Senior Knowledge Engineer, Ontology and Data Standards (Contract)

Description

Our Mission

Our mission is to restore cell health and resilience through cell rejuvenation to reverse disease, injury, and the disabilities that can occur throughout life.

For more information, see our website at altoslabs.com.

Our Value

Our Single Altos Value: Everyone Owns Achieving Our Inspiring Mission .

Responsibilities

• Knowledge Modeling & Ontology Engineering:
• Design, maintain, and extend internal LinkML / Biolink models and ontologies covering experimental and prior-knowledge metadata—driven by competency questions from user requirements and not by source-side convenience.
• Own mapping and alignment as a discipline: cross-ontology mappings with recorded justification and provenance, and upstream term requests as appropriate.
• Serve as reviewer of record for schema change, holding the line that reuse precedes coining anything new.
• Agentic & Automated Curation:
• Administer, steer, and refine our agentic curation framework and Model Context Protocol (MCP) service layer to scale data profiling, validation, and entity mapping far beyond manual capacity.
• Standardize tool definitions (FastMCP), prompt templates, and LLM-driven workflows that extract, normalize, and validate metadata from prior-knowledge sources and experimental assets.
• Biological Data Harmonization:
• Define mapping patterns and metadata conventions for diverse experimental modalities (genomics, single-cell, screening data) to conform to the canonical schema.
• Establish standardized conventions that allow both external prior-knowledge sources and internal experimental datasets to cleanly map into the LinkML graph architecture.
• Quality, Evaluation & Provenance:
• Establish and maintain automated validation, LLM-assisted quality control, and CI/CD under a "curation as code" paradigm—extending existing drift and coverage gates into the places where semantic review is still manual.
• Measure whether the knowledge is correct, not merely reproducible: gold-standard sets, inter-curator agreement, and precision/recall on automated extraction.

Requirements

• Education & Experience: PhD with 5+ years, or MS with 8+ years, in Bioinformatics, Computational Biology, Genomics, Systems Biology, or a related life science field. This is a senior individual-contributor role with organization-wide technical authority and no direct reports.
• Biological Data Lifecycle: Direct experience turning messy, real-world exploratory datasets (genomics, single-cell, screening, imaging) into structured metadata.
• Ontology & Semantic Web Expertise: Strong working knowledge of OBO Foundry standards, OWL, RDF, and SPARQL, with schema modeling experience in LinkML, Biolink, or BioCypher. Experience with Protégé, ROBOT, ODK, or SSSOM mapping sets is a plus.
• Python & Agentic AI Tooling: Proficient in modular Python (3.12, uv, pandas, Pydantic, pytest), and able to read and extend a substantial existing codebase rather than only scripting against it. Active hands-on experience with AI environments (e.g., Cursor, Claude Code) and building agentic LLM workflows, custom MCP tools, or RAG pipelines.
• Software & Data Management: Familiarity with Git, GitHub Actions, graph/relational databases, and cloud storage (e.g., AWS S3).
• The salary range for Redwood City, CA:
• Senior Engineer: $105/hr to $123/hr
• Exact compensation may vary based on skills, experience, and location.
• For UK applicants, before submitting your application: