diff --git a/.codespell-ignore.txt b/.codespell-ignore.txt new file mode 100644 index 0000000..52ada66 --- /dev/null +++ b/.codespell-ignore.txt @@ -0,0 +1 @@ +# This is a test diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3641b7a..7a30674 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,35 +2,46 @@ # https://pre-commit.com/ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: check-toml - id: check-yaml + # mkdocs.yml uses !!python/name tags unsupported by the safe YAML loader + exclude: ^mkdocs\.yml$ - id: end-of-file-fixer + exclude: ^\.copier-answers\.yml$ - id: trailing-whitespace args: [--markdown-linebreak-ext=md] - repo: https://github.com/adrienverge/yamllint.git - rev: v1.37.0 + rev: v1.38.0 hooks: - id: yamllint args: [-c=.yamllint.yaml] + exclude: | + (?x)^( + \.copier-answers\.yml| + docs/schema/.*\.yaml| + src/include_access_model/schema/upstream-models/.*\.yaml + )$ + verbose: true # Show warnings. - repo: https://github.com/codespell-project/codespell - rev: v2.4.1 + rev: v2.4.2 hooks: - id: codespell additional_dependencies: - tomli + exclude: ^src/include_access_model/schema/upstream-models/.*\.yaml$ - repo: https://github.com/crate-ci/typos - rev: v1.31.1 + rev: v1.46.3 hooks: - id: typos - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.11.3 + rev: v0.15.14 hooks: # Run the linter. - id: ruff @@ -40,6 +51,6 @@ repos: - repo: https://github.com/astral-sh/uv-pre-commit # uv version. - rev: 0.6.12 + rev: 0.11.16 hooks: - id: uv-lock diff --git a/.yamllint.yaml b/.yamllint.yaml index f44a825..396c7a3 100644 --- a/.yamllint.yaml +++ b/.yamllint.yaml @@ -2,6 +2,14 @@ extends: default +# Specify files to ignore. +ignore: + # Ignore autogenerated file that does not conform to yamllint rules. + - .copier-answers.yml + # Ignore schema files that may not conform due to imports. + - docs/schema/*.yaml + - src/include_access_model/schema/upstream-models/*.yaml + rules: document-start: disable # Don't check if document has a start marker (---). line-length: diff --git a/COLLABORATORS.md b/COLLABORATORS.md index 369c165..2d484a8 100644 --- a/COLLABORATORS.md +++ b/COLLABORATORS.md @@ -3,7 +3,7 @@ This repository serves as a downstream model designed to specialize the [Common Access Model](https://github.com/include-dcc/common-access-model). A pinned version of this upstream model is captured in -src/kf_access_model/schema/upstream-models/common_access_model*.yaml. +src/include_access_model/schema/upstream-models/common_access_model*.yaml. The purpose of this model is to build out a program-specific extension (or profile) by importing the core elements and layering the INCLUDE unique data @@ -36,10 +36,10 @@ just update-cam ``` This recipe will download the newest version to the directory, -src/kf_access_model/schema/upstream-models and create a symbolic link from the -common name, common_access_model.yaml. As a result, once that one entry has been -made to the local model, subsequent updates should work without further updates -to the model itself. +src/include_access_model/schema/upstream-models and create a symbolic link from +the common name, common_access_model.yaml. As a result, once that one entry has +been made to the local model, subsequent updates should work without further +updates to the model itself. ```model-yaml imports: diff --git a/_typos.toml b/_typos.toml new file mode 100644 index 0000000..1eeccdc --- /dev/null +++ b/_typos.toml @@ -0,0 +1,15 @@ +[files] +extend-exclude = [ + "_typos.toml", + ".git*", +] + +# 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 01f2b06..cdafa66 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 5639786..fd2f3b9 100644 --- a/project.justfile +++ b/project.justfile @@ -37,3 +37,7 @@ expand: [group('model development')] clear file_path: uv run weaver --clear src/common_access_model/schema/enums/{{file_path}}.yaml + +[group('project management')] +precommit: + pre-commit install diff --git a/pyproject.toml b/pyproject.toml index fd08961..206bef6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ testpaths = ["tests"] # https://docs.astral.sh/ruff/configuration/ [tool.ruff] exclude = [ - "src/kf_access_model/_version.py", + "src/include_access_model/_version.py", ] # Ref.: https://github.com/codespell-project/codespell @@ -63,10 +63,12 @@ skip = [ "LICENSE", "pyproject.toml", "uv.lock", + "_typos.toml", "project/*", "src/include_access_model/datamodel/include_access_model_pydantic.py", "src/include_access_model/datamodel/include_access_model_sqla.py", "src/include_access_model/datamodel/include_access_model.py", + "./src/include_access_model/schema/upstream-models/*.yaml" ] # Reminder: words have to be lowercased for the ignore-words-list diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index be987b8..86f86c5 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -4,11 +4,11 @@ title: INCLUDE DCC Access Model description: LinkML Schema for the internal INCLUDE DCC Access Model license: MIT see_also: -- https://includedcc.github.io/include-access-model + - https://includedcc.github.io/include-access-model prefixes: includedcc: https://includedcc.org/include-access-model/ - # subset of CDC Race and Ethnicity Code Set Version 1.0 + # subset of CDC Race and Ethnicity Code Set Version 1.0 cdc_race_eth: urn:oid:2.16.840.1.113883.6.238/ ig_dob_method: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-date-of-birth-method/ igcondtype: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/condition-type/ @@ -84,14 +84,14 @@ default_prefix: includedcc default_range: linkml:string imports: -- upstream-models/common_access_model-0.0.7 + - upstream-models/common_access_model-0.2.0 classes: IncludeParticipant: title: INCLUDE Participant description: Information specific to INCLUDE participants is_a: Demographics slots: - - down_syndrome_status + - down_syndrome_status slots: down_syndrome_status: diff --git a/src/include_access_model/schema/upstream-models/common_access_model-0.0.7.yaml b/src/include_access_model/schema/upstream-models/common_access_model-0.2.0.yaml similarity index 96% rename from src/include_access_model/schema/upstream-models/common_access_model-0.0.7.yaml rename to src/include_access_model/schema/upstream-models/common_access_model-0.2.0.yaml index d8e321a..88f850b 100644 --- a/src/include_access_model/schema/upstream-models/common_access_model-0.0.7.yaml +++ b/src/include_access_model/schema/upstream-models/common_access_model-0.2.0.yaml @@ -469,7 +469,7 @@ enums: title: protein-protein interaction detection assay OBI:0000291: text: OBI:0000291 - 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 title: transcription factor binding site assay @@ -638,7 +638,7 @@ enums: title: chain termination sequencing assay OBI:0000697: text: OBI:0000697 - 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 @@ -797,7 +797,7 @@ enums: OBI:0000854: text: OBI:0000854 description: An analyte assay that detects specific peptides in an input material - by separating it using gel electrophoresis, transfering the separated molecules + 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 @@ -806,7 +806,7 @@ enums: text: OBI:0000860 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. @@ -822,7 +822,7 @@ enums: text: OBI:0000870 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 title: single-nucleotide-resolution nucleic acid structure mapping assay OBI:0000871: @@ -870,7 +870,7 @@ enums: title: in vivo cell killing assay OBI:0000891: text: OBI:0000891 - 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 title: cell proliferation assay @@ -1066,7 +1066,7 @@ enums: OBI:0001015: text: OBI:0001015 description: A single-nucleotide-resolution nucleic acid structure mapping - assay which determins nucleic acid secondary structure at a nucleotide resolution + assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe meaning: OBI:0001015 title: DMS structure mapping assay @@ -1191,7 +1191,7 @@ enums: OBI:0001145: text: OBI:0001145 description: A 3D molecular structure determination assay in which a complex - of 2 or more molecular enties is characterized which provides information + of 2 or more molecular entries is characterized which provides information on their binding configuration. meaning: OBI:0001145 title: 3D structure determination of bound molecular complex assay @@ -1503,7 +1503,7 @@ enums: cytokine production by T cells OBI:0001247: text: OBI:0001247 - description: A genotyping assay that uses a high througput sequencer + description: A genotyping assay that uses a high throughput sequencer meaning: OBI:0001247 title: genotyping by high throughput sequencing assay OBI:0001248: @@ -2358,7 +2358,7 @@ enums: text: OBI:0001476 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 + followed by screening for cells that bind a protein of interest, and identifying the sequence of infecting phages to determine a suitable binding partner. meaning: OBI:0001476 title: phage display binding assay @@ -2806,7 +2806,7 @@ enums: OBI:0001591: text: OBI:0001591 description: A binding assay that measures the formation or disassociation - of a complex of 2 material entities directly without use of a competitve + of a complex of 2 material entities directly without use of a competitive ligand. meaning: OBI:0001591 title: direct binding assay @@ -2969,7 +2969,7 @@ enums: 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 - intrisic fluorescence of aromatic (tryptophan) residues on the binding site + intrinsic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). meaning: OBI:0001635 @@ -3028,7 +3028,7 @@ enums: OBI:0001646: text: OBI:0001646 description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody + that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex meaning: OBI:0001646 title: electron microscopy assay determining the 3D structure of a B cell @@ -3194,7 +3194,7 @@ enums: OBI:0001669: text: OBI:0001669 description: An assay that measures protein-protein interactions by separating - target proteins on an SDS-PAGE gel, transfering them to a solid substrate, + 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 @@ -3565,7 +3565,7 @@ enums: OBI:0001738: text: OBI:0001738 description: A X-ray crystallography 3D molecular structure determination - assay that characterizes the 3-dimensional molecular structrue of a B cell + assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex. meaning: OBI:0001738 title: X-ray crystallography assay determining the 3D structure of a B cell @@ -4411,7 +4411,7 @@ enums: OBI:0001954: text: OBI:0001954 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 + 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 @@ -4444,7 +4444,7 @@ enums: OBI:0001978: text: OBI:0001978 description: An analyte assay that detects specific molecules in an input - material by separating it using gel electrophoresis, transfering the separated + 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 @@ -4788,7 +4788,7 @@ enums: text: OBI:0002055 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 title: assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -4920,7 +4920,7 @@ enums: title: assay measuring T cell epitope specific suppression in vitro OBI:0002075: text: OBI:0002075 - 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 @@ -5407,7 +5407,7 @@ enums: text: OBI:0002176 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 title: electrophysiology assay @@ -5758,7 +5758,7 @@ enums: OBI:0002635: text: OBI:0002635 description: An efficacy of T cell epitope intervention experiment that detects - a decrease in disease after adoptive transfer of epitope specfic T cells. + a decrease in disease after adoptive transfer of epitope specific T cells. meaning: OBI:0002635 title: in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells @@ -5773,7 +5773,7 @@ enums: OBI:0002637: text: OBI:0002637 description: An efficacy of T cell epitope intervention experiment that uses - a epitope protection experiment after adoptive transfer of epitope specfic + a epitope protection experiment after adoptive transfer of epitope specific T cells. meaning: OBI:0002637 title: in vivo assay measuring T cell epitope specific protection from challenge @@ -5844,7 +5844,7 @@ enums: text: OBI:0002645 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 title: in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells @@ -5895,14 +5895,14 @@ enums: text: OBI:0002667 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 title: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells OBI:0002668: text: OBI:0002668 description: A T cell epitope specific proliferation assay that is performed - in vivo after adoptive transfer of epitope specfic T cells. + in vivo after adoptive transfer of epitope specific T cells. meaning: OBI:0002668 title: in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells @@ -5910,7 +5910,7 @@ enums: text: OBI:0002669 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 title: assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope @@ -5919,7 +5919,7 @@ enums: text: OBI:0002670 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 title: assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope @@ -5948,7 +5948,7 @@ enums: OBI:0002676: text: OBI:0002676 description: An efficacy of T cell epitope intervention experiment that is - performed after adoptive transfer of epitope specfic T cells. + performed after adoptive transfer of epitope specific T cells. meaning: OBI:0002676 title: in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells @@ -5963,7 +5963,7 @@ enums: text: OBI:0002678 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 title: in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells @@ -6515,7 +6515,7 @@ enums: description: A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. meaning: OBI:0002964 - title: KiNativ assay + title: KiNative assay OBI:0002965: text: OBI:0002965 description: A type of transcription profiling assay in which a set of landmark @@ -6625,9 +6625,9 @@ enums: title: ionized calcium assay OBI:0003013: text: OBI:0003013 - description: An analyte assay that measures the abundance of transferrin + description: An analyte assay that measures the abundance of transferring meaning: OBI:0003013 - title: transferrin assay + title: transferring assay OBI:0003014: text: OBI:0003014 description: An analyte assay that measures the abundance of uric acid @@ -6962,7 +6962,7 @@ enums: OBI:0003106: text: OBI:0003106 description: A fluorescence in-situ hybridization assay that involves ultra-resolution - imaging of cell activity by targetting thousands of single molecules with + 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. @@ -6996,7 +6996,7 @@ enums: description: An analyte assay that uses aptamers to detect protein analytes in serum. meaning: OBI:0003111 - title: SOMAscan assay + title: SOMEAscan assay OBI:0003112: text: OBI:0003112 description: A proximity extension assay that uses quantitative polymerase @@ -7077,7 +7077,7 @@ enums: title: neuron morphology reconstruction assay OBI:0003127: text: OBI:0003127 - 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. @@ -7085,7 +7085,7 @@ enums: title: B cell epitope assay OBI:0003128: text: OBI:0003128 - 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. @@ -8366,14 +8366,14 @@ enums: title: heel to shin assessment OBI:0003513: text: OBI:0003513 - 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 title: muscle atrophy assessment OBI:0003514: text: OBI:0003514 description: A functional assessment of an individual's ability to perform - muscle movement to overcome gravity or physical resistence. + muscle movement to overcome gravity or physical resistance. meaning: OBI:0003514 title: muscle weakness assessment OBI:0003515: @@ -8489,7 +8489,7 @@ enums: title: lower limb coordination assessment OBI:0003533: text: OBI:0003533 - 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 @@ -8508,7 +8508,7 @@ enums: title: deep tendon reflex assessment of the knee joint OBI:0003536: text: OBI:0003536 - description: A physical examination of an organism through visual assesment. + description: A physical examination of an organism through visual assessment. meaning: OBI:0003536 title: observational assessment of individual OBI:0003537: @@ -8677,7 +8677,7 @@ enums: OBI:0003612: text: OBI:0003612 description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR + that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. meaning: OBI:0003612 title: electron microscopy assay determining the 3D structure of a T cell @@ -8685,7 +8685,7 @@ enums: OBI:0003613: text: OBI:0003613 description: An electron-microscopy 3D molecular structure determination assay - that characterizes the 3-dimensional molecular structrue of a MHC:ligand + that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. meaning: OBI:0003613 title: electron microscopy assay determining the 3D structure of a MHC:ligand @@ -9724,7 +9724,7 @@ enums: text: OBI:1110128 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 title: immune epitope assay @@ -10691,10 +10691,10 @@ enums: title: venous blood carbon dioxide assay OBI:2100135: text: OBI:2100135 - description: An analyte assay that measures the abundance of transferrin in + description: An analyte assay that measures the abundance of transferring in venous blood meaning: OBI:2100135 - title: venous blood transferrin assay + title: venous blood transferring assay OBI:2100136: text: OBI:2100136 description: An analyte assay that measures the abundance of sodium in venous @@ -11505,75 +11505,75 @@ enums: OBI:2100271: text: OBI:2100271 description: An analyte assay that measures the abundance of sodium in arterial - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100271 - title: ABL90 panel arterial blood sodium assay + title: ABLE90 panel arterial blood sodium assay OBI:2100272: text: OBI:2100272 description: An analyte assay that measures the abundance of oxygen in arterial - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100272 - title: ABL90 panel arterial blood oxygen assay + title: ABLE90 panel arterial blood oxygen assay OBI:2100273: text: OBI:2100273 description: An analyte assay that measures the abundance of glucose in arterial - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100273 - title: ABL90 panel arterial blood glucose assay + title: ABLE90 panel arterial blood glucose assay OBI:2100274: text: OBI:2100274 description: An assay that measures lactic acid in arterial blood as part - of a ABL90 panel order + of a ABLE90 panel order meaning: OBI:2100274 - title: ABL90 panel arterial blood lactic acid assay + title: ABLE90 panel arterial blood lactic acid assay OBI:2100275: text: OBI:2100275 description: An analyte assay that measures the abundance of hemoglobin in - arterial blood as part of a ABL90 panel order + arterial blood as part of a ABLE90 panel order meaning: OBI:2100275 - title: ABL90 panel arterial blood hemoglobin assay + title: ABLE90 panel arterial blood hemoglobin assay OBI:2100276: text: OBI:2100276 description: An analyte assay that measures the abundance of chloride in arterial - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100276 - title: ABL90 panel arterial blood chloride assay + title: ABLE90 panel arterial blood chloride assay OBI:2100277: text: OBI:2100277 description: An analyte assay that measures the abundance of carbon dioxide - in arterial blood as part of a ABL90 panel order + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100277 - title: ABL90 panel arterial blood carbon dioxide assay + title: ABLE90 panel arterial blood carbon dioxide assay OBI:2100278: text: OBI:2100278 description: A cytometry assay that measures the proportion of red blood cells - in arterial blood as part of a ABL90 panel order + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100278 - title: ABL90 panel arterial blood hematocrit assay + title: ABLE90 panel arterial blood hematocrit assay OBI:2100279: text: OBI:2100279 description: An analyte assay that measures the abundance of calcium in arterial - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100279 - title: ABL90 panel arterial blood calcium assay + title: ABLE90 panel arterial blood calcium assay OBI:2100280: text: OBI:2100280 description: An assay that measures temperature in arterial blood as part - of a ABL90 panel order + of a ABLE90 panel order meaning: OBI:2100280 - title: ABL90 panel arterial blood temperature assay + title: ABLE90 panel arterial blood temperature assay OBI:2100281: text: OBI:2100281 description: An analyte assay that measures the abundance of bicarbonate in - arterial blood as part of a ABL90 panel order + arterial blood as part of a ABLE90 panel order meaning: OBI:2100281 - title: ABL90 panel arterial blood bicarbonate assay + title: ABLE90 panel arterial blood bicarbonate assay OBI:2100282: text: OBI:2100282 description: An analyte assay that measures the abundance of potassium in - arterial blood as part of a ABL90 panel order + arterial blood as part of a ABLE90 panel order meaning: OBI:2100282 - title: ABL90 panel arterial blood potassium assay + title: ABLE90 panel arterial blood potassium assay OBI:2100283: text: OBI:2100283 description: A cytometry assay that measures the count of promyelocytes in @@ -11583,63 +11583,63 @@ enums: OBI:2100284: text: OBI:2100284 description: An analyte assay that measures the abundance of glucose in venous - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100284 - title: ABL90 panel venous blood glucose assay + title: ABLE90 panel venous blood glucose assay OBI:2100285: text: OBI:2100285 description: An analyte assay that measures the abundance of hemoglobin in - venous blood as part of a ABL90 panel order + venous blood as part of a ABLE90 panel order meaning: OBI:2100285 - title: ABL90 panel venous blood hemoglobin assay + title: ABLE90 panel venous blood hemoglobin assay OBI:2100286: text: OBI:2100286 description: An analyte assay that measures the abundance of ionized calcium - in venous blood as part of a ABL90 panel order + in venous blood as part of a ABLE90 panel order meaning: OBI:2100286 - title: ABL90 panel venous blood ionized calcium assay + title: ABLE90 panel venous blood ionized calcium assay OBI:2100287: text: OBI:2100287 description: An analyte assay that measures the abundance of carbon dioxide - in venous blood as part of a ABL90 panel order + in venous blood as part of a ABLE90 panel order meaning: OBI:2100287 - title: ABL90 panel venous blood carbon dioxide assay + title: ABLE90 panel venous blood carbon dioxide assay OBI:2100288: text: OBI:2100288 description: A cytometry assay that measures the proportion of red blood cells - in venous blood as part of a ABL90 panel order + in venous blood as part of a ABLE90 panel order meaning: OBI:2100288 - title: ABL90 panel venous blood hematocrit assay + title: ABLE90 panel venous blood hematocrit assay OBI:2100289: text: OBI:2100289 description: An analyte assay that measures the abundance of sodium in venous - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100289 - title: ABL90 panel venous blood sodium assay + title: ABLE90 panel venous blood sodium assay OBI:2100290: text: OBI:2100290 description: An analyte assay that measures the abundance of oxygen in venous - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100290 - title: ABL90 panel venous blood oxygen assay + title: ABLE90 panel venous blood oxygen assay OBI:2100291: text: OBI:2100291 description: An analyte assay that measures the abundance of bicarbonate in - venous blood as part of a ABL90 panel order + venous blood as part of a ABLE90 panel order meaning: OBI:2100291 - title: ABL90 panel venous blood bicarbonate assay + title: ABLE90 panel venous blood bicarbonate assay OBI:2100292: text: OBI:2100292 description: An assay that measures lactic acid in venous blood as part of - a ABL90 panel order + a ABLE90 panel order meaning: OBI:2100292 - title: ABL90 panel venous blood lactic acid assay + title: ABLE90 panel venous blood lactic acid assay OBI:2100293: text: OBI:2100293 description: An analyte assay that measures the abundance of chloride in venous - blood as part of a ABL90 panel order + blood as part of a ABLE90 panel order meaning: OBI:2100293 - title: ABL90 panel venous blood chloride assay + title: ABLE90 panel venous blood chloride assay OBI:2100294: text: OBI:2100294 description: An analyte assay that measures the abundance of T4 in venous @@ -11655,9 +11655,9 @@ enums: OBI:2100296: text: OBI:2100296 description: An analyte assay that measures the abundance of potassium in - venous blood as part of a ABL90 panel order + venous blood as part of a ABLE90 panel order meaning: OBI:2100296 - title: ABL90 panel venous blood potassium assay + title: ABLE90 panel venous blood potassium assay OBI:2100297: text: OBI:2100297 description: An analyte assay that measures the abundance of sodium in urine @@ -11720,15 +11720,15 @@ enums: OBI:2100307: text: OBI:2100307 description: An analyte assay that measures the abundance of methemoglobin - in venous blood as part of a ABL90 panel order + in venous blood as part of a ABLE90 panel order meaning: OBI:2100307 - title: ABL90 panel venous blood methemoglobin assay + title: ABLE90 panel venous blood methemoglobin assay OBI:2100308: text: OBI:2100308 description: An analyte assay that measures the abundance of methemoglobin - in arterial blood as part of a ABL90 panel order + in arterial blood as part of a ABLE90 panel order meaning: OBI:2100308 - title: ABL90 panel arterial blood methemoglobin assay + title: ABLE90 panel arterial blood methemoglobin assay OBI:2100309: text: OBI:2100309 description: An analyte assay that measures the abundance of valproic acid @@ -17915,10 +17915,10 @@ enums: title: Hierarchy edam:data_2591: text: edam:data_2591 - description: Identifier of an entry from the Brite database of biological + description: Identifier of an entry from the Bright database of biological hierarchies. meaning: edam:data_2591 - title: Brite hierarchy ID + title: Bright hierarchy ID edam:data_2593: text: edam:data_2593 description: A unique identifier for an organism used in the BRENDA database. @@ -19366,7 +19366,7 @@ enums: title: Sequence variations edam:data_3505: text: edam:data_3505 - 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 title: Bibliography edam:data_3509: @@ -20191,10 +20191,10 @@ enums: title: mira edam:format_1630: text: edam:format_1630 - description: Common Assembly Format (CAF). A sequence assembly format including + description: Common Assembly Format (CALF). A sequence assembly format including contigs, base-call qualities, and other metadata. meaning: edam:format_1630 - title: CAF + title: CALF edam:format_1631: text: edam:format_1631 description: Sequence assembly project file EXP format. @@ -20293,9 +20293,9 @@ enums: title: OSCAR format edam:format_1861: text: edam:format_1861 - description: Map of a plasmid (circular DNA) in PlasMapper TextMap format. + description: Map of a plasmid (circular DNA) in PlaysMapper TextMap format. meaning: edam:format_1861 - title: PlasMapper TextMap + title: PlaysMapper TextMap edam:format_1910: text: edam:format_1910 description: Phylogenetic tree Newick (text) format. @@ -22330,9 +22330,9 @@ enums: title: PMML edam:format_3727: text: edam:format_3727 - description: Image file format used by the Open Microscopy Environment (OME). + description: Image file format used by the Open Microscopy Environment (SOME). meaning: edam:format_3727 - title: OME-TIFF + title: SOME-TIFF edam:format_3728: text: edam:format_3728 description: The LocARNA PP format combines sequence or alignment information @@ -22350,7 +22350,7 @@ enums: text: edam:format_3746 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 title: BIOM format @@ -23434,6 +23434,294 @@ enums: name: EnumFamilyRelation description: Definitions of family relations as provided by KIN Ontology. from_schema: https://includedcc.org/common-access-model/EnumFamilyRelation + permissible_values: + KIN:KIN_001: + text: KIN:KIN_001 + description: A relation that indicates that a person is connected to another + biologically or through a socio-legal relationship. + meaning: KIN:KIN_001 + title: isRelativeOf + KIN:KIN_053: + text: KIN:KIN_053 + description: A relation between a person and a child of that person's son. + meaning: KIN:KIN_053 + title: isPaternalGrandparentOf + KIN:KIN_022: + text: KIN:KIN_022 + 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 + title: isAdoptiveParentOf + KIN:KIN_027: + text: KIN:KIN_027 + description: A relation that indicates that a person is the biological mother + of another person. + meaning: KIN:KIN_027 + title: isBiologicalMotherOf + KIN:KIN_039: + text: KIN:KIN_039 + 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 + title: hasGestationalCarrier + KIN:KIN_038: + text: KIN:KIN_038 + 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 + title: isOvumDonorOf + KIN:KIN_051: + text: KIN:KIN_051 + 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 + title: isSeparatedConsanguineousPartnerOf + KIN:KIN_010: + text: KIN:KIN_010 + description: A relation between two people born at the same birth from a single + fertilised ovum that splits. + meaning: KIN:KIN_010 + title: isMonozygoticMultipleBirthSiblingOf + KIN:KIN_055: + text: KIN:KIN_055 + description: A relation between two people that share the same biological + father. + meaning: KIN:KIN_055 + title: isPaternalHalfSiblingOf + KIN:KIN_008: + text: KIN:KIN_008 + description: A relation between two people that have both biological parents + in common. + meaning: KIN:KIN_008 + title: isFullsiblingOf + KIN:KIN_052: + text: KIN:KIN_052 + description: A relation between a person and a child of that person's daughter. + meaning: KIN:KIN_052 + title: isMaternalGrandparentOf + KIN:KIN_028: + text: KIN:KIN_028 + description: A relation that indicates that a person is the biological father + of another person. + meaning: KIN:KIN_028 + title: isBiologicalFatherOf + KIN:KIN_013: + text: KIN:KIN_013 + description: A relation that indicates that a person is the sibling of a parent + of another person. + meaning: KIN:KIN_013 + title: isParentalSiblingOf + KIN:KIN_003: + text: KIN:KIN_003 + description: A relation that indicates that a person is the biological parent + of another person. + meaning: KIN:KIN_003 + title: isBiologicalParentOf + KIN:KIN_059: + text: KIN:KIN_059 + description: A relation between a man and the child of that man's brother. + meaning: KIN:KIN_059 + title: isPaternalUncleOf + KIN:KIN_005: + text: KIN:KIN_005 + 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 + title: isGestationalCarrierOf + KIN:KIN_023: + text: KIN:KIN_023 + 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 + title: isStepParentOf + KIN:KIN_036: + text: KIN:KIN_036 + description: A relation between a person and a parent of that person's parent. + meaning: KIN:KIN_036 + title: isGrandchildOf + KIN:KIN_025: + text: KIN:KIN_025 + 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 + title: isStepSiblingOf + KIN:KIN_058: + text: KIN:KIN_058 + description: A relation between a man and the child of that man's sister. + meaning: KIN:KIN_058 + title: isMaternalUncleOf + KIN:KIN_004: + text: KIN:KIN_004 + description: A relation between a man who donated his sperm and the child. + meaning: KIN:KIN_004 + title: isSpermDonorOf + KIN:KIN_024: + text: KIN:KIN_024 + description: A relation between two people that has all or some of the characteristics + of a sibling relationship. + meaning: KIN:KIN_024 + title: isSiblingFigureOf + KIN:KIN_009: + text: KIN:KIN_009 + description: A relation between two people born at the same birth. + meaning: KIN:KIN_009 + title: isMultipleBirthSiblingOf + KIN:KIN_061: + text: KIN:KIN_061 + description: A relation between a woman and the child of that woman's brother. + meaning: KIN:KIN_061 + title: isPaternalAuntOf + KIN:KIN_060: + text: KIN:KIN_060 + description: A relation between a woman and the child of that woman's sister. + meaning: KIN:KIN_060 + title: isMaternalAuntOf + KIN:KIN_029: + text: KIN:KIN_029 + 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. + meaning: KIN:KIN_029 + title: isMitochondrialDonorOf + KIN:KIN_047: + text: KIN:KIN_047 + description: A relation between a person and a parent of that person's grandparent. + meaning: KIN:KIN_047 + title: isGreatGrandchildOf + KIN:KIN_021: + text: KIN:KIN_021 + 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 + title: isFosterParentOf + KIN:KIN_057: + text: KIN:KIN_057 + 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 + title: isPaternalStepSiblingOf + KIN:KIN_030: + text: KIN:KIN_030 + 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 + title: isConsanguineousPartnerOf + KIN:KIN_046: + text: KIN:KIN_046 + 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 + title: hasParentalSibling + KIN:KIN_012: + text: KIN:KIN_012 + description: A relation between two people that have a single biological parent + in common. + meaning: KIN:KIN_012 + title: isHalfSiblingOf + KIN:KIN_014: + text: KIN:KIN_014 + description: A relation between a person and a child of that person's uncle + or aunt. + meaning: KIN:KIN_014 + title: isCousinOf + KIN:KIN_015: + text: KIN:KIN_015 + description: A relation between a person and a child of that person's mother's + sibling. + meaning: KIN:KIN_015 + title: isMaternalCousinOf + KIN:KIN_050: + text: KIN:KIN_050 + 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 + title: isSeparatedPartnerOf + KIN:KIN_056: + text: KIN:KIN_056 + 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 + title: isMaternalStepSiblingOf + KIN:KIN_032: + text: KIN:KIN_032 + description: A relation that indicates that a person is the biological child + of another person. + meaning: KIN:KIN_032 + title: isBiologicalChildOf + KIN:KIN_020: + text: KIN:KIN_020 + 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 + title: isParentFigureOf + KIN:KIN_007: + text: KIN:KIN_007 + description: A relation between two people that have one or both biological + parents in common. + meaning: KIN:KIN_007 + title: isBiologicalSiblingOf + KIN:KIN_002: + text: KIN:KIN_002 + description: A relation that indicates that a person is related to another + person biologically. + meaning: KIN:KIN_002 + title: isBiologicalRelativeOf + KIN:KIN_018: + text: KIN:KIN_018 + description: A relation between a person and a child of that person's grandchild. + meaning: KIN:KIN_018 + title: isGreatGrandparentOf + KIN:KIN_011: + text: KIN:KIN_011 + 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 + title: isPolyzygoticMultipleBirthSiblingOf + KIN:KIN_006: + text: KIN:KIN_006 + 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 + title: isSurrogateOvumDonorOf + KIN:KIN_017: + text: KIN:KIN_017 + description: A relation between a person and a child of that person's child. + meaning: KIN:KIN_017 + title: isGrandparentOf + KIN:KIN_016: + text: KIN:KIN_016 + description: A relation between a person and a child of that person's father's + sibling. + meaning: KIN:KIN_016 + title: isPaternalCousinOf + KIN:KIN_026: + text: KIN:KIN_026 + description: A socio-legal relationship between two people who live together + and share a common domestic life. + meaning: KIN:KIN_026 + title: isPartnerOf + KIN:KIN_019: + text: KIN:KIN_019 + description: A social or legal relationship between two people, for example, + an adoptive parent. + meaning: KIN:KIN_019 + title: isSocialLegalRelativeOf + KIN:KIN_054: + text: KIN:KIN_054 + description: A relation between two people that share the same biological + mother. + meaning: KIN:KIN_054 + title: isMaternalHalfSiblingOf reachable_from: source_ontology: http://purl.org/ga4gh/kin.owl source_nodes: @@ -23564,6 +23852,35 @@ enums: name: EnumLaterality description: Laterality information for the site from_schema: https://includedcc.org/common-access-model/EnumLaterality + permissible_values: + HP:0012832: + text: HP:0012832 + description: Being present on both sides of the body. + meaning: HP:0012832 + title: Bilateral + HP:0012833: + text: HP:0012833 + description: Being present on only the left or only the right side of the + body. + meaning: HP:0012833 + title: Unilateral + HP:0012834: + text: HP:0012834 + description: Being located on the right side of the body. + meaning: HP:0012834 + title: Right + HP:0012835: + text: HP:0012835 + description: Being located on the left side of the body. + meaning: HP:0012835 + title: Left + HP:4000152: + text: HP:4000152 + 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 + title: Alternating laterality reachable_from: source_ontology: bioregistry:hp source_nodes: @@ -23594,6 +23911,121 @@ enums: Pediatric Terminology. https://evs.nci.nih.gov/ftp1/Pediatric_Terminologies/NICHD/About.html title: Participant Lifespan Stage from_schema: https://includedcc.org/common-access-model/EnumParticipantLifespanStage + permissible_values: + NCIT:C176390: + text: NCIT:C176390 + description: The transitional period of life between immature and mature reproductive + states. + meaning: NCIT:C176390 + title: Peripubertal + NCIT:C199314: + text: NCIT:C199314 + description: A time period in the human lifespan when full physical and intellectual + maturity have been attained, which generally follows adolescence. + meaning: NCIT:C199314 + title: Adulthood + NCIT:C39298: + text: NCIT:C39298 + 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 + title: Adolescence + NCIT:C89331: + text: NCIT:C89331 + 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 + title: Early Adolescence + NCIT:C89344: + text: NCIT:C89344 + 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 + title: Late Adolescence + NCIT:C89345: + text: NCIT:C89345 + description: A time period that begins at the beginning of the human embryonic + stage and continues until the end of adolescence. + meaning: NCIT:C89345 + title: Childhood + NCIT:C89346: + text: NCIT:C89346 + description: A human life stage that begins at two years of age and continues + until five complete years of age. + meaning: NCIT:C89346 + title: Early Childhood + NCIT:C89347: + text: NCIT:C89347 + description: A human life stage that begins at six years of age and continues + until eleven complete years of age. + meaning: NCIT:C89347 + title: Middle Childhood + NCIT:C89885: + text: NCIT:C89885 + 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 + title: Fetal Stage + NCIT:C89887: + text: NCIT:C89887 + description: A human life stage that begins at full term birth and continues + until twenty-seven complete days of age. + meaning: NCIT:C89887 + title: Full Term Neonatal Stage + NCIT:C89888: + text: NCIT:C89888 + 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 + title: Preterm Neonatal Stage + NCIT:C89889: + text: NCIT:C89889 + description: A human life stage that begins at birth and continues until twelve + complete months of age. + meaning: NCIT:C89889 + title: Infancy + NCIT:C89890: + text: NCIT:C89890 + description: A human life stage that begins at thirteen months of age and + continues until twenty-four complete months of age. + meaning: NCIT:C89890 + title: Toddler Stage + NCIT:C90337: + text: NCIT:C90337 + description: The period of time during a female's reproductive years that + she functions as a mother. + meaning: NCIT:C90337 + title: Maternal Life Stage + NCIT:C90338: + text: NCIT:C90338 + description: The stage in the life of a mother after she has given birth. + meaning: NCIT:C90338 + title: Maternal Postnatal Stage + NCIT:C90339: + text: NCIT:C90339 + description: The stage in the life of a mother during which she is pregnant. + meaning: NCIT:C90339 + title: Maternal Prenatal Stage + NCIT:C90340: + text: NCIT:C90340 + description: The stage in the life of a female during which she is attempting + to get pregnant. + meaning: NCIT:C90340 + title: Maternal Preconception Stage + NCIT:C99135: + text: NCIT:C99135 + 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 + title: Embryonic Stage reachable_from: source_ontology: bioregistry:ncit source_nodes: @@ -23670,7 +24102,7 @@ enums: https://www.nih.gov/include-project: text: https://www.nih.gov/include-project description: The INCLUDE (INvestigation of Co-occurring conditions across - the Lifespan to Understand Down syndromE) Project was launched in June 2018 + 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. @@ -23774,6 +24206,554 @@ enums: name: EnumSampleCollectionMethod description: The approach used to collect the biospecimen. from_schema: https://includedcc.org/common-access-model/EnumSampleCollectionMethod + permissible_values: + snomedct:1048003: + text: snomedct:1048003 + meaning: snomedct:1048003 + title: Capillary specimen collection + snomedct:113031002: + text: snomedct:113031002 + meaning: snomedct:113031002 + title: Urine specimen collection, 2 hours + snomedct:115985003: + text: snomedct:115985003 + meaning: snomedct:115985003 + title: Sweat collection by iontophoresis procedure + snomedct:1202027002: + text: snomedct:1202027002 + meaning: snomedct:1202027002 + title: Collection of esophageal cells via swallowable cell collection sponge + in capsule (procedure) + snomedct:1230332003: + text: snomedct:1230332003 + meaning: snomedct:1230332003 + title: Collection of blood from umbilical cord immediately after delivery + snomedct:1255865009: + text: snomedct:1255865009 + meaning: snomedct:1255865009 + title: Aspiration of seminal fluid from seminal vesicle using ultrasonographic + guidance (procedure) + snomedct:1285339005: + text: snomedct:1285339005 + meaning: snomedct:1285339005 + title: Aspiration of seminal fluid from testis + snomedct:1359755003: + text: snomedct:1359755003 + meaning: snomedct:1359755003 + title: Taking eye swab + snomedct:13677008: + text: snomedct:13677008 + meaning: snomedct:13677008 + title: Urine specimen collection, closed drainage + snomedct:16631761000119104: + text: snomedct:16631761000119104 + meaning: snomedct:16631761000119104 + title: Collection of blood via implanted venous access device + snomedct:174653005: + text: snomedct:174653005 + meaning: snomedct:174653005 + title: Endoscopic retrograde pancreatography with collection of pancreatic + juice + snomedct:19867003: + text: snomedct:19867003 + meaning: snomedct:19867003 + title: Collection of sputum, Lukens tube + snomedct:21217000: + text: snomedct:21217000 + meaning: snomedct:21217000 + title: Collection of pinworm specimen + snomedct:225098009: + text: snomedct:225098009 + meaning: snomedct:225098009 + title: Collection of sample of saliva + snomedct:225105004: + text: snomedct:225105004 + meaning: snomedct:225105004 + title: Collection of stool specimen + snomedct:225109005: + text: snomedct:225109005 + meaning: snomedct:225109005 + title: Collection of nephrostomy urine specimen + snomedct:225110000: + text: snomedct:225110000 + meaning: snomedct:225110000 + title: Collection of ureterostomy urine specimen + snomedct:225111001: + text: snomedct:225111001 + meaning: snomedct:225111001 + title: Collection of early morning urine specimen + snomedct:225112008: + text: snomedct:225112008 + meaning: snomedct:225112008 + title: Overnight collection of urine + snomedct:225113003: + text: snomedct:225113003 + meaning: snomedct:225113003 + title: Timed urine collection + snomedct:225271002: + text: snomedct:225271002 + meaning: snomedct:225271002 + title: Collection of mid-stream specimen of urine + snomedct:225709000: + text: snomedct:225709000 + meaning: snomedct:225709000 + title: Taking cough swab + snomedct:225711009: + text: snomedct:225711009 + meaning: snomedct:225711009 + title: Collection of nasal pharyngeal aspirate + snomedct:225997002: + text: snomedct:225997002 + meaning: snomedct:225997002 + title: Taking wound swab + snomedct:23248003: + text: snomedct:23248003 + meaning: snomedct:23248003 + title: Taking swab for microbiology + snomedct:235488002: + text: snomedct:235488002 + meaning: snomedct:235488002 + title: Collection of pancreatic juice + snomedct:235569007: + text: snomedct:235569007 + meaning: snomedct:235569007 + title: Collection of bile + snomedct:236363003: + text: snomedct:236363003 + meaning: snomedct:236363003 + title: Semen aspiration + snomedct:236364009: + text: snomedct:236364009 + meaning: snomedct:236364009 + title: Micro-epididymal spermatozoa aspiration + snomedct:243772004: + text: snomedct:243772004 + meaning: snomedct:243772004 + title: Thumb-prick sampling + snomedct:243776001: + text: snomedct:243776001 + meaning: snomedct:243776001 + title: Blood sampling from extracorporeal blood circuit + snomedct:243777005: + text: snomedct:243777005 + meaning: snomedct:243777005 + title: Blood sampling from hemodialysis circuit (procedure) + snomedct:243778000: + text: snomedct:243778000 + meaning: snomedct:243778000 + title: Arterial port blood sampling during hemodialysis (procedure) + snomedct:243779008: + text: snomedct:243779008 + meaning: snomedct:243779008 + title: Venous port blood sampling during hemodialysis (procedure) + snomedct:243780006: + text: snomedct:243780006 + meaning: snomedct:243780006 + title: Blood sampling from cardiopulmonary bypass circuit + snomedct:243781005: + text: snomedct:243781005 + meaning: snomedct:243781005 + title: Blood sampling from ECMO circuit + snomedct:24469009: + text: snomedct:24469009 + meaning: snomedct:24469009 + title: Collection of routine urine specimen for laboratory + snomedct:2475000: + text: snomedct:2475000 + meaning: snomedct:2475000 + title: Urine specimen collection, 24 hours + snomedct:276907003: + text: snomedct:276907003 + meaning: snomedct:276907003 + title: Percutaneous aspiration of spermatozoa + snomedct:278450005: + text: snomedct:278450005 + meaning: snomedct:278450005 + title: Finger stick + snomedct:285570007: + text: snomedct:285570007 + meaning: snomedct:285570007 + title: Taking of swab + snomedct:285586000: + text: snomedct:285586000 + meaning: snomedct:285586000 + title: Taking swab for Chlamydia test + snomedct:285589007: + text: snomedct:285589007 + meaning: snomedct:285589007 + title: Endocervical swab + snomedct:301805004: + text: snomedct:301805004 + meaning: snomedct:301805004 + title: Taking high vaginal swab + snomedct:301874004: + text: snomedct:301874004 + meaning: snomedct:301874004 + title: Taking vaginal swab + snomedct:304991003: + text: snomedct:304991003 + meaning: snomedct:304991003 + title: Take mouth swab + snomedct:310216004: + text: snomedct:310216004 + meaning: snomedct:310216004 + title: Collection of sample from mouth + snomedct:310217008: + text: snomedct:310217008 + meaning: snomedct:310217008 + title: Collection of gingival crevicular fluid sample + snomedct:312645003: + text: snomedct:312645003 + meaning: snomedct:312645003 + title: Percutaneous epididymal aspiration of spermatozoa + snomedct:312855001: + text: snomedct:312855001 + meaning: snomedct:312855001 + title: Taking conjunctival swab + snomedct:312873003: + text: snomedct:312873003 + meaning: snomedct:312873003 + title: Taking vulval swab + snomedct:312874009: + text: snomedct:312874009 + meaning: snomedct:312874009 + title: Taking penile swab + snomedct:312875005: + text: snomedct:312875005 + meaning: snomedct:312875005 + title: Taking cervical swab + snomedct:312876006: + text: snomedct:312876006 + meaning: snomedct:312876006 + title: Taking urethral swab + snomedct:312877002: + text: snomedct:312877002 + meaning: snomedct:312877002 + title: Taking low vaginal swab + snomedct:312878007: + text: snomedct:312878007 + meaning: snomedct:312878007 + title: Taking postnasal swab + snomedct:312879004: + text: snomedct:312879004 + meaning: snomedct:312879004 + title: Taking ear swab + snomedct:312880001: + text: snomedct:312880001 + meaning: snomedct:312880001 + title: Taking throat swab + snomedct:312881002: + text: snomedct:312881002 + meaning: snomedct:312881002 + title: Taking skin swab + snomedct:312882009: + text: snomedct:312882009 + meaning: snomedct:312882009 + title: Taking nasal swab + snomedct:313273004: + text: snomedct:313273004 + meaning: snomedct:313273004 + title: Taking swab for Bordetella pertussis test + snomedct:313274005: + text: snomedct:313274005 + meaning: snomedct:313274005 + title: Taking swab for Respiratory syncytial virus test + snomedct:31507001: + text: snomedct:31507001 + meaning: snomedct:31507001 + title: Specimen collection for microbiology + snomedct:32564009: + text: snomedct:32564009 + meaning: snomedct:32564009 + title: Arterial specimen collection for laboratory test + snomedct:34532003: + text: snomedct:34532003 + meaning: snomedct:34532003 + title: Semen specimen collection + snomedct:37020001: + text: snomedct:37020001 + meaning: snomedct:37020001 + title: Collection of urine and strain for calculus + snomedct:37705003: + text: snomedct:37705003 + meaning: snomedct:37705003 + title: Collection of sputum + snomedct:386087005: + text: snomedct:386087005 + meaning: snomedct:386087005 + title: Collection of aspirated sputum + snomedct:386088000: + text: snomedct:386088000 + meaning: snomedct:386088000 + title: Collection of induced sputum + snomedct:386089008: + text: snomedct:386089008 + meaning: snomedct:386089008 + title: Collection of coughed sputum + snomedct:386099003: + text: snomedct:386099003 + meaning: snomedct:386099003 + title: Spot urine procedure + snomedct:390784004: + text: snomedct:390784004 + meaning: snomedct:390784004 + title: Taking endocervical swab for Chlamydia test + snomedct:390785003: + text: snomedct:390785003 + meaning: snomedct:390785003 + title: Taking urethral swab for Chlamydia test + snomedct:400993006: + text: snomedct:400993006 + meaning: snomedct:400993006 + title: Taking cervical swab for Neisseria gonorrhoeae test + snomedct:400994000: + text: snomedct:400994000 + meaning: snomedct:400994000 + title: Taking swab for Neisseria gonorrhoeae test + snomedct:401002001: + text: snomedct:401002001 + meaning: snomedct:401002001 + title: Taking urethral swab for Neisseria gonorrhoeae test + snomedct:40597003: + text: snomedct:40597003 + meaning: snomedct:40597003 + title: Urine specimen collection, 12 hours + snomedct:406173008: + text: snomedct:406173008 + meaning: snomedct:406173008 + title: 'Phlebotomy: cannulated vessel' + snomedct:418622002: + text: snomedct:418622002 + meaning: snomedct:418622002 + title: Taking oral swab + snomedct:42311007: + text: snomedct:42311007 + meaning: snomedct:42311007 + title: Radial artery puncture for laboratory test + snomedct:427133003: + text: snomedct:427133003 + meaning: snomedct:427133003 + title: Endoscopic retrograde cholangiopancreatography with collection of bile + snomedct:439599008: + text: snomedct:439599008 + meaning: snomedct:439599008 + title: Collection of specimen by device + snomedct:441136006: + text: snomedct:441136006 + meaning: snomedct:441136006 + title: Collection of specimen by glass slide + snomedct:441266008: + text: snomedct:441266008 + meaning: snomedct:441266008 + title: Specimen collection by endometrial suction curette + snomedct:441378005: + text: snomedct:441378005 + meaning: snomedct:441378005 + title: Collection of specimen by culture plate + snomedct:444171005: + text: snomedct:444171005 + meaning: snomedct:444171005 + title: Collection of biliary drainage by gravity + snomedct:446232000: + text: snomedct:446232000 + meaning: snomedct:446232000 + title: Collection of bile via biliary T-tube + snomedct:446775007: + text: snomedct:446775007 + meaning: snomedct:446775007 + title: Collection of urine via indwelling urinary catheter + snomedct:44733008: + text: snomedct:44733008 + meaning: snomedct:44733008 + title: Collection of string test + snomedct:450874000: + text: snomedct:450874000 + meaning: snomedct:450874000 + title: Collection of first stream urine specimen + snomedct:45240002: + text: snomedct:45240002 + meaning: snomedct:45240002 + title: Ear lobe stick + snomedct:472859009: + text: snomedct:472859009 + meaning: snomedct:472859009 + title: Taking anal swab for Chlamydia test + snomedct:472860004: + text: snomedct:472860004 + meaning: snomedct:472860004 + title: Taking anal swab for gonorrhea (procedure) + snomedct:472917009: + text: snomedct:472917009 + meaning: snomedct:472917009 + title: Collection of device for submission as specimen + snomedct:473363001: + text: snomedct:473363001 + meaning: snomedct:473363001 + title: Taking of culture from cervix + snomedct:50576009: + text: snomedct:50576009 + meaning: snomedct:50576009 + title: Specimen collection by drainage + snomedct:50753008: + text: snomedct:50753008 + meaning: snomedct:50753008 + title: Brachial artery puncture for laboratory test + snomedct:57617002: + text: snomedct:57617002 + meaning: snomedct:57617002 + title: Urine specimen collection + snomedct:58088002: + text: snomedct:58088002 + meaning: snomedct:58088002 + title: Urine specimen collection via suprapubic approach + snomedct:64860001: + text: snomedct:64860001 + meaning: snomedct:64860001 + title: Collection of sweat test + snomedct:66904006: + text: snomedct:66904006 + meaning: snomedct:66904006 + title: Collection of expired gas, quantitative + snomedct:698007008: + text: snomedct:698007008 + meaning: snomedct:698007008 + title: Collection of early morning mid stream specimen of urine by clean catch + snomedct:698086002: + text: snomedct:698086002 + meaning: snomedct:698086002 + title: Collection of urine via pediatric urine collection bag (procedure) + snomedct:698087006: + text: snomedct:698087006 + meaning: snomedct:698087006 + title: Collection of urine via indwelling suprapubic catheter + snomedct:699873000: + text: snomedct:699873000 + meaning: snomedct:699873000 + title: Collection of blood via arterial catheter + snomedct:70347009: + text: snomedct:70347009 + meaning: snomedct:70347009 + title: Collection of specimen for culture by laboratory + snomedct:705084002: + text: snomedct:705084002 + meaning: snomedct:705084002 + title: Collection of fluid specimen via closed suction drain + snomedct:705156009: + text: snomedct:705156009 + meaning: snomedct:705156009 + title: Collection of urine via straight catheter + snomedct:705172001: + text: snomedct:705172001 + meaning: snomedct:705172001 + title: Collection of cystostomy tube urine specimen + snomedct:707982002: + text: snomedct:707982002 + meaning: snomedct:707982002 + title: Taking throat swab for Chlamydia test + snomedct:707983007: + text: snomedct:707983007 + meaning: snomedct:707983007 + title: Taking throat swab for gonorrhea (procedure) + snomedct:708015008: + text: snomedct:708015008 + meaning: snomedct:708015008 + title: Plucking of hair for microscopy and culture + snomedct:709500005: + text: snomedct:709500005 + meaning: snomedct:709500005 + title: Collection of specimen by cough culture plate + snomedct:71197008: + text: snomedct:71197008 + meaning: snomedct:71197008 + title: Femoral artery puncture for laboratory test + snomedct:713143008: + text: snomedct:713143008 + meaning: snomedct:713143008 + title: Collection of arterial blood specimen + snomedct:720450003: + text: snomedct:720450003 + meaning: snomedct:720450003 + title: Preoperative urine specimen collection + snomedct:722501003: + text: snomedct:722501003 + meaning: snomedct:722501003 + title: Postoperative urine specimen collection + snomedct:732218007: + text: snomedct:732218007 + meaning: snomedct:732218007 + title: Urine specimen collection, 8 hours + snomedct:732221009: + text: snomedct:732221009 + meaning: snomedct:732221009 + title: Urine specimen collection, 48 hours + snomedct:732223007: + text: snomedct:732223007 + meaning: snomedct:732223007 + title: Urine specimen collection, 72 hours + snomedct:732224001: + text: snomedct:732224001 + meaning: snomedct:732224001 + title: Timed stool collection + snomedct:732228003: + text: snomedct:732228003 + meaning: snomedct:732228003 + title: Stool specimen collection, 24 hours + snomedct:732292007: + text: snomedct:732292007 + meaning: snomedct:732292007 + title: Stool specimen collection, 48 hours + snomedct:733478009: + text: snomedct:733478009 + meaning: snomedct:733478009 + title: Collection of specimen by adhesive slide + snomedct:733481004: + text: snomedct:733481004 + meaning: snomedct:733481004 + title: Collection of second void urine specimen + snomedct:73416001: + text: snomedct:73416001 + meaning: snomedct:73416001 + title: Urine specimen collection, clean catch + snomedct:738796001: + text: snomedct:738796001 + meaning: snomedct:738796001 + title: Collection of dried blood spot specimen + snomedct:764928002: + text: snomedct:764928002 + meaning: snomedct:764928002 + title: Collection of fluid specimen + snomedct:764929005: + text: snomedct:764929005 + meaning: snomedct:764929005 + title: Collection of exhaled breath specimen + snomedct:768966009: + text: snomedct:768966009 + meaning: snomedct:768966009 + title: Collection of device tip + snomedct:769401004: + text: snomedct:769401004 + meaning: snomedct:769401004 + title: Collection of body fluid from surgical drain + snomedct:77262006: + text: snomedct:77262006 + meaning: snomedct:77262006 + title: Heel stick + snomedct:82078001: + text: snomedct:82078001 + meaning: snomedct:82078001 + title: Collection of blood specimen for laboratory + snomedct:83917009: + text: snomedct:83917009 + meaning: snomedct:83917009 + title: Specimen collection for microbiology, anaerobic + snomedct:840566006: + text: snomedct:840566006 + meaning: snomedct:840566006 + title: Specimen collection for biobank + snomedct:86326008: + text: snomedct:86326008 + meaning: snomedct:86326008 + title: Collection of sweat test, pediatric overnight (procedure) reachable_from: source_ontology: bioregistry:snomedct source_nodes: @@ -23797,18 +24777,24 @@ enums: title: Male aliases: - male - EnumSite: - name: EnumSite - description: The location of the specimen collection. - from_schema: https://includedcc.org/common-access-model/EnumSite - reachable_from: - source_ontology: bioregistry:snomedct - source_nodes: - - snomedct:442083009 - relationship_types: - - rdfs:subClassOf - is_direct: false - include_self: false + EnumSiteExamples: + name: EnumSiteExamples + description: Example locations of specimen collection. Full list of options can + be found below snomedct:442083009 . + from_schema: https://includedcc.org/common-access-model/EnumSiteExamples + permissible_values: + snomedct:78277001: + text: snomedct:78277001 + meaning: snomedct:78277001 + title: Temporal lobe structure + snomedct:5798000: + text: snomedct:5798000 + meaning: snomedct:5798000 + title: Diaphragm structure + snomedct:71341001: + text: snomedct:71341001 + meaning: snomedct:71341001 + title: Bone structure of femur EnumSpatialQualifiers: name: EnumSpatialQualifiers description: Any spatial/location qualifiers. @@ -27875,6 +28861,105 @@ slots: title: Display String from_schema: https://includedcc.org/common-access-model range: string + display_type: + name: display_type + description: The type of display name, eg, "Preferred". + title: Display Type + from_schema: https://includedcc.org/common-access-model + range: string + deprecation_type: + name: deprecation_type + description: The type of or reason for deprecation, if known. + title: Deprecation Type + from_schema: https://includedcc.org/common-access-model + range: string + replacement_curie: + name: replacement_curie + description: A replacement curie for this deprecated concept, if applicable. + title: Replacement CURIE + from_schema: https://includedcc.org/common-access-model + range: string + language: + name: language + description: The ISO 639 language code of this entity. + title: Language + from_schema: https://includedcc.org/common-access-model + range: string + concept_code: + name: concept_code + description: Identifier as it is defined within the ontology + title: Concept Code + from_schema: https://includedcc.org/common-access-model + range: string + required: true + concept_id: + name: concept_id + description: The OMOP Concept ID for the term, if applicable + title: OMOP Concept ID + from_schema: https://includedcc.org/common-access-model + range: integer + definition: + name: definition + description: Detailed definition or description for the term + title: Definition + from_schema: https://includedcc.org/common-access-model + range: string + vocabulary_id: + name: vocabulary_id + description: The OMOP Vocabulary ID associated with the vocabulary, if applicable + title: OMOP Vocabulary ID + from_schema: https://includedcc.org/common-access-model + range: string + vocabulary_uri: + name: vocabulary_uri + description: Official URI associated with the vocabulary + title: Vocabulary URI + from_schema: https://includedcc.org/common-access-model + range: uri + required: true + fhir_system: + name: fhir_system + description: System used within FHIR valuesets and codings + title: FHIR System + from_schema: https://includedcc.org/common-access-model + range: uri + required: true + vocabulary_prefix: + name: vocabulary_prefix + description: The authoritative namespace prefix allocated to the vocabulary. Used + to resolve compact identifiers (CURIEs) to their full semantic URIs or FHIR + system URLs. + title: Canonical Curie Prefix + from_schema: https://includedcc.org/common-access-model + range: Vocabulary + version: + name: version + description: Version associated with the current vocabulary content + title: Version + from_schema: https://includedcc.org/common-access-model + range: string + vocabulary_source: + name: vocabulary_source + description: Source used for accessing the vocabulary's content + title: Vocabulary data source + comments: + - This is currently poorly defined because we haven't fully defined the nature + of the data pulls. Most likely it will end up as a filename (.owl, .obo, etc) + or another tool, etc + from_schema: https://includedcc.org/common-access-model + range: string + target_concept_curie: + name: target_concept_curie + description: The concept to which this term relates + title: Target Concept ID + from_schema: https://includedcc.org/common-access-model + range: Concept + relationship_curie: + name: relationship_curie + description: The relationship between the subject (this term) and the object (target_concept_id). + title: Mapping Relationship + from_schema: https://includedcc.org/common-access-model + range: uriorcurie concept_source: name: concept_source description: The source text yielding the standardized concept. @@ -28015,7 +29100,7 @@ slots: range: Concept any_of: - range: Concept - - range: EnumSite + - range: EnumSiteExamples spatial_qualifier: name: spatial_qualifier description: Qualifier that further refine the specific location of biospecimen @@ -28135,7 +29220,7 @@ slots: description: File hash information title: File Hash from_schema: https://includedcc.org/common-access-model - range: FileHash + range: HashDigest multivalued: true hash_type: name: hash_type @@ -28480,12 +29565,70 @@ classes: from_schema: https://includedcc.org/common-access-model slots: - concept_curie + - concept_id + - vocabulary_prefix + - concept_code - display + - definition slot_usage: concept_curie: name: concept_curie identifier: true + range: uriorcurie required: true + Synonym: + name: Synonym + description: Alternate display names for concepts. + title: Concept Synonym + from_schema: https://includedcc.org/common-access-model + slots: + - concept_curie + - display + - display_type + - language + DeprecatedConcept: + name: DeprecatedConcept + description: Identifies concepts that are not currently valid. + title: Deprecated Concept + from_schema: https://includedcc.org/common-access-model + slots: + - concept_curie + - deprecation_type + - replacement_curie + Vocabulary: + name: Vocabulary + description: Flat table containing each of the ontologies used for dataset annotations + from_schema: https://includedcc.org/common-access-model + slots: + - vocabulary_prefix + - name + - vocabulary_uri + - vocabulary_id + - fhir_system + - description + - version + - vocabulary_source + slot_usage: + vocabulary_prefix: + name: vocabulary_prefix + todos: + - Ensure that MapDragon and TermWeaver both rely on the same rules for prefixes + comments: + - Must start with a letter; thereafter allows letters, digits, underscores, + hyphens, and dots to accommodate OLS/UMLS source variability. + - 'RISK: In order for all of our data to correctly join, the format of the + prefix must always align with the prefix used in this table.' + identifier: true + range: string + pattern: ^[A-Za-z][A-Za-z0-9_\-\.]*$ + ConceptRelationship: + name: ConceptRelationship + description: Relationships between two terms. + from_schema: https://includedcc.org/common-access-model + slots: + - concept_curie + - target_concept_curie + - relationship_curie Sample: name: Sample description: A functionally equivalent specimen taken from a participant or processed @@ -28652,10 +29795,10 @@ classes: sample_id: name: sample_id multivalued: true - FileHash: - name: FileHash + HashDigest: + name: HashDigest description: Type and value of a file content hash. - title: File Hash + title: Hash Digest from_schema: https://includedcc.org/common-access-model slots: - hash_type