Skip to content
View SkyeAv's full-sized avatar
10 followers · 9 following

Organizations

@NCATSTranslator

Block or report SkyeAv

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
SkyeAv/README.md

Skye Lane Goetz

Applied AI & Knowledge Graph Engineer @ Institute for Systems Biology

Polyglot engineer building AI/ML systems, data pipelines, and backend services across a range of languages. My focus area is biomedical knowledge graphs: I build the Tablassert ecosystem, which turns messy tabular data into NCATS Translator-compliant knowledge graphs, including an autonomous agent pipeline that derives table configurations with GEPA prompt optimization. I also contribute to the open-source Translator stack (biolink-model, Babel, RTX, shepherd).

Skills

  • Languages: Python, Rust, Go, Elixir, SQL, Shell
  • AI/ML: Deep learning (PyTorch), LLM agents & MCP (LangGraph, LangChain), model fine-tuning (Transformers, PEFT), gradient boosting (LightGBM), classical ML & NLP (Scikit-learn, spaCy, sentence transformers)
  • Knowledge Graphs & Ontologies: Ontology mapping & modeling (Biolink, LinkML, KGX), graph construction & analysis (Neo4j, NetworkX), analytical & relational stores (DuckDB, Polars, PostgreSQL, Redis), ETL pipeline design
  • Backend & Infrastructure: API services (FastAPI, Gin), Nix/NixOS & nix-darwin, Docker, virtualization (QEMU/KVM), CI/CD (GitHub Actions)
  • Biomedical Domain: Multi-omics, clinical-trial data, biomedical entity resolution & knowledge integration (NCATS Translator / Biolink)

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 258 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