Senior Knowledge Engineer, Ontology and Data Standards (Contract)

The role

You will drive how the team represents biological knowledge by acting as the scientific translation layer between biological discovery and AI platform engineering. You will design and maintain LinkML/Biolink models, manage agentic curation frameworks, and harmonize biological data.

What you will do

• Design, maintain, and extend internal LinkML / Biolink models and ontologies
• Own mapping and alignment as a discipline
• Serve as reviewer of record for schema change
• Administer, steer, and refine the agentic curation framework and MCP service layer
• Standardize tool definitions, prompt templates, and LLM-driven workflows
• Define mapping patterns and metadata conventions for diverse experimental modalities
• Establish standardized conventions for external and internal datasets
• Establish and maintain automated validation and LLM-assisted quality control

Required qualifications

• PhD with 5+ years, or MS with 8+ years, in Bioinformatics, Computational Biology, Genomics, Systems Biology, or a related life science field
• Direct experience turning messy, real-world exploratory datasets into structured metadata
• Strong working knowledge of OBO Foundry standards, OWL, RDF, and SPARQL
• Schema modeling experience in LinkML, Biolink, or BioCypher
• Proficient in modular Python (3.12, uv, pandas, Pydantic, pytest)
• Active hands-on experience with AI environments and building agentic LLM workflows, custom MCP tools, or RAG pipelines
• Familiarity with Git, GitHub Actions, graph/relational databases, and cloud storage (e.g., AWS S3)

Nice to have

• Experience with Protégé, ROBOT, ODK, or SSSOM mapping sets

About the company

Altos Labs is a biotech company whose mission is to restore cell health and resilience through cell rejuvenation to reverse disease, injury, and disabilities. The company focuses on a culture of belonging and scientific excellence.