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SkyeAv/README.md

Skye Lane Goetz

Applied AI & Knowledge Graph Engineer @ Institute for Systems Biology

I build the Tablassert ecosystem (tools that turn messy tabular biomedical data into NCATS Translator-compliant knowledge graphs) and contribute to open-source projects across the Translator ecosystem.

Skills

  • Languages: Python, Rust, Go, Elixir, Julia, TypeScript, SQL, Shell, LaTeX
  • AI/ML: PyTorch, LightGBM, Scikit-learn, LangGraph, MCP, Transformers, PEFT, Diffusers, Ollama, Snorkel
  • Data & Storage: Polars, DuckDB, PostgreSQL, Redis, SQLite, ChromaDB, NumPy
  • Knowledge Graphs: Biolink, KGX, LinkML, Ontology Mapping, Neo4j, NetworkX, Centrality Algorithms
  • NLP: spaCy, Autoencoders, Sentence Transformers, BERT, Text Classification, PCA, KernelPCA
  • DevOps/Infra: Nix/NixOS, Docker, QEMU/KVM, FastAPI, Gin, GitHub Packages/Actions
  • Domain: Multi-Omics, Clinical Trials, Polygenic Risk Scores, Quantum Chemistry, TD-DFT

Contact

LinkedIn · sgoetz@isbscience.org

Pinned Loading

  1. Tablassert Tablassert Public

    Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.

    Python 5

  2. NCATSTranslator/Babel NCATSTranslator/Babel Public

    Babel creates cliques of equivalent identifiers across many biomedical vocabularies.

    Python 17 5

  3. biolink/biolink-model biolink/biolink-model Public

    Schema and generated objects for biolink data model and upper ontology

    Python 257 89

  4. NCATSTranslator/Translator_component_toolkit NCATSTranslator/Translator_component_toolkit Public

    Forked from gloriachin/Translator_component_toolkit

    Jupyter Notebook 5 5

  5. RTXteam/RTX RTXteam/RTX Public

    Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)

    Python 46 27

  6. BioPack-team/shepherd BioPack-team/shepherd Public

    Shepherd is a shared platform for Translator ARA implementation.

    Python 3 5