Senior Knowledge Engineer, Ontology and Data Standards (Contract)
Core
Drive the representation of biological knowledge by governing and administering a canonical LinkML/Biolink schema and agentic curation framework to scale data profiling and validation beyond manual capacity.
Role type
Senior individual-contributor knowledge engineer (ontology and data standards)
Builds
A large canonical LinkML/Biolink schema, REST/MCP/CLI service layer, and agentic/human-in-the-loop curation framework for biological data
Domain
Biotechnology, Bioinformatics, Semantic Web, AI/LLM workflows
Deliverable
production ML models
Required skills
Ontology engineering (LinkML, Biolink, OBO Foundry, OWL, RDF, SPARQL), Python (3.12, uv, pandas, Pydantic), Agentic AI tooling (MCP, LLM workflows, RAG), Data harmonization (genomics, single-cell, screening), CI/CD for curation
Preferred skills
Protégé, ROBOT, ODK, SSSOM mapping sets, graph/relational databases, cloud storage (AWS S3)
Technologies
LinkML, Biolink, Python, FastMCP, Git, GitHub Actions, AWS S3
Responsibilities
Design and extend internal LinkML/Biolink models and ontologies; Own mapping and alignment as a discipline with recorded justification; Administer and refine the agentic curation framework and Model Context Protocol (MCP) service layer; Define mapping patterns and metadata conventions for diverse experimental modalities; Establish automated validation, LLM-assisted quality control, and CI/CD under a "curation as code" paradigm
Seniority
Senior, hands-on IC
