: Format of results of a search of the InterPro database showing + description: + Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. meaning: edam:format_1342 edam:format_1343: title: InterPro match table format - description: Format of results of a search of the InterPro database showing + description: + Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. meaning: edam:format_1343 edam:format_1349: @@ -202,7 +235,8 @@ enums: meaning: edam:format_1350 edam:format_1351: title: HMMER emission and transition - description: Format of a report from the HMMER package on the emission and + description: + Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. meaning: edam:format_1351 edam:format_1356: @@ -219,12 +253,14 @@ enums: meaning: edam:format_1360 edam:format_1366: title: prosite-profile - description: Sequence profile (sequence classifier) format used in the PROSITE + description: + Sequence profile (sequence classifier) format used in the PROSITE database. meaning: edam:format_1366 edam:format_1367: title: JASPAR format - description: A profile (sequence classifier) in the format used in the JASPAR + description: + A profile (sequence classifier) in the format used in the JASPAR database. meaning: edam:format_1367 edam:format_1369: @@ -233,12 +269,14 @@ enums: meaning: edam:format_1369 edam:format_1370: title: HMMER format - description: Format of a hidden Markov model representation used by the HMMER + description: + Format of a hidden Markov model representation used by the HMMER package. meaning: edam:format_1370 edam:format_1391: title: HMMER-aln - description: FASTA-style format for multiple sequences aligned by HMMER package + description: + FASTA-style format for multiple sequences aligned by HMMER package to an HMM. meaning: edam:format_1391 edam:format_1392: @@ -247,23 +285,27 @@ enums: meaning: edam:format_1392 edam:format_1393: title: daf - description: EMBASSY 'domain alignment file' (DAF) format, containing a sequence + description: + EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. meaning: edam:format_1393 edam:format_1419: title: Sequence-MEME profile alignment - description: Format for alignment of molecular sequences to MEME profiles + description: + Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. meaning: edam:format_1419 edam:format_1421: title: HMMER profile alignment (sequences versus HMMs) - description: Format used by the HMMER package for an alignment of a sequence + description: + Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. meaning: edam:format_1421 edam:format_1422: title: HMMER profile alignment (HMM versus sequences) - description: Format used by the HMMER package for of an alignment of a hidden + description: + Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. meaning: edam:format_1422 edam:format_1423: @@ -276,7 +318,8 @@ enums: meaning: edam:format_1424 edam:format_1425: title: Phylip tree raw - description: Raw data file format used by Phylip from which a phylogenetic + description: + Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. meaning: edam:format_1425 edam:format_1430: @@ -301,37 +344,44 @@ enums: meaning: edam:format_1435 edam:format_1436: title: TreeBASE format - description: The format of an entry from the TreeBASE database of phylogenetic + description: + The format of an entry from the TreeBASE database of phylogenetic data. meaning: edam:format_1436 edam:format_1437: title: TreeFam format - description: The format of an entry from the TreeFam database of phylogenetic + description: + The format of an entry from the TreeFam database of phylogenetic data. meaning: edam:format_1437 edam:format_1445: title: Phylip tree distance format - description: Format for distances, such as Branch Score distance, between + description: + Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. meaning: edam:format_1445 edam:format_1454: title: dssp - description: Format of an entry from the DSSP database (Dictionary of Secondary + description: + Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). meaning: edam:format_1454 edam:format_1455: title: hssp - description: Entry format of the HSSP database (Homology-derived Secondary + description: + Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). meaning: edam:format_1455 edam:format_1457: title: Dot-bracket format - description: Format of RNA secondary structure in dot-bracket notation, originally + description: + Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. meaning: edam:format_1457 edam:format_1458: title: Vienna local RNA secondary structure format - description: Format of local RNA secondary structure components with free + description: + Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. meaning: edam:format_1458 edam:format_1475: @@ -356,7 +406,8 @@ enums: meaning: edam:format_1504 edam:format_1551: title: Pcons report format - description: Format of output of the Pcons Model Quality Assessment Program + description: + Format of output of the Pcons Model Quality Assessment Program (MQAP). meaning: edam:format_1551 edam:format_1552: @@ -365,18 +416,21 @@ enums: meaning: edam:format_1552 edam:format_1582: title: findkm - description: A report format for the kinetics of enzyme-catalysed reaction(s) + description: + A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). meaning: edam:format_1582 edam:format_1627: title: Primer3 primer - description: Report format on PCR primers and hybridisation oligos as generated + description: + Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. meaning: edam:format_1627 edam:format_1628: title: ABI - description: A format of raw sequence read data from an Applied Biosystems + description: + A format of raw sequence read data from an Applied Biosystems sequencing machine. meaning: edam:format_1628 edam:format_1629: @@ -384,8 +438,9 @@ enums: description: Format of MIRA sequence trace information file. meaning: edam:format_1629 edam:format_1630: - title: CAF - description: Common Assembly Format (CAF). A sequence assembly format including + title: CALF + description: + Common Assembly Format (CALF). A sequence assembly format including contigs, base-call qualities, and other metadata. meaning: edam:format_1630 edam:format_1631: @@ -394,12 +449,14 @@ enums: meaning: edam:format_1631 edam:format_1632: title: SCF - description: Staden Chromatogram Files format (SCF) of base-called sequence + description: + Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. meaning: edam:format_1632 edam:format_1633: title: PHD - description: PHD sequence trace format to store serialised chromatogram data + description: + PHD sequence trace format to store serialised chromatogram data (reads). meaning: edam:format_1633 edam:format_1637: @@ -408,22 +465,26 @@ enums: meaning: edam:format_1637 edam:format_1638: title: cel - description: Format of Affymetrix data file of information about (raw) expression + description: + Format of Affymetrix data file of information about (raw) expression levels of the individual probes. meaning: edam:format_1638 edam:format_1639: title: affymetrix - description: Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) + description: + Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. meaning: edam:format_1639 edam:format_1641: title: affymetrix-exp - description: Affymetrix data file format for information about experimental + description: + Affymetrix data file format for information about experimental conditions and protocols. meaning: edam:format_1641 edam:format_1644: title: CHP - description: Format of Affymetrix data file of information about (normalised) + description: + Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. meaning: edam:format_1644 edam:format_1665: @@ -432,7 +493,8 @@ enums: meaning: edam:format_1665 edam:format_1705: title: HET group dictionary entry format - description: The format of an entry from the HET group dictionary (HET groups + description: + The format of an entry from the HET group dictionary (HET groups from PDB files). meaning: edam:format_1705 edam:format_1734: @@ -441,17 +503,20 @@ enums: meaning: edam:format_1734 edam:format_1735: title: Medline Display Format - description: Format for abstracts of scientific articles from the Medline + description: + Format for abstracts of scientific articles from the Medline database. meaning: edam:format_1735 edam:format_1736: title: CiteXplore-core - description: CiteXplore 'core' citation format including title, journal, authors + description: + CiteXplore 'core' citation format including title, journal, authors and abstract. meaning: edam:format_1736 edam:format_1737: title: CiteXplore-all - description: CiteXplore 'all' citation format includes all known details such + description: + CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. meaning: edam:format_1737 edam:format_1739: @@ -460,7 +525,8 @@ enums: meaning: edam:format_1739 edam:format_1740: title: iHOP format - description: The format of iHOP (Information Hyperlinked over Proteins) text-mining + description: + The format of iHOP (Information Hyperlinked over Proteins) text-mining result. meaning: edam:format_1740 edam:format_1741: @@ -468,8 +534,8 @@ enums: description: OSCAR format of annotated chemical text. meaning: edam:format_1741 edam:format_1861: - title: PlasMapper TextMap - description: Map of a plasmid (circular DNA) in PlasMapper TextMap format. + title: PlaysMapper TextMap + description: Map of a plasmid (circular DNA) in PlaysMapper TextMap format. meaning: edam:format_1861 edam:format_1910: title: newick @@ -633,7 +699,8 @@ enums: meaning: edam:format_1960 edam:format_1961: title: Stockholm format - description: Stockholm multiple sequence alignment format (used by Pfam and + description: + Stockholm multiple sequence alignment format (used by Pfam and Rfam). meaning: edam:format_1961 edam:format_1962: @@ -662,7 +729,8 @@ enums: meaning: edam:format_1968 edam:format_1969: title: debug-seq - description: EMBOSS debugging trace sequence format of full internal data + description: + EMBOSS debugging trace sequence format of full internal data content. meaning: edam:format_1969 edam:format_1970: @@ -699,7 +767,8 @@ enums: meaning: edam:format_1982 edam:format_1983: title: debug - description: EMBOSS alignment format for debugging trace of full internal + description: + EMBOSS alignment format for debugging trace of full internal data content. meaning: edam:format_1983 edam:format_1984: @@ -728,7 +797,8 @@ enums: meaning: edam:format_1989 edam:format_1990: title: match - description: Alignment format for start and end of matches between sequence + description: + Alignment format for start and end of matches between sequence pairs. meaning: edam:format_1990 edam:format_1991: @@ -813,7 +883,8 @@ enums: meaning: edam:format_2030 edam:format_2031: title: Gene annotation format - description: Format of a report on a particular locus, gene, gene system or + description: + Format of a report on a particular locus, gene, gene system or groups of genes. meaning: edam:format_2031 edam:format_2032: @@ -866,7 +937,8 @@ enums: meaning: edam:format_2055 edam:format_2056: title: Microarray experiment data format - description: Format for information about a microarray experimental per se + description: + Format for information about a microarray experimental per se (not the data generated from that experiment). meaning: edam:format_2056 edam:format_2057: @@ -875,17 +947,20 @@ enums: meaning: edam:format_2057 edam:format_2058: title: Gene expression report format - description: Format of a file of gene expression data, e.g. a gene expression + description: + Format of a file of gene expression data, e.g. a gene expression matrix or profile. meaning: edam:format_2058 edam:format_2060: title: Map format - description: Format of a map of (typically one) molecular sequence annotated + description: + Format of a map of (typically one) molecular sequence annotated with features. meaning: edam:format_2060 edam:format_2061: title: Nucleic acid features (primers) format - description: Format of a report on PCR primers or hybridisation oligos in + description: + Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. meaning: edam:format_2061 edam:format_2062: @@ -898,12 +973,14 @@ enums: meaning: edam:format_2064 edam:format_2065: title: Protein structure report (quality evaluation) format - description: Format of a report on the quality of a protein three-dimensional + description: + Format of a report on the quality of a protein three-dimensional model. meaning: edam:format_2065 edam:format_2066: title: Database hits (sequence) format - description: Format of a report on sequence hits and associated data from + description: + Format of a report on sequence hits and associated data from searching a sequence database. meaning: edam:format_2066 edam:format_2067: @@ -928,17 +1005,20 @@ enums: meaning: edam:format_2074 edam:format_2075: title: HMM emission and transition counts format - description: Data format for the emission and transition counts of a hidden + description: + Data format for the emission and transition counts of a hidden Markov model. meaning: edam:format_2075 edam:format_2076: title: RNA secondary structure format - description: Format for secondary structure (predicted or real) of an RNA + description: + Format for secondary structure (predicted or real) of an RNA molecule. meaning: edam:format_2076 edam:format_2077: title: Protein secondary structure format - description: Format for secondary structure (predicted or real) of a protein + description: + Format for secondary structure (predicted or real) of a protein molecule. meaning: edam:format_2077 edam:format_2078: @@ -947,32 +1027,38 @@ enums: meaning: edam:format_2078 edam:format_2094: title: pure - description: Alphabet for molecular sequence with possible unknown positions + description: + Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. meaning: edam:format_2094 edam:format_2095: title: unpure - description: Alphabet for a molecular sequence with possible unknown positions + description: + Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. meaning: edam:format_2095 edam:format_2096: title: unambiguous sequence - description: Alphabet for a molecular sequence with possible unknown positions + description: + Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. meaning: edam:format_2096 edam:format_2097: title: ambiguous - description: Alphabet for a molecular sequence with possible unknown positions + description: + Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. meaning: edam:format_2097 edam:format_2155: title: Sequence features (repeats) format - description: Format used for map of repeats in molecular (typically nucleotide) + description: + Format used for map of repeats in molecular (typically nucleotide) sequences. meaning: edam:format_2155 edam:format_2158: title: Nucleic acid features (restriction sites) format - description: Format used for report on restriction enzyme recognition sites + description: + Format used for report on restriction enzyme recognition sites in nucleotide sequences. meaning: edam:format_2158 edam:format_2170: @@ -1005,7 +1091,8 @@ enums: meaning: edam:format_2184 edam:format_2185: title: INSDSeq - description: INSDSeq provides the elements of a sequence as presented in the + description: + INSDSeq provides the elements of a sequence as presented in the GenBank/EMBL/DDBJ-style flatfile formats, with a small amount of additional structure. meaning: edam:format_2185 @@ -1027,12 +1114,14 @@ enums: meaning: edam:format_2195 edam:format_2196: title: OBO format - description: A serialisation format conforming to the Open Biomedical Ontologies + description: + A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. meaning: edam:format_2196 edam:format_2197: title: OWL format - description: A serialisation format conforming to the Web Ontology Language + description: + A serialisation format conforming to the Web Ontology Language (OWL) model. meaning: edam:format_2197 edam:format_2200: @@ -1089,19 +1178,22 @@ enums: meaning: edam:format_2333 edam:format_2350: title: Format (by type of data) - description: A placeholder concept for visual navigation by dividing data + description: + A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented. meaning: edam:format_2350 edam:format_2352: title: BioXSD (XML) - description: BioXSD-schema-based XML format of sequence-based data and some + description: + BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming. meaning: edam:format_2352 edam:format_2376: title: RDF format - description: A serialisation format conforming to the Resource Description + description: + A serialisation format conforming to the Resource Description Framework (RDF) model. meaning: edam:format_2376 edam:format_2532: @@ -1178,27 +1270,32 @@ enums: meaning: edam:format_2561 edam:format_2566: title: completely unambiguous - description: Alphabet for a molecular sequence without any unknown positions + description: + Alphabet for a molecular sequence without any unknown positions or ambiguity characters. meaning: edam:format_2566 edam:format_2567: title: completely unambiguous pure - description: Alphabet for a molecular sequence without unknown positions, + description: + Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. meaning: edam:format_2567 edam:format_2568: title: completely unambiguous pure nucleotide - description: Alphabet for a nucleotide sequence (characters ACGTU only) without + description: + Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . meaning: edam:format_2568 edam:format_2569: title: completely unambiguous pure dna - description: Alphabet for a DNA sequence (characters ACGT only) without unknown + description: + Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. meaning: edam:format_2569 edam:format_2570: title: completely unambiguous pure rna sequence - description: Alphabet for an RNA sequence (characters ACGU only) without unknown + description: + Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. meaning: edam:format_2570 edam:format_2571: @@ -1207,26 +1304,30 @@ enums: meaning: edam:format_2571 edam:format_2572: title: BAM - description: BAM format, the binary, BGZF-formatted compressed version of + description: + BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. meaning: edam:format_2572 edam:format_2573: title: SAM - description: Sequence Alignment/Map (SAM) format for alignment of nucleotide + description: + Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. meaning: edam:format_2573 edam:format_2585: title: SBML - description: Systems Biology Markup Language (SBML), the standard XML format + description: + Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. meaning: edam:format_2585 edam:format_2607: title: completely unambiguous pure protein - description: Alphabet for any protein sequence without unknown positions, + description: + Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. meaning: edam:format_2607 edam:format_2848: @@ -1239,7 +1340,8 @@ enums: meaning: edam:format_2919 edam:format_2920: title: Alignment format (pair only) - description: Data format for molecular sequence alignment information that + description: + Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. meaning: edam:format_2920 edam:format_2921: @@ -1260,55 +1362,65 @@ enums: meaning: edam:format_2924 edam:format_3000: title: AB1 - description: AB1 binary format of raw DNA sequence reads (output of Applied + description: + AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. meaning: edam:format_3000 edam:format_3001: title: ACE - description: ACE sequence assembly format including contigs, base-call qualities, + description: + ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). meaning: edam:format_3001 edam:format_3003: title: BED - description: Browser Extensible Data (BED) format of sequence annotation track, + description: + Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. meaning: edam:format_3003 edam:format_3004: title: bigBed - description: bigBed format for large sequence annotation tracks, similar to + description: + bigBed format for large sequence annotation tracks, similar to textual BED format. meaning: edam:format_3004 edam:format_3005: title: WIG - description: Wiggle format (WIG) of a sequence annotation track that consists + description: + Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. meaning: edam:format_3005 edam:format_3006: title: bigWig - description: bigWig format for large sequence annotation tracks that consist + description: + bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. meaning: edam:format_3006 edam:format_3007: title: PSL - description: PSL format of alignments, typically generated by BLAT or psLayout. + description: + PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. meaning: edam:format_3007 edam:format_3008: title: MAF - description: Multiple Alignment Format (MAF) supporting alignments of whole + description: + Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. meaning: edam:format_3008 edam:format_3009: title: 2bit - description: 2bit binary format of nucleotide sequences using 2 bits per nucleotide. + description: + 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. meaning: edam:format_3009 edam:format_3010: title: .nib - description: .nib (nibble) binary format of a nucleotide sequence using 4 + description: + .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. meaning: edam:format_3010 edam:format_3011: @@ -1317,7 +1429,8 @@ enums: meaning: edam:format_3011 edam:format_3012: title: pgSnp - description: Personal Genome SNP (pgSnp) format for sequence variation tracks + description: + Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. meaning: edam:format_3012 edam:format_3013: @@ -1330,33 +1443,39 @@ enums: meaning: edam:format_3014 edam:format_3015: title: Pileup - description: Pileup format of alignment of sequences (e.g. sequencing reads) + description: + Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). meaning: edam:format_3015 edam:format_3016: title: VCF - description: Variant Call Format (VCF) is tabular format for storing genomic + description: + Variant Call Format (VCF) is tabular format for storing genomic sequence variations. meaning: edam:format_3016 edam:format_3017: title: SRF - description: Sequence Read Format (SRF) of sequence trace data. Supports submission + description: + Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. meaning: edam:format_3017 edam:format_3018: title: ZTR - description: ZTR format for storing chromatogram data from DNA sequencing + description: + ZTR format for storing chromatogram data from DNA sequencing instruments. meaning: edam:format_3018 edam:format_3019: title: GVF - description: Genome Variation Format (GVF). A GFF3-compatible format with + description: + Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. meaning: edam:format_3019 edam:format_3020: title: BCF - description: BCF is the binary version of Variant Call Format (VCF) for sequence + description: + BCF is the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). meaning: edam:format_3020 edam:format_3033: @@ -1365,7 +1484,8 @@ enums: meaning: edam:format_3033 edam:format_3097: title: Protein domain classification format - description: Format of data concerning the classification of the sequences + description: + Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). meaning: edam:format_3097 edam:format_3098: @@ -1378,33 +1498,39 @@ enums: meaning: edam:format_3099 edam:format_3100: title: CATH domain report format - description: Format of summary of domain classification information for a + description: + Format of summary of domain classification information for a CATH domain. meaning: edam:format_3100 edam:format_3155: title: SBRML - description: Systems Biology Result Markup Language (SBRML), the standard + description: + Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. meaning: edam:format_3155 edam:format_3156: title: BioPAX - description: BioPAX is an exchange format for pathway data, with its data + description: + BioPAX is an exchange format for pathway data, with its data model defined in OWL. meaning: edam:format_3156 edam:format_3157: title: EBI Application Result XML - description: EBI Application Result XML is a format returned by sequence similarity + description: + EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. meaning: edam:format_3157 edam:format_3158: title: PSI MI XML (MIF) - description: XML Molecular Interaction Format (MIF), standardised by HUPO + description: + XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. meaning: edam:format_3158 edam:format_3159: title: phyloXML - description: phyloXML is a standardised XML format for phylogenetic trees, + description: + phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. meaning: edam:format_3159 edam:format_3160: @@ -1413,30 +1539,35 @@ enums: meaning: edam:format_3160 edam:format_3161: title: MAGE-ML - description: MAGE-ML XML format for microarray expression data, standardised + description: + MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). meaning: edam:format_3161 edam:format_3162: title: MAGE-TAB - description: MAGE-TAB textual format for microarray expression data, standardised + description: + MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). meaning: edam:format_3162 edam:format_3163: title: GCDML - description: GCDML XML format for genome and metagenome metadata according + description: + GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). meaning: edam:format_3163 edam:format_3164: title: GTrack - description: GTrack is a generic and optimised tabular format for genome or + description: + GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability"). meaning: edam:format_3164 edam:format_3166: title: Biological pathway or network report format - description: Data format for a report of information derived from a biological + description: + Data format for a report of information derived from a biological pathway or network. meaning: edam:format_3166 edam:format_3167: @@ -1453,54 +1584,64 @@ enums: meaning: edam:format_3239 edam:format_3240: title: CellML - description: CellML, the format for mathematical models of biological and + description: + CellML, the format for mathematical models of biological and other networks. meaning: edam:format_3240 edam:format_3242: title: PSI MI TAB (MITAB) - description: Tabular Molecular Interaction format (MITAB), standardised by + description: + Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. meaning: edam:format_3242 edam:format_3243: title: PSI-PAR - description: Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. + description: + Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. meaning: edam:format_3243 edam:format_3244: title: mzML - description: mzML format for raw spectrometer output data, standardised by + description: + mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. meaning: edam:format_3244 edam:format_3245: title: Mass spectrometry data format - description: Format for mass pectra and derived data, include peptide sequences + description: + Format for mass pectra and derived data, include peptide sequences etc. meaning: edam:format_3245 edam:format_3246: title: TraML - description: TraML (Transition Markup Language) is the format for mass spectrometry + description: + TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. meaning: edam:format_3246 edam:format_3247: title: mzIdentML - description: mzIdentML is the exchange format for peptides and proteins identified + description: + mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. meaning: edam:format_3247 edam:format_3248: title: mzQuantML - description: mzQuantML is the format for quantitation values associated with + description: + mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. meaning: edam:format_3248 edam:format_3249: title: GelML - description: GelML is the format for describing the process of gel electrophoresis, + description: + GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. meaning: edam:format_3249 edam:format_3250: title: spML - description: spML is the format for describing proteomics sample processing, + description: + spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. meaning: edam:format_3250 @@ -1514,23 +1655,27 @@ enums: meaning: edam:format_3253 edam:format_3254: title: KRSS2 Syntax - description: A superset of the "Description-Logic Knowledge Representation + description: + A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". meaning: edam:format_3254 edam:format_3255: title: Turtle - description: The Terse RDF Triple Language (Turtle) is a human-friendly serialisation + description: + The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. meaning: edam:format_3255 edam:format_3256: title: N-Triples - description: A plain text serialisation format for RDF (Resource Description + description: + A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. meaning: edam:format_3256 edam:format_3257: title: Notation3 - description: A shorthand non-XML serialisation of Resource Description Framework + description: + A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind. meaning: edam:format_3257 edam:format_3261: @@ -1543,14 +1688,16 @@ enums: meaning: edam:format_3262 edam:format_3281: title: A2M - description: The A2M format is used as the primary format for multiple alignments + description: + The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. meaning: edam:format_3281 edam:format_3284: title: SFF - description: Standard flowgram format (SFF) is a binary file format used to + description: + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. meaning: edam:format_3284 @@ -1560,12 +1707,14 @@ enums: meaning: edam:format_3285 edam:format_3286: title: PED - description: The PED file describes individuals and genetic data and is used + description: + The PED file describes individuals and genetic data and is used by the Plink package. meaning: edam:format_3286 edam:format_3287: title: Individual genetic data format - description: Data format for a metadata on an individual and their genetic + description: + Data format for a metadata on an individual and their genetic data. meaning: edam:format_3287 edam:format_3288: @@ -1574,7 +1723,8 @@ enums: meaning: edam:format_3288 edam:format_3309: title: CT - description: File format of a CT (Connectivity Table) file from the RNAstructure + description: + File format of a CT (Connectivity Table) file from the RNAstructure package. meaning: edam:format_3309 edam:format_3310: @@ -1591,7 +1741,8 @@ enums: meaning: edam:format_3312 edam:format_3313: title: BLC - description: A multiple alignment in vertical format, as used in the AMPS + description: + A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) package. meaning: edam:format_3313 edam:format_3326: @@ -1612,7 +1763,8 @@ enums: meaning: edam:format_3329 edam:format_3330: title: PO - description: PO is the output format of Partial Order Alignment program (POA) + description: + PO is the output format of Partial Order Alignment program (POA) performing Multiple Sequence Alignment (MSA). meaning: edam:format_3330 edam:format_3331: @@ -1625,7 +1777,8 @@ enums: meaning: edam:format_3462 edam:format_3464: title: JSON - description: JavaScript Object Notation format; a lightweight, text-based + description: + JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs. meaning: edam:format_3464 edam:format_3466: @@ -1646,7 +1799,8 @@ enums: meaning: edam:format_3475 edam:format_3477: title: Cytoscape input file format - description: Format of the cytoscape input file of gene expression ratios + description: + Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. meaning: edam:format_3477 edam:format_3484: @@ -1679,7 +1833,8 @@ enums: meaning: edam:format_3506 edam:format_3507: title: Document format - description: Format of documents including word processor, spreadsheet and + description: + Format of documents including word processor, spreadsheet and presentation. meaning: edam:format_3507 edam:format_3508: @@ -1692,44 +1847,52 @@ enums: meaning: edam:format_3547 edam:format_3548: title: DICOM format - description: Medical image format corresponding to the Digital Imaging and + description: + Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. meaning: edam:format_3548 edam:format_3549: title: nii - description: An open file format from the Neuroimaging Informatics Technology + description: + An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI) commonly used to store brain imaging data obtained using Magnetic Resonance Imaging (MRI) methods. meaning: edam:format_3549 edam:format_3550: title: mhd - description: Text-based tagged file format for medical images generated using + description: + Text-based tagged file format for medical images generated using the MetaImage software package. meaning: edam:format_3550 edam:format_3551: title: nrrd - description: Nearly Raw Rasta Data format designed to support scientific visualisation + description: + Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. meaning: edam:format_3551 edam:format_3554: title: R file format - description: File format used for scripts written in the R programming language + description: + File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. meaning: edam:format_3554 edam:format_3555: title: SPSS - description: File format used for scripts for the Statistical Package for + description: + File format used for scripts for the Statistical Package for the Social Sciences. meaning: edam:format_3555 edam:format_3556: title: MHTML - description: MIME HTML format for Web pages, which can include external resources, + description: + MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. meaning: edam:format_3556 edam:format_3578: title: IDAT - description: Proprietary file format for (raw) BeadArray data used by genomewide + description: + Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. meaning: edam:format_3578 @@ -1739,34 +1902,40 @@ enums: meaning: edam:format_3579 edam:format_3580: title: rcc - description: Reporter Code Count-A data file (.csv) output by the Nanostring + description: + Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts. meaning: edam:format_3580 edam:format_3581: title: arff - description: ARFF (Attribute-Relation File Format) is an ASCII text file format + description: + ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes. meaning: edam:format_3581 edam:format_3582: title: afg - description: AFG is a single text-based file assembly format that holds read + description: + AFG is a single text-based file assembly format that holds read and consensus information together. meaning: edam:format_3582 edam:format_3583: title: bedgraph - description: The bedGraph format allows display of continuous-valued data + description: + The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. meaning: edam:format_3583 edam:format_3584: title: bedstrict - description: Browser Extensible Data (BED) format of sequence annotation track + description: + Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. meaning: edam:format_3584 edam:format_3585: title: bed6 - description: BED file format where each feature is described by chromosome, + description: + BED file format where each feature is described by chromosome, start, end, name, score, and strand. meaning: edam:format_3585 edam:format_3586: @@ -1787,7 +1956,8 @@ enums: meaning: edam:format_3589 edam:format_3590: title: HDF5 - description: HDF5 is a data model, library, and file format for storing and + description: + HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF). meaning: edam:format_3590 edam:format_3591: @@ -1800,55 +1970,65 @@ enums: meaning: edam:format_3592 edam:format_3593: title: im - description: IM is a format used by LabEye and other applications based on + description: + IM is a format used by LabEye and other applications based on the IFUNC image processing library. meaning: edam:format_3593 edam:format_3594: title: pcd - description: Photo CD format, which is the highest resolution format for images + description: + Photo CD format, which is the highest resolution format for images on a CD. meaning: edam:format_3594 edam:format_3595: title: pcx - description: PCX is an image file format that uses a simple form of run-length + description: + PCX is an image file format that uses a simple form of run-length encoding. It is lossless. meaning: edam:format_3595 edam:format_3596: title: ppm - description: The PPM format is a lowest common denominator color image file + description: + The PPM format is a lowest common denominator color image file format. meaning: edam:format_3596 edam:format_3597: title: psd - description: PSD (Photoshop Document) is a proprietary file that allows the + description: + PSD (Photoshop Document) is a proprietary file that allows the user to work with the images' individual layers even after the file has been saved. meaning: edam:format_3597 edam:format_3598: title: xbm - description: X BitMap is a plain text binary image format used by the X Window + description: + X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. meaning: edam:format_3598 edam:format_3599: title: xpm - description: X PixMap (XPM) is an image file format used by the X Window System, + description: + X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. meaning: edam:format_3599 edam:format_3600: title: rgb - description: RGB file format is the native raster graphics file format for + description: + RGB file format is the native raster graphics file format for Silicon Graphics workstations. meaning: edam:format_3600 edam:format_3601: title: pbm - description: The PBM format is a lowest common denominator monochrome file + description: + The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. meaning: edam:format_3601 edam:format_3602: title: pgm - description: The PGM format is a lowest common denominator grayscale file + description: + The PGM format is a lowest common denominator grayscale file format. meaning: edam:format_3602 edam:format_3603: @@ -1857,42 +2037,50 @@ enums: meaning: edam:format_3603 edam:format_3604: title: SVG - description: Scalable Vector Graphics (SVG) is an XML-based vector image format + description: + Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. meaning: edam:format_3604 edam:format_3605: title: rast - description: Sun Raster is a raster graphics file format used on SunOS by + description: + Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems. meaning: edam:format_3605 edam:format_3606: title: Sequence quality report format (text) - description: Textual report format for sequence quality for reports from sequencing + description: + Textual report format for sequence quality for reports from sequencing machines. meaning: edam:format_3606 edam:format_3607: title: qual - description: FASTQ format subset for Phred sequencing quality score data only + description: + FASTQ format subset for Phred sequencing quality score data only (no sequences). meaning: edam:format_3607 edam:format_3608: title: qualsolexa - description: FASTQ format subset for Phred sequencing quality score data only + description: + FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format. meaning: edam:format_3608 edam:format_3609: title: qualillumina - description: FASTQ format subset for Phred sequencing quality score data only + description: + FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8. meaning: edam:format_3609 edam:format_3610: title: qualsolid - description: FASTQ format subset for Phred sequencing quality score data only + description: + FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data. meaning: edam:format_3610 edam:format_3611: title: qual454 - description: FASTQ format subset for Phred sequencing quality score data only + description: + FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. meaning: edam:format_3611 edam:format_3612: @@ -1925,12 +2113,14 @@ enums: meaning: edam:format_3618 edam:format_3619: title: sif - description: SIF (simple interaction file) Format - a network/pathway format + description: + SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. meaning: edam:format_3619 edam:format_3620: title: xlsx - description: MS Excel spreadsheet format consisting of a set of XML documents + description: + MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. meaning: edam:format_3620 edam:format_3621: @@ -1939,12 +2129,14 @@ enums: meaning: edam:format_3621 edam:format_3622: title: Gemini SQLite format - description: Data format used by the SQLite database conformant to the Gemini + description: + Data format used by the SQLite database conformant to the Gemini schema. meaning: edam:format_3622 edam:format_3624: title: snpeffdb - description: An index of a genome database, indexed for use by the snpeff + description: + An index of a genome database, indexed for use by the snpeff tool. meaning: edam:format_3624 edam:format_3626: @@ -1953,18 +2145,21 @@ enums: meaning: edam:format_3626 edam:format_3650: title: NetCDF - description: Format used by netCDF software library for writing and reading + description: + Format used by netCDF software library for writing and reading chromatography-MS data files. Also used to store trajectory atom coordinates information, such as the ones obtained by Molecular Dynamics simulations. meaning: edam:format_3650 edam:format_3651: title: MGF - description: Mascot Generic Format. Encodes multiple MS/MS spectra in a single + description: + Mascot Generic Format. Encodes multiple MS/MS spectra in a single file. meaning: edam:format_3651 edam:format_3652: title: dta - description: Spectral data format file where each spectrum is written to a + description: + Spectral data format file where each spectrum is written to a separate file. meaning: edam:format_3652 edam:format_3653: @@ -1973,62 +2168,73 @@ enums: meaning: edam:format_3653 edam:format_3654: title: mzXML - description: Common file format for proteomics mass spectrometric data developed + description: + Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. meaning: edam:format_3654 edam:format_3655: title: pepXML - description: Open data format for the storage, exchange, and processing of + description: + Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. meaning: edam:format_3655 edam:format_3657: title: GPML - description: Graphical Pathway Markup Language (GPML) is an XML format used + description: + Graphical Pathway Markup Language (GPML) is an XML format used for exchanging biological pathways. meaning: edam:format_3657 edam:format_3665: title: K-mer countgraph - description: A list of k-mers and their occurrences in a dataset. Can also + description: + A list of k-mers and their occurrences in a dataset. Can also be used as an implicit De Bruijn graph. meaning: edam:format_3665 edam:format_3681: title: mzTab - description: mzTab is a light-weight, tab-delimited format for mass spectrometry-based + description: + mzTab is a light-weight, tab-delimited format for mass spectrometry-based proteomics data. meaning: edam:format_3681 edam:format_3682: title: imzML metadata file - description: imzML metadata is a data format for mass spectrometry imaging + description: + imzML metadata is a data format for mass spectrometry imaging metadata. meaning: edam:format_3682 edam:format_3683: title: qcML - description: qcML is an XML format for quality-related data of mass spectrometry + description: + qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements. meaning: edam:format_3683 edam:format_3684: title: PRIDE XML - description: PRIDE XML is an XML format for mass spectra, peptide and protein + description: + PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment. meaning: edam:format_3684 edam:format_3685: title: SED-ML - description: Simulation Experiment Description Markup Language (SED-ML) is + description: + Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements. meaning: edam:format_3685 edam:format_3686: title: COMBINE OMEX - description: Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating + description: + Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology. meaning: edam:format_3686 edam:format_3687: title: ISA-Tab - description: ISA-Tab stands for Investigation / Study / Assay (ISA) tab-delimited + description: + ISA-Tab stands for Investigation / Study / Assay (ISA) tab-delimited (Tab) format, and it is comprised of metadata describing observational or experimental scientific studies. meaning: edam:format_3687 @@ -2038,27 +2244,32 @@ enums: meaning: edam:format_3688 edam:format_3689: title: BCML - description: Biological Connection Markup Language (BCML) is an XML format + description: + Biological Connection Markup Language (BCML) is an XML format for biological pathways. meaning: edam:format_3689 edam:format_3690: title: BDML - description: Biological Dynamics Markup Language (BDML) is an XML format for + description: + Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. meaning: edam:format_3690 edam:format_3691: title: BEL - description: Biological Expression Language (BEL) is a textual format for + description: + Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. meaning: edam:format_3691 edam:format_3692: title: SBGN-ML - description: SBGN-ML is an XML format for Systems Biology Graphical Notation + description: + SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. meaning: edam:format_3692 edam:format_3693: title: AGP - description: AGP is a tabular format for a sequence assembly (a contig, a + description: + AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome). meaning: edam:format_3693 edam:format_3696: @@ -2067,23 +2278,27 @@ enums: meaning: edam:format_3696 edam:format_3698: title: SRA format - description: SRA archive format (SRA) is the archive format used for input + description: + SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. meaning: edam:format_3698 edam:format_3699: title: VDB - description: VDB ('vertical database') is the native format used for export + description: + VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. meaning: edam:format_3699 edam:format_3701: title: Sequin format - description: A five-column, tab-delimited table of feature locations and qualifiers + description: + A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). meaning: edam:format_3701 edam:format_3702: title: MSF - description: Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer + description: + Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. meaning: edam:format_3702 edam:format_3706: @@ -2092,13 +2307,15 @@ enums: meaning: edam:format_3706 edam:format_3708: title: ABCD format - description: Exchange format of the Access to Biological Collections Data + description: + Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). meaning: edam:format_3708 edam:format_3709: title: GCT/Res format - description: Tab-delimited text files of GenePattern that contain a column + description: + Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample. meaning: edam:format_3709 @@ -2108,12 +2325,14 @@ enums: meaning: edam:format_3710 edam:format_3711: title: X!Tandem XML - description: Output format used by X! series search engines that is based + description: + Output format used by X! series search engines that is based on the XML language BIOML. meaning: edam:format_3711 edam:format_3712: title: Thermo RAW - description: Proprietary file format for mass spectrometry data from Thermo + description: + Proprietary file format for mass spectrometry data from Thermo Scientific. meaning: edam:format_3712 edam:format_3713: @@ -2122,71 +2341,83 @@ enums: meaning: edam:format_3713 edam:format_3714: title: MaxQuant APL peaklist format - description: Format of peak list files from Andromeda search engine (MaxQuant) + description: + Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. meaning: edam:format_3714 edam:format_3725: title: SBOL - description: Synthetic Biology Open Language (SBOL) is an XML format for the + description: + Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. meaning: edam:format_3725 edam:format_3726: title: PMML - description: PMML uses XML to represent mining models. The structure of the + description: + PMML uses XML to represent mining models. The structure of the models is described by an XML Schema. meaning: edam:format_3726 edam:format_3727: - title: OME-TIFF - description: Image file format used by the Open Microscopy Environment (OME). + title: SOME-TIFF + description: Image file format used by the Open Microscopy Environment (SOME). meaning: edam:format_3727 edam:format_3728: title: LocARNA PP - description: The LocARNA PP format combines sequence or alignment information + description: + The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record. meaning: edam:format_3728 edam:format_3729: title: dbGaP format - description: Input format used by the Database of Genotypes and Phenotypes + description: + Input format used by the Database of Genotypes and Phenotypes (dbGaP). meaning: edam:format_3729 edam:format_3746: title: BIOM format - description: The BIological Observation Matrix (BIOM) is a format for representing + description: + The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative - omics. The primary use of this format is to represent OTU tables and metagenome + omics. The primary use of this format is to represent OUT tables and metagenome tables. meaning: edam:format_3746 edam:format_3747: title: protXML - description: A format for storage, exchange, and processing of protein identifications + description: + A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data. meaning: edam:format_3747 edam:format_3748: title: Linked data format - description: A linked data format enables publishing structured data as linked + description: + A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries. meaning: edam:format_3748 edam:format_3749: title: JSON-LD - description: JSON-LD, or JavaScript Object Notation for Linked Data, is a + description: + JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON. meaning: edam:format_3749 edam:format_3750: title: YAML - description: YAML (YAML Ain't Markup Language) is a human-readable tree-structured + description: + YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. meaning: edam:format_3750 edam:format_3751: title: DSV - description: Tabular data represented as values in a text file delimited by + description: + Tabular data represented as values in a text file delimited by some character. meaning: edam:format_3751 edam:format_3752: title: CSV - description: Tabular data represented as comma-separated values in a text + description: + Tabular data represented as comma-separated values in a text file. meaning: edam:format_3752 edam:format_3758: @@ -2195,90 +2426,106 @@ enums: meaning: edam:format_3758 edam:format_3764: title: idXML - description: XML file format for files containing information about peptide + description: + XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. meaning: edam:format_3764 edam:format_3765: title: KNIME datatable format - description: Data table formatted such that it can be passed/streamed within + description: + Data table formatted such that it can be passed/streamed within the KNIME platform. meaning: edam:format_3765 edam:format_3770: title: UniProtKB XML - description: UniProtKB XML sequence features format is an XML format available + description: + UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. meaning: edam:format_3770 edam:format_3771: title: UniProtKB RDF - description: UniProtKB RDF sequence features format is an RDF format available + description: + UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). meaning: edam:format_3771 edam:format_3772: title: BioJSON (BioXSD) - description: BioJSON is a BioXSD-schema-based JSON format of sequence-based + description: + BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming. meaning: edam:format_3772 edam:format_3773: title: BioYAML - description: BioYAML is a BioXSD-schema-based YAML format of sequence-based + description: + BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editing, and object-oriented programming. meaning: edam:format_3773 edam:format_3774: title: BioJSON (Jalview) - description: BioJSON is a JSON format of single multiple sequence alignments, + description: + BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench. meaning: edam:format_3774 edam:format_3775: title: GSuite - description: GSuite is a tabular format for collections of genome or sequence + description: + GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata. meaning: edam:format_3775 edam:format_3776: title: BTrack - description: BTrack is an HDF5-based binary format for genome or sequence + description: + BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats. meaning: edam:format_3776 edam:format_3777: title: MCPD - description: The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) + description: + The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. meaning: edam:format_3777 edam:format_3780: title: Annotated text format - description: Data format of an annotated text, e.g. with recognised entities, + description: + Data format of an annotated text, e.g. with recognised entities, concepts, and relations. meaning: edam:format_3780 edam:format_3781: title: PubAnnotation format - description: JSON format of annotated scientific text used by PubAnnotations + description: + JSON format of annotated scientific text used by PubAnnotations and other tools. meaning: edam:format_3781 edam:format_3782: title: BioC - description: BioC is a standardised XML format for sharing and integrating + description: + BioC is a standardised XML format for sharing and integrating text data and annotations. meaning: edam:format_3782 edam:format_3783: title: PubTator format - description: Native textual export format of annotated scientific text from + description: + Native textual export format of annotated scientific text from PubTator. meaning: edam:format_3783 edam:format_3784: title: Open Annotation format - description: A format of text annotation using the linked-data Open Annotation + description: + A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD. meaning: edam:format_3784 edam:format_3785: title: BioNLP Shared Task format - description: A family of similar formats of text annotation, used by BRAT + description: + A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar. @@ -2289,20 +2536,23 @@ enums: meaning: edam:format_3787 edam:format_3788: title: SQL - description: SQL (Structured Query Language) is the de-facto standard query + description: + SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. meaning: edam:format_3788 edam:format_3789: title: XQuery - description: XQuery (XML Query) is a query language (format of queries) for + description: + XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.). meaning: edam:format_3789 edam:format_3790: title: SPARQL - description: SPARQL (SPARQL Protocol and RDF Query Language) is a semantic + description: + SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. meaning: edam:format_3790 @@ -2312,7 +2562,8 @@ enums: meaning: edam:format_3804 edam:format_3811: title: XMFA - description: XMFA format stands for eXtended Multi-FastA format and is used + description: + XMFA format stands for eXtended Multi-FastA format and is used to store collinear sub-alignments that constitute a single genome alignment. meaning: edam:format_3811 edam:format_3812: @@ -2321,23 +2572,27 @@ enums: meaning: edam:format_3812 edam:format_3813: title: SAMPLE file format - description: The SAMPLE file format contains information about each individual + description: + The SAMPLE file format contains information about each individual i.e. individual IDs, covariates, phenotypes and missing data proportions, from a GWAS study. meaning: edam:format_3813 edam:format_3814: title: SDF - description: SDF is one of a family of chemical-data file formats developed + description: + SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information. meaning: edam:format_3814 edam:format_3815: title: Molfile - description: An MDL Molfile is a file format for holding information about + description: + An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. meaning: edam:format_3815 edam:format_3816: title: Mol2 - description: Complete, portable representation of a SYBYL molecule. ASCII + description: + Complete, portable representation of a SYBYL molecule. ASCII file which contains all the information needed to reconstruct a SYBYL molecule. meaning: edam:format_3816 edam:format_3817: @@ -2346,18 +2601,21 @@ enums: meaning: edam:format_3817 edam:format_3818: title: ELAND format - description: Tab-delimited text file format used by Eland - the read-mapping + description: + Tab-delimited text file format used by Eland - the read-mapping program distributed by Illumina with its sequencing analysis pipeline - which maps short Solexa sequence reads to the human reference genome. meaning: edam:format_3818 edam:format_3819: title: Relaxed PHYLIP Interleaved - description: Phylip multiple alignment sequence format, less stringent than + description: + Phylip multiple alignment sequence format, less stringent than PHYLIP format. meaning: edam:format_3819 edam:format_3820: title: Relaxed PHYLIP Sequential - description: Phylip multiple alignment sequence format, less stringent than + description: + Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998). meaning: edam:format_3820 edam:format_3821: @@ -2366,34 +2624,40 @@ enums: meaning: edam:format_3821 edam:format_3822: title: GML - description: GML (Graph Modeling Language) is a text file format supporting + description: + GML (Graph Modeling Language) is a text file format supporting network data with a very easy syntax. It is used by Graphlet, Pajek, yEd, LEDA and NetworkX. meaning: edam:format_3822 edam:format_3823: title: FASTG - description: FASTG is a format for faithfully representing genome assemblies + description: + FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. meaning: edam:format_3823 edam:format_3824: title: NMR data format - description: Data format for raw data from a nuclear magnetic resonance (NMR) + description: + Data format for raw data from a nuclear magnetic resonance (NMR) spectroscopy experiment. meaning: edam:format_3824 edam:format_3825: title: nmrML - description: nmrML is an MSI supported XML-based open access format for metabolomics + description: + nmrML is an MSI supported XML-based open access format for metabolomics NMR raw and processed spectral data. It is accompanies by an nmrCV (controlled vocabulary) to allow ontology-based annotations. meaning: edam:format_3825 edam:format_3826: title: proBAM - description: . proBAM is an adaptation of BAM (format_2572), which was extended + description: + . proBAM is an adaptation of BAM (format_2572), which was extended to meet specific requirements entailed by proteomics data. meaning: edam:format_3826 edam:format_3827: title: proBED - description: . proBED is an adaptation of BED (format_3003), which was extended + description: + . proBED is an adaptation of BED (format_3003), which was extended to meet specific requirements entailed by proteomics data. meaning: edam:format_3827 edam:format_3828: @@ -2402,7 +2666,8 @@ enums: meaning: edam:format_3828 edam:format_3829: title: GPR - description: GenePix Results (GPR) text file format developed by Axon Instruments + description: + GenePix Results (GPR) text file format developed by Axon Instruments that is used to save GenePix Results data. meaning: edam:format_3829 edam:format_3830: @@ -2411,7 +2676,8 @@ enums: meaning: edam:format_3830 edam:format_3832: title: consensusXML - description: OpenMS format for grouping features in one map or across several + description: + OpenMS format for grouping features in one map or across several maps. meaning: edam:format_3832 edam:format_3833: @@ -2420,12 +2686,14 @@ enums: meaning: edam:format_3833 edam:format_3834: title: mzData - description: Now deprecated data format of the HUPO Proteomics Standards Initiative. + description: + Now deprecated data format of the HUPO Proteomics Standards Initiative. Replaced by mzML (format_3244). meaning: edam:format_3834 edam:format_3835: title: TIDE TXT - description: Format supported by the Tide tool for identifying peptides from + description: + Format supported by the Tide tool for identifying peptides from tandem mass spectra. meaning: edam:format_3835 edam:format_3836: @@ -2446,18 +2714,21 @@ enums: meaning: edam:format_3841 edam:format_3843: title: BEAST - description: XML input file format for BEAST Software (Bayesian Evolutionary + description: + XML input file format for BEAST Software (Bayesian Evolutionary Analysis Sampling Trees). meaning: edam:format_3843 edam:format_3844: title: Chado-XML - description: Chado-XML format is a direct mapping of the Chado relational + description: + Chado-XML format is a direct mapping of the Chado relational schema into XML. meaning: edam:format_3844 edam:format_3845: title: HSAML - description: 'An alignment format generated by PRANK/PRANKSTER consisting - of four elements: newick, nodes, selection and model.' + description: + "An alignment format generated by PRANK/PRANKSTER consisting + of four elements: newick, nodes, selection and model." meaning: edam:format_3845 edam:format_3846: title: InterProScan XML @@ -2465,35 +2736,41 @@ enums: meaning: edam:format_3846 edam:format_3847: title: KGML - description: The KEGG Markup Language (KGML) is an exchange format of the + description: + The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. meaning: edam:format_3847 edam:format_3848: title: PubMed XML - description: XML format for collected entries from bibliographic databases + description: + XML format for collected entries from bibliographic databases MEDLINE and PubMed. meaning: edam:format_3848 edam:format_3849: title: MSAML - description: A set of XML compliant markup components for describing multiple + description: + A set of XML compliant markup components for describing multiple sequence alignments. meaning: edam:format_3849 edam:format_3850: title: OrthoXML - description: OrthoXML is designed broadly to allow the storage and comparison + description: + OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format. meaning: edam:format_3850 edam:format_3851: title: PSDML - description: Tree structure of Protein Sequence Database Markup Language generated + description: + Tree structure of Protein Sequence Database Markup Language generated using Matra software. meaning: edam:format_3851 edam:format_3852: title: SeqXML - description: SeqXML is an XML Schema to describe biological sequences, developed + description: + SeqXML is an XML Schema to describe biological sequences, developed by the Stockholm Bioinformatics Centre. meaning: edam:format_3852 edam:format_3853: @@ -2506,7 +2783,8 @@ enums: meaning: edam:format_3854 edam:format_3857: title: CWL - description: Common Workflow Language (CWL) format for description of command-line + description: + Common Workflow Language (CWL) format for description of command-line tools and workflows. meaning: edam:format_3857 edam:format_3858: @@ -2515,7 +2793,8 @@ enums: meaning: edam:format_3858 edam:format_3859: title: JCAMP-DX - description: A standardized file format for data exchange in mass spectrometry, + description: + A standardized file format for data exchange in mass spectrometry, initially developed for infrared spectrometry. meaning: edam:format_3859 edam:format_3862: @@ -2528,39 +2807,46 @@ enums: meaning: edam:format_3863 edam:format_3864: title: mirGFF3 - description: mirGFF3 is a common format for microRNA data resulting from small-RNA + description: + mirGFF3 is a common format for microRNA data resulting from small-RNA RNA-Seq workflows. meaning: edam:format_3864 edam:format_3865: title: RNA annotation format - description: A "placeholder" concept for formats of annotated RNA data, including + description: + A "placeholder" concept for formats of annotated RNA data, including e.g. microRNA and RNA-Seq data. meaning: edam:format_3865 edam:format_3866: title: Trajectory format - description: File format to store trajectory information for a 3D structure + description: + File format to store trajectory information for a 3D structure . meaning: edam:format_3866 edam:format_3867: title: Trajectory format (binary) - description: Binary file format to store trajectory information for a 3D structure + description: + Binary file format to store trajectory information for a 3D structure . meaning: edam:format_3867 edam:format_3868: title: Trajectory format (text) - description: Textual file format to store trajectory information for a 3D + description: + Textual file format to store trajectory information for a 3D structure . meaning: edam:format_3868 edam:format_3873: title: HDF - description: HDF is the name of a set of file formats and libraries designed + description: + HDF is the name of a set of file formats and libraries designed to store and organize large amounts of numerical data, originally developed at the National Center for Supercomputing Applications at the University of Illinois. meaning: edam:format_3873 edam:format_3874: title: PCAzip - description: PCAZip format is a binary compressed file to store atom coordinates + description: + PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA). meaning: edam:format_3874 edam:format_3875: @@ -2569,50 +2855,58 @@ enums: meaning: edam:format_3875 edam:format_3876: title: TNG - description: Trajectory Next Generation (TNG) is a format for storage of molecular + description: + Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format. meaning: edam:format_3876 edam:format_3877: title: XYZ - description: The XYZ chemical file format is widely supported by many programs, + description: + The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number. meaning: edam:format_3877 edam:format_3878: title: mdcrd - description: AMBER trajectory (also called mdcrd), with 10 coordinates per + description: + AMBER trajectory (also called mdcrd), with 10 coordinates per line and format F8.3 (fixed point notation with field width 8 and 3 decimal places). meaning: edam:format_3878 edam:format_3879: title: Topology format - description: Format of topology files; containing the static information of + description: + Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation. meaning: edam:format_3879 edam:format_3880: title: GROMACS top - description: GROMACS MD package top textual files define an entire structure + description: + GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files. meaning: edam:format_3880 edam:format_3881: title: AMBER top - description: AMBER Prmtop file (version 7) is a structure topology text file + description: + AMBER Prmtop file (version 7) is a structure topology text file divided in several sections designed to be parsed easily using simple Fortran code. Each section contains particular topology information, such as atom name, charge, mass, angles, dihedrals, etc. meaning: edam:format_3881 edam:format_3882: title: PSF - description: 'X-Plor Protein Structure Files (PSF) are structure topology + description: + "X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD and CHARMM molecular simulations programs. PSF files contain six main sections of interest: atoms, bonds, angles, dihedrals, - improper dihedrals (force terms used to maintain planarity) and cross-terms.' + improper dihedrals (force terms used to maintain planarity) and cross-terms." meaning: edam:format_3882 edam:format_3883: title: GROMACS itp - description: GROMACS itp files (include topology) contain structure topology + description: + GROMACS itp files (include topology) contain structure topology information, and are typically included in GROMACS topology files (GROMACS top). Itp files are used to define individual (or multiple) components of a topology as a separate file. This is particularly useful if there is a @@ -2621,85 +2915,99 @@ enums: meaning: edam:format_3883 edam:format_3884: title: FF parameter format - description: Format of force field parameter files, which store the set of + description: + Format of force field parameter files, which store the set of parameters (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential for the proper description and simulation of a molecular system. meaning: edam:format_3884 edam:format_3885: title: BinPos - description: Scripps Research Institute BinPos format is a binary formatted + description: + Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates. meaning: edam:format_3885 edam:format_3886: title: RST - description: AMBER coordinate/restart file with 6 coordinates per line and + description: + AMBER coordinate/restart file with 6 coordinates per line and decimal format F12.7 (fixed point notation with field width 12 and 7 decimal places). meaning: edam:format_3886 edam:format_3887: title: CHARMM rtf - description: Format of CHARMM Residue Topology Files (RTF), which define groups + description: + Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information. meaning: edam:format_3887 edam:format_3888: title: AMBER frcmod - description: AMBER frcmod (Force field Modification) is a file format to store + description: + AMBER frcmod (Force field Modification) is a file format to store any modification to the standard force field needed for a particular molecule to be properly represented in the simulation. meaning: edam:format_3888 edam:format_3889: title: AMBER off - description: AMBER Object File Format library files (OFF library files) store + description: + AMBER Object File Format library files (OFF library files) store residue libraries (forcefield residue parameters). meaning: edam:format_3889 edam:format_3906: title: NMReDATA - description: 'MReData is a text based data standard for processed NMR data. + description: + 'MReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or "NMReDATA") includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc.' meaning: edam:format_3906 edam:format_3909: title: BpForms - description: BpForms is a string format for concretely representing the primary + description: + BpForms is a string format for concretely representing the primary structures of biopolymers, including DNA, RNA, and proteins that include non-canonical nucleic and amino acids. See https://www.bpforms.org for more information. meaning: edam:format_3909 edam:format_3910: title: trr - description: Format of trr files that contain the trajectory of a simulation + description: + Format of trr files that contain the trajectory of a simulation experiment used by GROMACS. meaning: edam:format_3910 edam:format_3911: title: msh - description: Mash sketch is a format for sequence / sequence checksum information. + description: + Mash sketch is a format for sequence / sequence checksum information. To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random identifier. By sorting these hashes, a small subset from the top of the sorted list can represent the entire sequence. meaning: edam:format_3911 edam:format_3913: title: Loom - description: The Loom file format is based on HDF5, a standard for storing + description: + The Loom file format is based on HDF5, a standard for storing large numerical datasets. The Loom format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns. meaning: edam:format_3913 edam:format_3915: title: Zarr - description: The Zarr format is an implementation of chunked, compressed, + description: + The Zarr format is an implementation of chunked, compressed, N-dimensional arrays for storing data. meaning: edam:format_3915 edam:format_3916: title: MTX - description: The Matrix Market matrix (MTX) format stores numerical or pattern + description: + The Matrix Market matrix (MTX) format stores numerical or pattern matrices in a dense (array format) or sparse (coordinate format) representation. meaning: edam:format_3916 edam:format_3951: title: BcForms - description: BcForms is a format for abstractly describing the molecular structure + description: + BcForms is a format for abstractly describing the molecular structure (atoms and bonds) of macromolecular complexes as a collection of subunits and crosslinks. Each subunit can be described with BpForms (http://edamontology.org/format_3909) or SMILES (http://edamontology.org/data_2301). BcForms uses an ontology @@ -2708,19 +3016,22 @@ enums: meaning: edam:format_3951 edam:format_3956: title: N-Quads - description: N-Quads is a line-based, plain text format for encoding an RDF + description: + N-Quads is a line-based, plain text format for encoding an RDF dataset. It includes information about the graph each triple belongs to. meaning: edam:format_3956 edam:format_3969: title: Vega - description: Vega is a visualization grammar, a declarative language for creating, + description: + Vega is a visualization grammar, a declarative language for creating, saving, and sharing interactive visualization designs. With Vega, you can describe the visual appearance and interactive behavior of a visualization in a JSON format, and generate web-based views using Canvas or SVG. meaning: edam:format_3969 edam:format_3970: title: Vega-lite - description: Vega-Lite is a high-level grammar of interactive graphics. It + description: + Vega-Lite is a high-level grammar of interactive graphics. It provides a concise JSON syntax for rapidly generating visualizations to support analysis. Vega-Lite specifications can be compiled to Vega specifications. meaning: edam:format_3970 @@ -2730,33 +3041,38 @@ enums: meaning: edam:format_3971 edam:format_3972: title: BNGL - description: BioNetGen is a format for the specification and simulation of + description: + BioNetGen is a format for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. meaning: edam:format_3972 edam:format_3973: title: Docker image - description: A Docker image is a file, comprised of multiple layers, that + description: + A Docker image is a file, comprised of multiple layers, that is used to execute code in a Docker container. An image is essentially built from the instructions for a complete and executable version of an application, which relies on the host OS kernel. meaning: edam:format_3973 edam:format_3975: title: GFA 1 - description: Graphical Fragment Assembly captures sequence graphs as the product + description: + Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. meaning: edam:format_3975 edam:format_3976: title: GFA 2 - description: Graphical Fragment Assembly captures sequence graphs as the product + description: + Graphical Fragment Assembly captures sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. GFA2 is an update of GFA1 which is not compatible with GFA1. meaning: edam:format_3976 edam:format_3977: title: ObjTables - description: ObjTables is a toolkit for creating reusable datasets that are + description: + ObjTables is a toolkit for creating reusable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances @@ -2767,19 +3083,22 @@ enums: meaning: edam:format_3977 edam:format_3978: title: CONTIG - description: The CONTIG format used for output of the SOAPdenovo alignment + description: + The CONTIG format used for output of the SOAPdenovo alignment program. It contains contig sequences generated without using mate pair information. meaning: edam:format_3978 edam:format_3979: title: WEGO - description: WEGO native format used by the Web Gene Ontology Annotation Plot + description: + WEGO native format used by the Web Gene Ontology Annotation Plot application. Tab-delimited format with gene names and others GO IDs (columns) with one annotation record per line. meaning: edam:format_3979 edam:format_3980: title: RPKM - description: Tab-delimited format for gene expression levels table, calculated + description: + Tab-delimited format for gene expression levels table, calculated as Reads Per Kilobase per Million (RPKM) mapped reads. meaning: edam:format_3980 edam:format_3981: @@ -2788,17 +3107,20 @@ enums: meaning: edam:format_3981 edam:format_3982: title: CHAIN - description: The CHAIN format describes a pairwise alignment that allow gaps + description: + The CHAIN format describes a pairwise alignment that allow gaps in both sequences simultaneously and is used by the UCSC Genome Browser. meaning: edam:format_3982 edam:format_3983: title: NET - description: The NET file format is used to describe the data that underlie + description: + The NET file format is used to describe the data that underlie the net alignment annotations in the UCSC Genome Browser. meaning: edam:format_3983 edam:format_3984: title: QMAP - description: Format of QMAP files generated for methylation data from an internal + description: + Format of QMAP files generated for methylation data from an internal BGI pipeline. meaning: edam:format_3984 edam:format_3985: @@ -2807,7 +3129,8 @@ enums: meaning: edam:format_3985 edam:format_3986: title: WMV - description: The proprietary native video format of various Microsoft programs + description: + The proprietary native video format of various Microsoft programs such as Windows Media Player. meaning: edam:format_3986 edam:format_3987: @@ -2820,34 +3143,40 @@ enums: meaning: edam:format_3988 edam:format_3989: title: GZIP format - description: GNU zip compressed file format common to Unix-based operating + description: + GNU zip compressed file format common to Unix-based operating systems. meaning: edam:format_3989 edam:format_3990: title: AVI - description: Audio Video Interleaved (AVI) format is a multimedia container + description: + Audio Video Interleaved (AVI) format is a multimedia container format for AVI files, that allows synchronous audio-with-video playback. meaning: edam:format_3990 edam:format_3991: title: TrackDB - description: A declaration file format for UCSC browsers track dataset display + description: + A declaration file format for UCSC browsers track dataset display characteristics. meaning: edam:format_3991 edam:format_3992: title: CIGAR format - description: Compact Idiosyncratic Gapped Alignment Report format is a compressed + description: + Compact Idiosyncratic Gapped Alignment Report format is a compressed (run-length encoded) pairwise alignment format. It is useful for representing long (e.g. genomic) pairwise alignments. meaning: edam:format_3992 edam:format_3993: title: Stereolithography format - description: STL is a file format native to the stereolithography CAD software + description: + STL is a file format native to the stereolithography CAD software created by 3D Systems. The format is used to save and share surface-rendered 3D images and also for 3D printing. meaning: edam:format_3993 edam:format_3994: title: U3D - description: U3D (Universal 3D) is a compressed file format and data structure + description: + U3D (Universal 3D) is a compressed file format and data structure for 3D computer graphics. It contains 3D model information such as triangle meshes, lighting, shading, motion data, lines and points with color and structure. @@ -2858,51 +3187,60 @@ enums: meaning: edam:format_3995 edam:format_3996: title: Python script - description: Format for scripts writtenin Python - a widely used high-level + description: + Format for scripts writtenin Python - a widely used high-level programming language for general-purpose programming. meaning: edam:format_3996 edam:format_3997: title: MPEG-4 - description: A digital multimedia container format most commonly used to store + description: + A digital multimedia container format most commonly used to store video and audio. meaning: edam:format_3997 edam:format_3998: title: Perl script - description: Format for scripts written in Perl - a family of high-level, + description: + Format for scripts written in Perl - a family of high-level, general-purpose, interpreted, dynamic programming languages. meaning: edam:format_3998 edam:format_3999: title: R script - description: Format for scripts written in the R language - an open source + description: + Format for scripts written in the R language - an open source programming language and software environment for statistical computing and graphics that is supported by the R Foundation for Statistical Computing. meaning: edam:format_3999 edam:format_4000: title: R markdown - description: A file format for making dynamic documents (R Markdown scripts) + description: + A file format for making dynamic documents (R Markdown scripts) with the R language. meaning: edam:format_4000 edam:format_4002: title: pickle - description: Format used by Python pickle module for serializing and de-serializing + description: + Format used by Python pickle module for serializing and de-serializing a Python object structure. meaning: edam:format_4002 edam:format_4003: title: NumPy format - description: The standard binary file format used by NumPy - a fundamental + description: + The standard binary file format used by NumPy - a fundamental package for scientific computing with Python - for persisting a single arbitrary NumPy array on disk. The format stores all of the shape and dtype information necessary to reconstruct the array correctly. meaning: edam:format_4003 edam:format_4004: title: SimTools repertoire file format - description: Format of repertoire (archive) files that can be read by SimToolbox + description: + Format of repertoire (archive) files that can be read by SimToolbox (a MATLAB toolbox for structured illumination fluorescence microscopy) or alternatively extracted with zip file archiver software. meaning: edam:format_4004 edam:format_4005: title: Configuration file format - description: A configuration file used by various programs to store settings + description: + A configuration file used by various programs to store settings that are specific to their respective software. meaning: edam:format_4005 edam:format_4006: @@ -2915,12 +3253,14 @@ enums: meaning: edam:format_4007 edam:format_4015: title: PEtab - description: A data format for specifying parameter estimation problems in + description: + A data format for specifying parameter estimation problems in systems biology. meaning: edam:format_4015 edam:format_4018: title: gVCF - description: Genomic Variant Call Format (gVCF) is a version of VCF that includes + description: + Genomic Variant Call Format (gVCF) is a version of VCF that includes not only the positions that are variant when compared to a reference genome, but also the non-variant positions as ranges, including metrics of confidence that the positions in the range are actually non-variant e.g. minimum read-depth @@ -2928,18 +3268,21 @@ enums: meaning: edam:format_4018 edam:format_4023: title: cml - description: Chemical Markup Language (CML) is an XML-based format for encoding + description: + Chemical Markup Language (CML) is an XML-based format for encoding detailed information about a wide range of chemical concepts. meaning: edam:format_4023 edam:format_4024: title: cif - description: Crystallographic Information File (CIF) is a data exchange standard + description: + Crystallographic Information File (CIF) is a data exchange standard file format for Crystallographic Information and related Structural Science data. meaning: edam:format_4024 edam:format_4025: title: BioSimulators format for the specifications of biosimulation tools - description: Format for describing the capabilities of a biosimulation tool + description: + Format for describing the capabilities of a biosimulation tool including the modeling frameworks, simulation algorithms, and modeling formats that it supports, as well as metadata such as a list of the interfaces, programming languages, and operating systems supported by the tool; a link @@ -2947,20 +3290,24 @@ enums: to the tool. meaning: edam:format_4025 edam:format_4026: - title: BioSimulators standard for command-line interfaces for biosimulation + title: + BioSimulators standard for command-line interfaces for biosimulation tools - description: Outlines the syntax and semantics of the input and output arguments + description: + Outlines the syntax and semantics of the input and output arguments for command-line interfaces for biosimulation tools. meaning: edam:format_4026 edam:format_4035: title: PQR - description: Data format derived from the standard PDB format, which enables + description: + Data format derived from the standard PDB format, which enables user to incorporate parameters for charge and radius to the existing PDB data file. meaning: edam:format_4035 edam:format_4036: title: PDBQT - description: Data format used in AutoDock 4 for storing atomic coordinates, + description: + Data format used in AutoDock 4 for storing atomic coordinates, partial atomic charges and AutoDock atom types for both receptors and ligands. meaning: edam:format_4036 edam:format_4039: @@ -2969,17 +3316,20 @@ enums: meaning: edam:format_4039 edam:format_4041: title: maDMP - description: maDMP stands for machine-actionable data management plan, a standard + description: + maDMP stands for machine-actionable data management plan, a standard for DMPs developed by the Research Data Alliance (RDA). meaning: edam:format_4041 edam:format_4048: title: Nextflow - description: Nextflow is a workflow system for creating scalable, portable, + description: + Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. meaning: edam:format_4048 edam:format_4049: title: Snakemake - description: The Snakemake workflow management system is a tool to create + description: + The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. meaning: edam:format_4049 edam:format_4050: @@ -2988,61 +3338,71 @@ enums: meaning: edam:format_4050 edam:format_4058: title: mzTab-M - description: mzTab-M is a light-weight, tab-delimited format for mass spectrometry-based + description: + mzTab-M is a light-weight, tab-delimited format for mass spectrometry-based chemical profiling data, including metabolomics. meaning: edam:format_4058 edam:format_4059: title: mzTab-L - description: mzTab-L is a light-weight, tab-delimited format for mass spectrometry-based + description: + mzTab-L is a light-weight, tab-delimited format for mass spectrometry-based lipidomics data. It is a compatible version of mzTab-M, with additional rules and information standard (reporting guidelines). meaning: edam:format_4059 edam:format_4066: title: ISA-Tab Investigation file - description: ISA-Tab Investigation file (i_Investigation.txt) contains metadata + description: + ISA-Tab Investigation file (i_Investigation.txt) contains metadata describing the overall goals, means, and context of an investigation/experiment, including references to associated Study and Assay files. meaning: edam:format_4066 edam:format_4067: title: ISA-Tab Study file - description: ISA-Tab Study file (s_*.txt) contains sample metadata describing + description: + ISA-Tab Study file (s_*.txt) contains sample metadata describing the subjects under study, their sources, characteristics, sampling methodology, and any treatments or manipulations applied. meaning: edam:format_4067 edam:format_4068: title: ISA-Tab Assay file - description: ISA-Tab Assay file (a_*.txt) contains assay metadata describing + description: + ISA-Tab Assay file (a_*.txt) contains assay metadata describing test steps and analytical measurements performed on the sample material, including measurement types, technology used, and references to raw and derived data files. meaning: edam:format_4068 edam:format_4069: title: ISA-JSON - description: ISA-JSON stands for Investigation / Study / Assay (ISA) JavaScript + description: + ISA-JSON stands for Investigation / Study / Assay (ISA) JavaScript Object Notation (JSON) format, and it is comprised of metadata describing observational or experimental scientific studies. meaning: edam:format_4069 edam:format_4070: title: mwTab - description: mwTab is a tab-delimited text format developed by the Metabolomics + description: + mwTab is a tab-delimited text format developed by the Metabolomics Workbench to facilitate programmatic processing of metabolomics data and metadata suitable for submission to the repository. meaning: edam:format_4070 edam:format_4071: title: MHD - description: MHD (MetabolomicsHub Common Data Model) is a JSON-based format + description: + MHD (MetabolomicsHub Common Data Model) is a JSON-based format providing a standardised, FAIR-compliant data model for the exchange, discovery, and reuse of metabolomics dataset metadata across international repositories. meaning: edam:format_4071 edam:format_4072: title: MHD announcement - description: The MHD announcement file is a JSON-based format used to notify + description: + The MHD announcement file is a JSON-based format used to notify MetabolomicsHub of new or updated dataset submissions, serving as a manifest or notification file within the MHD data flow. meaning: edam:format_4072 edam:format_4073: title: MetaboLights MAF - description: MetaboLights MAF (Metabolite Annotation File) is a tab-separated + description: + MetaboLights MAF (Metabolite Annotation File) is a tab-separated file format used to report metabolites identified or annotated in a metabolomics study, including compound identifiers, chemical structure representations, mass-to-charge ratios, retention times, and per-sample quantitative measurements. diff --git a/src/common_access_model/schema/enums/EnumEthnicity.yaml b/src/common_access_model/schema/enums/EnumEthnicity.yaml index 5b12af9..42621d8 100644 --- a/src/common_access_model/schema/enums/EnumEthnicity.yaml +++ b/src/common_access_model/schema/enums/EnumEthnicity.yaml @@ -1,7 +1,7 @@ id: https://includedcc.org/common-access-model/EnumEthnicity name: EnumEthnicity enums: -# Could set these up for concept expansion in theory. + # Could set these up for concept expansion in theory. EnumEthnicity: description: Participant ethnicity, specific to Hispanic or Latino. permissible_values: diff --git a/src/common_access_model/schema/enums/EnumFamilyRelation.yaml b/src/common_access_model/schema/enums/EnumFamilyRelation.yaml index 95f57c7..ed0cf5d 100644 --- a/src/common_access_model/schema/enums/EnumFamilyRelation.yaml +++ b/src/common_access_model/schema/enums/EnumFamilyRelation.yaml @@ -15,7 +15,8 @@ enums: permissible_values: KIN:KIN_001: title: isRelativeOf - description: A relation that indicates that a person is connected to another + description: + A relation that indicates that a person is connected to another biologically or through a socio-legal relationship. meaning: KIN:KIN_001 KIN:KIN_053: @@ -24,44 +25,52 @@ enums: meaning: KIN:KIN_053 KIN:KIN_022: title: isAdoptiveParentOf - description: A legal relation between a person and a child that is adopted + description: + A legal relation between a person and a child that is adopted by that person. The adopted child is given the rights, privileges, and duties of a biological child by the adoptive person. meaning: KIN:KIN_022 KIN:KIN_027: title: isBiologicalMotherOf - description: A relation that indicates that a person is the biological mother + description: + A relation that indicates that a person is the biological mother of another person. meaning: KIN:KIN_027 KIN:KIN_039: title: hasGestationalCarrier - description: A relation between the child and a woman who carried a fertilised + description: + A relation between the child and a woman who carried a fertilised egg in her womb and gave birth to a child on behalf of the mother. meaning: KIN:KIN_039 KIN:KIN_038: title: isOvumDonorOf - description: A relation between a fertile woman who donated an egg to another + description: + A relation between a fertile woman who donated an egg to another woman to help her conceive and the child. meaning: KIN:KIN_038 KIN:KIN_051: title: isSeparatedConsanguineousPartnerOf - description: A socio-legal relationship between two people who used to live + description: + A socio-legal relationship between two people who used to live together, share a common domestic life and are closely related biologically (second cousins or closer), and have now separated. meaning: KIN:KIN_051 KIN:KIN_010: title: isMonozygoticMultipleBirthSiblingOf - description: A relation between two people born at the same birth from a single + description: + A relation between two people born at the same birth from a single fertilised ovum that splits. meaning: KIN:KIN_010 KIN:KIN_055: title: isPaternalHalfSiblingOf - description: A relation between two people that share the same biological + description: + A relation between two people that share the same biological father. meaning: KIN:KIN_055 KIN:KIN_008: title: isFullsiblingOf - description: A relation between two people that have both biological parents + description: + A relation between two people that have both biological parents in common. meaning: KIN:KIN_008 KIN:KIN_052: @@ -70,17 +79,20 @@ enums: meaning: KIN:KIN_052 KIN:KIN_028: title: isBiologicalFatherOf - description: A relation that indicates that a person is the biological father + description: + A relation that indicates that a person is the biological father of another person. meaning: KIN:KIN_028 KIN:KIN_013: title: isParentalSiblingOf - description: A relation that indicates that a person is the sibling of a parent + description: + A relation that indicates that a person is the sibling of a parent of another person. meaning: KIN:KIN_013 KIN:KIN_003: title: isBiologicalParentOf - description: A relation that indicates that a person is the biological parent + description: + A relation that indicates that a person is the biological parent of another person. meaning: KIN:KIN_003 KIN:KIN_059: @@ -89,12 +101,14 @@ enums: meaning: KIN:KIN_059 KIN:KIN_005: title: isGestationalCarrierOf - description: A relation between the woman who carried a fertilised egg in + description: + A relation between the woman who carried a fertilised egg in her womb and gave birth to a child on behalf of the mother, and the child. meaning: KIN:KIN_005 KIN:KIN_023: title: isStepParentOf - description: A relation between a person and a child, where the person is + description: + A relation between a person and a child, where the person is married to the father or mother of a child but who is not that child's own father or mother. meaning: KIN:KIN_023 @@ -104,7 +118,8 @@ enums: meaning: KIN:KIN_036 KIN:KIN_025: title: isStepSiblingOf - description: A relation between children born of two different families who + description: + A relation between children born of two different families who have been joined by marriage, defacto or otherwise, of at least one of their respective parents. meaning: KIN:KIN_025 @@ -118,7 +133,8 @@ enums: meaning: KIN:KIN_004 KIN:KIN_024: title: isSiblingFigureOf - description: A relation between two people that has all or some of the characteristics + description: + A relation between two people that has all or some of the characteristics of a sibling relationship. meaning: KIN:KIN_024 KIN:KIN_009: @@ -135,7 +151,8 @@ enums: meaning: KIN:KIN_060 KIN:KIN_029: title: isMitochondrialDonorOf - description: A relation between a woman that has donated mitochondria and + description: + A relation between a woman that has donated mitochondria and a child. Mitochondrial donation involves removing the nuclear DNA from a woman’s ovum containing faulty mitochondria and inserting it into a healthy donor ovum, which has had its nuclear DNA removed. @@ -146,72 +163,85 @@ enums: meaning: KIN:KIN_047 KIN:KIN_021: title: isFosterParentOf - description: A relation between a person and a child that temporarily enters + description: + A relation between a person and a child that temporarily enters into his or her family for a period of time, without becoming the child's legal parent. meaning: KIN:KIN_021 KIN:KIN_057: title: isPaternalStepSiblingOf - description: A relation between children born of two different families who + description: + A relation between children born of two different families who have been joined by marriage, defacto or otherwise. One is a biological child and the other is a step child of the same man. meaning: KIN:KIN_057 KIN:KIN_030: title: isConsanguineousPartnerOf - description: A socio-legal relationship between two people who live together, + description: + A socio-legal relationship between two people who live together, share a common domestic life and are closely related biologically (second cousins or closer). meaning: KIN:KIN_030 KIN:KIN_046: title: hasParentalSibling - description: A relation that indicates that a person has a parental sibling + description: + A relation that indicates that a person has a parental sibling relationship with another person, i.e., the other person is the sibling of a parent. meaning: KIN:KIN_046 KIN:KIN_012: title: isHalfSiblingOf - description: A relation between two people that have a single biological parent + description: + A relation between two people that have a single biological parent in common. meaning: KIN:KIN_012 KIN:KIN_014: title: isCousinOf - description: A relation between a person and a child of that person's uncle + description: + A relation between a person and a child of that person's uncle or aunt. meaning: KIN:KIN_014 KIN:KIN_015: title: isMaternalCousinOf - description: A relation between a person and a child of that person's mother's + description: + A relation between a person and a child of that person's mother's sibling. meaning: KIN:KIN_015 KIN:KIN_050: title: isSeparatedPartnerOf - description: A socio-legal relationship between two people who used to live + description: + A socio-legal relationship between two people who used to live together and share a common domestic life, but have now separated. meaning: KIN:KIN_050 KIN:KIN_056: title: isMaternalStepSiblingOf - description: A relation between children born of two different families who + description: + A relation between children born of two different families who have been joined by marriage, defacto or otherwise. One is a biological child and the other is a step child of the same woman. meaning: KIN:KIN_056 KIN:KIN_032: title: isBiologicalChildOf - description: A relation that indicates that a person is the biological child + description: + A relation that indicates that a person is the biological child of another person. meaning: KIN:KIN_032 KIN:KIN_020: title: isParentFigureOf - description: A relation between a person who is regarded as having all or + description: + A relation between a person who is regarded as having all or some of the characteristics of a parent and the child. meaning: KIN:KIN_020 KIN:KIN_007: title: isBiologicalSiblingOf - description: A relation between two people that have one or both biological + description: + A relation between two people that have one or both biological parents in common. meaning: KIN:KIN_007 KIN:KIN_002: title: isBiologicalRelativeOf - description: A relation that indicates that a person is related to another + description: + A relation that indicates that a person is related to another person biologically. meaning: KIN:KIN_002 KIN:KIN_018: @@ -220,12 +250,14 @@ enums: meaning: KIN:KIN_018 KIN:KIN_011: title: isPolyzygoticMultipleBirthSiblingOf - description: A relation between two people born at the same birth from fertilisation + description: + A relation between two people born at the same birth from fertilisation of more than two ovums discharged in a single ovarian cycle. meaning: KIN:KIN_011 KIN:KIN_006: title: isSurrogateOvumDonorOf - description: A relation between the woman who carried her fertilised egg in + description: + A relation between the woman who carried her fertilised egg in her womb and gave birth to a child on behalf of the mother, and the child. meaning: KIN:KIN_006 KIN:KIN_017: @@ -234,21 +266,25 @@ enums: meaning: KIN:KIN_017 KIN:KIN_016: title: isPaternalCousinOf - description: A relation between a person and a child of that person's father's + description: + A relation between a person and a child of that person's father's sibling. meaning: KIN:KIN_016 KIN:KIN_026: title: isPartnerOf - description: A socio-legal relationship between two people who live together + description: + A socio-legal relationship between two people who live together and share a common domestic life. meaning: KIN:KIN_026 KIN:KIN_019: title: isSocialLegalRelativeOf - description: A social or legal relationship between two people, for example, + description: + A social or legal relationship between two people, for example, an adoptive parent. meaning: KIN:KIN_019 KIN:KIN_054: title: isMaternalHalfSiblingOf - description: A relation between two people that share the same biological + description: + A relation between two people that share the same biological mother. meaning: KIN:KIN_054 diff --git a/src/common_access_model/schema/enums/EnumFamilyRole.yaml b/src/common_access_model/schema/enums/EnumFamilyRole.yaml index 71a2e6c..7c0a6cc 100644 --- a/src/common_access_model/schema/enums/EnumFamilyRole.yaml +++ b/src/common_access_model/schema/enums/EnumFamilyRole.yaml @@ -7,12 +7,11 @@ enums: snomedct:85900004: title: Proband aliases: - - proband + - proband KIN:027: title: isBiologicalMotherOf description: A relation that indicates that a person is the biological mother of another person. snomedct:72705000: title: Mother aliases: - - mother - + - mother diff --git a/src/common_access_model/schema/enums/EnumFamilyType.yaml b/src/common_access_model/schema/enums/EnumFamilyType.yaml index 42088ac..4a5e7f1 100644 --- a/src/common_access_model/schema/enums/EnumFamilyType.yaml +++ b/src/common_access_model/schema/enums/EnumFamilyType.yaml @@ -19,17 +19,17 @@ enums: title: Duo description: This family study includes at a minimum one parent and one affected child. aliases: - - duo + - duo CAMO:0000004: title: Trio description: This family study includes at a minimum two parents of one affected child. aliases: - - trio + - trio CAMO:0000005: title: Trio+ description: This family study includes at a minimum two parents of one affected child and at least one other child. aliases: - - trio_plus + - trio_plus CAMO:0000006: title: Case Only description: This family study includes only one or more cases. @@ -37,9 +37,9 @@ enums: title: Proband Only description: This family study includes only one or more probands. aliases: - - proband_only + - proband_only CAMO:0000008: title: Control Only - description: This family study includes only one or more controls. + description: This family study includes only one or more controls. aliases: - - control_only + - control_only diff --git a/src/common_access_model/schema/enums/EnumFileHashType.yaml b/src/common_access_model/schema/enums/EnumFileHashType.yaml index e081181..4bbc3c1 100644 --- a/src/common_access_model/schema/enums/EnumFileHashType.yaml +++ b/src/common_access_model/schema/enums/EnumFileHashType.yaml @@ -14,29 +14,29 @@ enums: permissible_values: MS:1000568: title: MD5 - description: MD5 (Message-Digest algorithm 5) is a (now deprecated) - cryptographic hash function with a 128-bit hash value used to check + description: MD5 (Message-Digest algorithm 5) is a (now deprecated) + cryptographic hash function with a 128-bit hash value used to check the integrity of files. aliases: - - md5 + - md5 CAMO:0000022: title: ETag - description: The entity tag is a hash of the object. The ETag reflects - changes only to the contents of an object, not its metadata. The + description: The entity tag is a hash of the object. The ETag reflects + changes only to the contents of an object, not its metadata. The ETag may or may not be an MD5 digest of the object data. aliases: - - etag + - etag MS:1000569: title: SHA-1 - description: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash - function designed by the National Security Agency (NSA). It is also - used to verify file integrity. Since 2011 it has been deprecated by + description: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash + function designed by the National Security Agency (NSA). It is also + used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. aliases: - - sha1 + - sha1 MS:1003151: title: SHA-256 - description: SHA-256 (member of Secure Hash Algorithm-2 family) is a + description: SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency - (NSA) and published by the NIST as a U. S. government standard. It + (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. diff --git a/src/common_access_model/schema/enums/EnumLaterality.yaml b/src/common_access_model/schema/enums/EnumLaterality.yaml index 487159d..6c93f18 100644 --- a/src/common_access_model/schema/enums/EnumLaterality.yaml +++ b/src/common_access_model/schema/enums/EnumLaterality.yaml @@ -19,7 +19,8 @@ enums: meaning: HP:0012832 HP:0012833: title: Unilateral - description: Being present on only the left or only the right side of the + description: + Being present on only the left or only the right side of the body. meaning: HP:0012833 HP:0012834: @@ -32,7 +33,8 @@ enums: meaning: HP:0012835 HP:4000152: title: Alternating laterality - description: Occurring on the left and right in succession. This term can + description: + Occurring on the left and right in succession. This term can refer to alternating sides of the body (e.g., Alternating hemiplegia) or alternative sides of the visual field (e.g., some migraine auras). meaning: HP:4000152 diff --git a/src/common_access_model/schema/enums/EnumOrganism.yaml b/src/common_access_model/schema/enums/EnumOrganism.yaml index 7fd0004..7b39d97 100644 --- a/src/common_access_model/schema/enums/EnumOrganism.yaml +++ b/src/common_access_model/schema/enums/EnumOrganism.yaml @@ -13,4 +13,4 @@ enums: title: Mus musculus aliases: - mouse - - house_mouse \ No newline at end of file + - house_mouse diff --git a/src/common_access_model/schema/enums/EnumParticipantLifespanStage.yaml b/src/common_access_model/schema/enums/EnumParticipantLifespanStage.yaml index cc777cc..e2645d6 100644 --- a/src/common_access_model/schema/enums/EnumParticipantLifespanStage.yaml +++ b/src/common_access_model/schema/enums/EnumParticipantLifespanStage.yaml @@ -4,7 +4,8 @@ name: EnumParticipantLifespanStage enums: EnumParticipantLifespanStage: title: Participant Lifespan Stage - description: Stages of life during which participants may be recruited. From NICHD + description: + Stages of life during which participants may be recruited. From NICHD Pediatric Terminology. https://evs.nci.nih.gov/ftp1/Pediatric_Terminologies/NICHD/About.html reachable_from: source_ontology: bioregistry:ncit @@ -17,79 +18,93 @@ enums: permissible_values: NCIT:C176390: title: Peripubertal - description: The transitional period of life between immature and mature reproductive + description: + The transitional period of life between immature and mature reproductive states. meaning: NCIT:C176390 NCIT:C199314: title: Adulthood - description: A time period in the human lifespan when full physical and intellectual + description: + A time period in the human lifespan when full physical and intellectual maturity have been attained, which generally follows adolescence. meaning: NCIT:C199314 NCIT:C39298: title: Adolescence - description: A human life stage that begins at twelve years of age and continues + description: + A human life stage that begins at twelve years of age and continues until twenty-one complete years of age, generally marked by the beginning of puberty and lasting to the beginning of adulthood. meaning: NCIT:C39298 NCIT:C89331: title: Early Adolescence - description: A human life stage that begins at twelve years of age and continues + description: + A human life stage that begins at twelve years of age and continues until eighteen complete years of age. This phase marks the start of physical, physiological and psychological changes that characterize pubertal growth and development. meaning: NCIT:C89331 NCIT:C89344: title: Late Adolescence - description: A human life stage that begins at nineteen years of age and continues + description: + A human life stage that begins at nineteen years of age and continues until twenty-one complete years of age. This phase includes the final stages of pubertal growth and development as well as the attainment of significant psycho-social milestones. meaning: NCIT:C89344 NCIT:C89345: title: Childhood - description: A time period that begins at the beginning of the human embryonic + description: + A time period that begins at the beginning of the human embryonic stage and continues until the end of adolescence. meaning: NCIT:C89345 NCIT:C89346: title: Early Childhood - description: A human life stage that begins at two years of age and continues + description: + A human life stage that begins at two years of age and continues until five complete years of age. meaning: NCIT:C89346 NCIT:C89347: title: Middle Childhood - description: A human life stage that begins at six years of age and continues + description: + A human life stage that begins at six years of age and continues until eleven complete years of age. meaning: NCIT:C89347 NCIT:C89885: title: Fetal Stage - description: A human life stage, during prenatal development, that typically + description: + A human life stage, during prenatal development, that typically begins at the beginning of nine weeks after fertilization (full formation of the embryo) and continues until birth. meaning: NCIT:C89885 NCIT:C89887: title: Full Term Neonatal Stage - description: A human life stage that begins at full term birth and continues + description: + A human life stage that begins at full term birth and continues until twenty-seven complete days of age. meaning: NCIT:C89887 NCIT:C89888: title: Preterm Neonatal Stage - description: A human life stage that begins at birth prior to thirty-seven + description: + A human life stage that begins at birth prior to thirty-seven weeks of full gestation (full term) and continues until twenty-seven complete days after birth. meaning: NCIT:C89888 NCIT:C89889: title: Infancy - description: A human life stage that begins at birth and continues until twelve + description: + A human life stage that begins at birth and continues until twelve complete months of age. meaning: NCIT:C89889 NCIT:C89890: title: Toddler Stage - description: A human life stage that begins at thirteen months of age and + description: + A human life stage that begins at thirteen months of age and continues until twenty-four complete months of age. meaning: NCIT:C89890 NCIT:C90337: title: Maternal Life Stage - description: The period of time during a female's reproductive years that + description: + The period of time during a female's reproductive years that she functions as a mother. meaning: NCIT:C90337 NCIT:C90338: @@ -102,12 +117,14 @@ enums: meaning: NCIT:C90339 NCIT:C90340: title: Maternal Preconception Stage - description: The stage in the life of a female during which she is attempting + description: + The stage in the life of a female during which she is attempting to get pregnant. meaning: NCIT:C90340 NCIT:C99135: title: Embryonic Stage - description: A human life stage, during prenatal development, that begins + description: + A human life stage, during prenatal development, that begins at fertilization and typically continues until the end of eight weeks after fertilization, with full formation of the embryo. meaning: NCIT:C99135 diff --git a/src/common_access_model/schema/enums/EnumPresentAbsent.yaml b/src/common_access_model/schema/enums/EnumPresentAbsent.yaml index 1efa682..4eff369 100644 --- a/src/common_access_model/schema/enums/EnumPresentAbsent.yaml +++ b/src/common_access_model/schema/enums/EnumPresentAbsent.yaml @@ -3,7 +3,8 @@ id: https://includedcc.org/common-access-model/EnumPresentAbsent name: EnumPresentAbsent enums: EnumPresentAbsent: - description: Options for describing presence or absence. Derived from SNOMED CT + description: + Options for describing presence or absence. Derived from SNOMED CT Known codes. The "Known" codes and "Not suspected" are the broadest terms and suitable for general use. reachable_from: diff --git a/src/common_access_model/schema/enums/EnumProgram.yaml b/src/common_access_model/schema/enums/EnumProgram.yaml index 5a7b34d..4ec26fd 100644 --- a/src/common_access_model/schema/enums/EnumProgram.yaml +++ b/src/common_access_model/schema/enums/EnumProgram.yaml @@ -7,20 +7,22 @@ enums: permissible_values: https://www.nih.gov/include-project: title: INCLUDE - description: The INCLUDE (INvestigation of Co-occurring conditions across the - Lifespan to Understand Down syndromE) Project was launched in June 2018 in - support of a Congressional directive in the fiscal year (FY) 2018 Omnibus - Appropriations. The directive called for a new trans-NIH research initiative + description: + The INCLUDE (INvestigation of Co-occurring conditions across the + Lifespan to Understand Down syndromeE) Project was launched in June 2018 in + support of a Congressional directive in the fiscal year (FY) 2018 Omnibus + Appropriations. The directive called for a new trans-NIH research initiative on critical health and quality-of-life needs for individuals with Down syndrome. aliases: - - include + - include https://commonfund.nih.gov/KidsFirst: title: Kids First - description: The goal of the Gabriella Miller Kids First Pediatric Research Program - (Kids First) is to help researchers uncover new insights into the biology of childhood - cancer and congenital anomalies, including the discovery of shared genetic pathways - between these disorders. Children with birth defects have an increased risk of developing - childhood cancer. This suggests there are shared genetic pathways underlying some types - of childhood cancer and congenital anomalies. + description: + The goal of the Gabriella Miller Kids First Pediatric Research Program + (Kids First) is to help researchers uncover new insights into the biology of childhood + cancer and congenital anomalies, including the discovery of shared genetic pathways + between these disorders. Children with birth defects have an increased risk of developing + childhood cancer. This suggests there are shared genetic pathways underlying some types + of childhood cancer and congenital anomalies. aliases: - - kf \ No newline at end of file + - kf diff --git a/src/common_access_model/schema/enums/EnumRace.yaml b/src/common_access_model/schema/enums/EnumRace.yaml index f14eecc..72e7e23 100644 --- a/src/common_access_model/schema/enums/EnumRace.yaml +++ b/src/common_access_model/schema/enums/EnumRace.yaml @@ -2,7 +2,7 @@ id: https://includedcc.org/common-access-model/EnumRace name: EnumRace enums: EnumRace: - # Could set these up for concept expansion in theory. + # Could set these up for concept expansion in theory. description: Participant Race permissible_values: CDCREC:1002-5: diff --git a/src/common_access_model/schema/enums/EnumSampleCollectionMethod.yaml b/src/common_access_model/schema/enums/EnumSampleCollectionMethod.yaml index 89e21c7..64070d5 100644 --- a/src/common_access_model/schema/enums/EnumSampleCollectionMethod.yaml +++ b/src/common_access_model/schema/enums/EnumSampleCollectionMethod.yaml @@ -23,14 +23,16 @@ enums: title: Sweat collection by iontophoresis procedure meaning: snomedct:115985003 snomedct:1202027002: - title: Collection of esophageal cells via swallowable cell collection sponge + title: + Collection of esophageal cells via swallowable cell collection sponge in capsule (procedure) meaning: snomedct:1202027002 snomedct:1230332003: title: Collection of blood from umbilical cord immediately after delivery meaning: snomedct:1230332003 snomedct:1255865009: - title: Aspiration of seminal fluid from seminal vesicle using ultrasonographic + title: + Aspiration of seminal fluid from seminal vesicle using ultrasonographic guidance (procedure) meaning: snomedct:1255865009 snomedct:1285339005: @@ -46,7 +48,8 @@ enums: title: Collection of blood via implanted venous access device meaning: snomedct:16631761000119104 snomedct:174653005: - title: Endoscopic retrograde pancreatography with collection of pancreatic + title: + Endoscopic retrograde pancreatography with collection of pancreatic juice meaning: snomedct:174653005 snomedct:19867003: @@ -248,7 +251,7 @@ enums: title: Urine specimen collection, 12 hours meaning: snomedct:40597003 snomedct:406173008: - title: 'Phlebotomy: cannulated vessel' + title: "Phlebotomy: cannulated vessel" meaning: snomedct:406173008 snomedct:418622002: title: Taking oral swab diff --git a/src/common_access_model/schema/enums/EnumStudyDesign.yaml b/src/common_access_model/schema/enums/EnumStudyDesign.yaml index 4ed88fe..578e5a4 100644 --- a/src/common_access_model/schema/enums/EnumStudyDesign.yaml +++ b/src/common_access_model/schema/enums/EnumStudyDesign.yaml @@ -4,7 +4,8 @@ name: EnumStudyDesign enums: EnumStudyDesign: title: Study Design - description: Approaches for collecting data, investigating interventions, and/or + description: + Approaches for collecting data, investigating interventions, and/or analyzing data. reachable_from: source_ontology: bioregistry:mesh @@ -18,31 +19,36 @@ enums: permissible_values: mesh:D003430: title: Cross-Sectional Studies - description: Studies in which the presence or absence of disease or other + description: + Studies in which the presence or absence of disease or other health-related variables are determined in each member of the study population or in a representative sample at one particular time. This contrasts with LONGITUDINAL STUDIES which are followed over a period of time. meaning: mesh:D003430 mesh:D005500: title: Follow-Up Studies - description: Studies in which individuals or populations are followed to assess + description: + Studies in which individuals or populations are followed to assess the outcome of exposures, procedures, or effects of a characteristic, e.g., occurrence of disease. meaning: mesh:D005500 mesh:D008137: title: Longitudinal Studies - description: Studies in which variables relating to an individual or group + description: + Studies in which variables relating to an individual or group of individuals are assessed over a period of time. meaning: mesh:D008137 mesh:D011446: title: Prospective Studies - description: Observation of a population for a sufficient number of persons + description: + Observation of a population for a sufficient number of persons over a sufficient number of years to generate incidence or mortality rates subsequent to the selection of the study group. meaning: mesh:D011446 mesh:D012189: title: Retrospective Studies - description: Studies used to test etiologic hypotheses in which inferences + description: + Studies used to test etiologic hypotheses in which inferences about an exposure to putative causal factors are derived from data relating to characteristics of persons under study or to events or experiences in their past. The essential feature is that some of the persons under study @@ -51,7 +57,8 @@ enums: meaning: mesh:D012189 mesh:D015331: title: Cohort Studies - description: Studies in which subsets of a defined population are identified. + description: + Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt @@ -59,14 +66,16 @@ enums: meaning: mesh:D015331 mesh:D015528: title: HIV Seroprevalence - description: Studies of the number of cases where human immunodeficiency virus + description: + Studies of the number of cases where human immunodeficiency virus (HIV) is present in a specific population at a designated time. The presence in a given individual is determined by the finding of HIV antibodies in the serum (HIV SEROPOSITIVITY). meaning: mesh:D015528 mesh:D016022: title: Case-Control Studies - description: Comparisons that start with the identification of persons with + description: + Comparisons that start with the identification of persons with the disease or outcome of interest and a control (comparison, referent) group without the disease or outcome of interest. The relationship of an attribute is examined by comparing both groups with regard to the frequency @@ -74,39 +83,45 @@ enums: meaning: mesh:D016022 mesh:D016036: title: Seroepidemiologic Studies - description: EPIDEMIOLOGIC STUDIES based on the detection through serological + description: + EPIDEMIOLOGIC STUDIES based on the detection through serological testing of characteristic change in the serum level of specific ANTIBODIES. Latent subclinical infections and carrier states can thus be detected in addition to clinically overt cases. meaning: mesh:D016036 mesh:D063588: title: National Longitudinal Study of Adolescent Health - description: Longitudinal study of a nationally representative sample of adolescents + description: + Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. The Add Health cohort has been followed into young adulthood. (from http://www.cpc.unc.edu/projects/addhealth accessed 08/2012) meaning: mesh:D063588 mesh:D065186: title: Interrupted Time Series Analysis - description: A study that uses observations at multiple time points before + description: + A study that uses observations at multiple time points before and after an intervention (the interruption), in an attempt to detect whether the intervention has had an effect significantly greater than any underlying trend over time. meaning: mesh:D065186 mesh:D065187: title: Controlled Before-After Studies - description: A study in which observations are made before and after an intervention, + description: + A study in which observations are made before and after an intervention, both in a group that receives the intervention and in a control group that does not. meaning: mesh:D065187 mesh:D065386: title: Historically Controlled Study - description: A study that compares a group of participants receiving an intervention + description: + A study that compares a group of participants receiving an intervention with a similar group from the past who did not. meaning: mesh:D065386 mesh:D000068397: title: Clinical Study - description: A work that reports on the results of a research study to evaluate + description: + A work that reports on the results of a research study to evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. While most clinical studies concern humans, @@ -115,25 +130,29 @@ enums: meaning: mesh:D000068397 mesh:D000073843: title: Equivalence Trial - description: Trial that aims to show a new treatment is no better and no worse + description: + Trial that aims to show a new treatment is no better and no worse than the standard treatment. meaning: mesh:D000073843 mesh:D000076362: title: Adaptive Clinical Trial - description: Clinical study in which a prospectively planned opportunity is + description: + Clinical study in which a prospectively planned opportunity is included to modify trial designs and hypotheses based on analysis of data from subjects in the study. meaning: mesh:D000076362 mesh:D000077522: title: Clinical Trial, Veterinary - description: A work in which animal participants are assigned to receive one + description: + A work in which animal participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. meaning: mesh:D000077522 mesh:D000078182: title: Systematic Review - description: A review of primary literature in health and health policy that + description: + A review of primary literature in health and health policy that attempts to identify, appraise, and synthesize all the empirical evidence that meets specified eligibility criteria to answer a given research question. Its conduct uses explicit methods aimed at minimizing bias in order to produce @@ -142,20 +161,23 @@ enums: meaning: mesh:D000078182 mesh:D000078323: title: Observational Study, Veterinary - description: Reports on studies of the results of a clinical study in which + description: + Reports on studies of the results of a clinical study in which animal subjects may receive diagnostic, therapeutic, or other types of interventions, where the investigator does not assign participants to specific interventions. meaning: mesh:D000078323 mesh:D000078325: title: Clinical Trial Protocol - description: The written description of a clinical study. It contains the + description: + The written description of a clinical study. It contains the study's objectives, design, and methods including subject target and/or enrollment criteria. It may also present relevant scientific background and statistical information. meaning: mesh:D000078325 mesh:D000081262: title: Randomized Controlled Trial, Veterinary - description: A work that reports on a clinical trial with animal subjects + description: + A work that reports on a clinical trial with animal subjects that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, @@ -163,18 +185,21 @@ enums: meaning: mesh:D000081262 mesh:D000098368: title: Human Challenge Trials - description: Trials in which participants are intentionally challenged (whether + description: + Trials in which participants are intentionally challenged (whether or not they have been vaccinated) with exposure to an infectious disease organism. meaning: mesh:D000098368 mesh:D000098583: title: Scoping Review - description: Review to identify knowledge gaps, scope a body of literature, + description: + Review to identify knowledge gaps, scope a body of literature, clarify concepts or to investigate research conduct. meaning: mesh:D000098583 mesh:D000099094: title: Network Meta-Analysis - description: Works consisting of meta-analysis of randomized trials in which + description: + Works consisting of meta-analysis of randomized trials in which estimates of comparative treatment effects are visualized and interpreted from a network of interventions that may or may not have been evaluated directly against each other. Common considerations in network meta-analysis @@ -182,24 +207,28 @@ enums: meaning: mesh:D000099094 mesh:D002363: title: Case Reports - description: Clinical presentations that may be followed by evaluative studies + description: + Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis. meaning: mesh:D002363 mesh:D003160: title: Comparative Study - description: Comparison of outcomes, results, responses, etc for different + description: + Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs. meaning: mesh:D003160 mesh:D016426: title: Scientific Integrity Review - description: Work consisting of reports by the United States Office of Research + description: + Work consisting of reports by the United States Office of Research Integrity, identifying questionable research published in articles or books. Notification of the questionable data is carried in the NIH Guide for Grants and Contracts. meaning: mesh:D016426 mesh:D016429: title: Clinical Conference - description: Work that consists of a conference of physicians on their observations + description: + Work that consists of a conference of physicians on their observations of a patient at the bedside, regarding the physical state, laboratory and other diagnostic findings, clinical manifestations, results of current therapy, etc. A clinical conference usually ends with a confirmation or correction @@ -208,7 +237,8 @@ enums: meaning: mesh:D016429 mesh:D016430: title: Clinical Trial - description: A work that reports on the results of a clinical study in which + description: + A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive @@ -218,23 +248,27 @@ enums: meaning: mesh:D016430 mesh:D016446: title: Consensus Development Conference - description: Official statements of the findings or recommendations expressing + description: + Official statements of the findings or recommendations expressing the outcome of a meeting convened to evaluate current thought and research on a subject of interest. meaning: mesh:D016446 mesh:D016447: title: Consensus Development Conference, NIH - description: Official statements of the finding or recommendations expressing + description: + Official statements of the finding or recommendations expressing the outcome from a conference sponsored by NIH. meaning: mesh:D016447 mesh:D016448: title: Multicenter Study - description: A work that reports on a study executed by several cooperating + description: + A work that reports on a study executed by several cooperating institutions. meaning: mesh:D016448 mesh:D016449: title: Randomized Controlled Trial - description: A work that reports on a clinical trial that involves at least + description: + A work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of @@ -242,7 +276,8 @@ enums: meaning: mesh:D016449 mesh:D017418: title: Meta-Analysis - description: Works consisting of studies using a quantitative method of combining + description: + Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview @@ -251,7 +286,8 @@ enums: meaning: mesh:D017418 mesh:D017426: title: Clinical Trial, Phase I - description: Work that is the report of a pre-planned, usually controlled, + description: + Work that is the report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on a small number of healthy persons and conducted over the period of about a year in either the United @@ -259,7 +295,8 @@ enums: meaning: mesh:D017426 mesh:D017427: title: Clinical Trial, Phase II - description: Work that is a report of a pre-planned, usually controlled, clinical + description: + Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on several hundred volunteers, including a limited number of patients, and conducted over a period of about two years @@ -267,7 +304,8 @@ enums: meaning: mesh:D017427 mesh:D017428: title: Clinical Trial, Phase III - description: Work that is a report of a pre-planned, usually controlled, clinical + description: + Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques after phase II trials. A large enough group of patients is studied and closely monitored by physicians for adverse response @@ -276,7 +314,8 @@ enums: meaning: mesh:D017428 mesh:D017429: title: Clinical Trial, Phase IV - description: Work that is a report of a planned post-marketing study of diagnostic, + description: + Work that is a report of a planned post-marketing study of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques that have been approved for general sale after clinical trials, phases I, II, and III. These studies, conducted in the United States or a foreign country, often @@ -284,12 +323,14 @@ enums: meaning: mesh:D017429 mesh:D018486: title: Twin Study - description: Work consisting of reporting using a method of detecting genetic + description: + Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins. meaning: mesh:D018486 mesh:D018848: title: Controlled Clinical Trial - description: A work that reports on a clinical trial involving one or more + description: + A work that reports on a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or @@ -302,23 +343,27 @@ enums: meaning: mesh:D018848 mesh:D023361: title: Validation Study - description: Works consisting of research using processes by which the reliability + description: + Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established. meaning: mesh:D023361 mesh:D023362: title: Evaluation Study - description: Works consisting of studies determining the effectiveness or + description: + Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment. meaning: mesh:D023362 mesh:D064888: title: Observational Study - description: A work that reports on the results of a clinical study in which + description: + A work that reports on the results of a clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study). meaning: mesh:D064888 mesh:D065007: title: Pragmatic Clinical Trial - description: Randomized clinical trials that compare interventions in clinical + description: + Randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts. meaning: mesh:D065007 diff --git a/src/common_access_model/schema/enums/EnumSubjectType.yaml b/src/common_access_model/schema/enums/EnumSubjectType.yaml index c0b9933..f1ae4d1 100644 --- a/src/common_access_model/schema/enums/EnumSubjectType.yaml +++ b/src/common_access_model/schema/enums/EnumSubjectType.yaml @@ -16,23 +16,22 @@ enums: title: Participant description: Study participant with consent, assent, or waiver of consent. aliases: - - participant + - participant CAMO:0000025: title: Non-Participant description: An individual not directly participating in a study, eg, the subject of a reported family history. aliases: - - non_participant + - non_participant CAMO:0000026: title: Cell Line aliases: - - cell_line + - cell_line CAMO:0000027: title: Animal Model aliases: - - animal_model + - animal_model CAMO:0000028: title: Group description: A group of entities or things being assessed as a whole. aliases: - - group - + - group diff --git a/src/common_access_model/schema/enums/EnumUnknown.yaml b/src/common_access_model/schema/enums/EnumUnknown.yaml index 644b64d..2bf9a8c 100644 --- a/src/common_access_model/schema/enums/EnumUnknown.yaml +++ b/src/common_access_model/schema/enums/EnumUnknown.yaml @@ -8,5 +8,3 @@ enums: title: Unknown aliases: - unknown - - diff --git a/src/common_access_model/schema/enums/EnumUnknownOther.yaml b/src/common_access_model/schema/enums/EnumUnknownOther.yaml index 3f4993b..32a4060 100644 --- a/src/common_access_model/schema/enums/EnumUnknownOther.yaml +++ b/src/common_access_model/schema/enums/EnumUnknownOther.yaml @@ -11,4 +11,4 @@ enums: snomedct:74964007: title: Other aliases: - - other \ No newline at end of file + - other