{"id":2738513,"url":"https://alion.io/job/altos-labs-senior-knowledge-engineer-ontology-and-data-standards-contract","title":"Senior Knowledge Engineer, Ontology and Data Standards (Contract)","company":{"id":449654,"name":"Altos Labs","domain":"altoslabs.com","url":"https://alion.io/company/altos-labs","size_band":"1001-5000","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Greenhouse","truth_index":{"grade":"B","score":83,"open_postings":4,"ghost_share":0,"stale_share":0.5,"repost_share":0,"time_to_fill_p50_days":73,"computed_at":"2026-11-14T05:58:10Z"}},"role":"Industrial Engineering","role_family":"Industrial Engineering","seniority":"senior","employment_type":"contractor","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["San Francisco, United States","Redwood City, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":105,"max":123,"currency":"USD","period":"hour","gross":null,"usd_annual":246000},"salary_estimate":null,"experience_years_min":8,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Agentic Workflows","optional":false},{"name":"AI Agents","optional":false},{"name":"CI/CD","optional":false},{"name":"Human-in-the-Loop","optional":false},{"name":"LLM","optional":false},{"name":"Model Context Protocol","optional":false},{"name":"Platform Engineering","optional":false},{"name":"Rest API","optional":false},{"name":"Amazon S3","optional":true},{"name":"AWS","optional":true},{"name":"Claude Code","optional":true},{"name":"Cursor","optional":true},{"name":"Git","optional":true},{"name":"GitHub Actions","optional":true},{"name":"Pydantic","optional":true},{"name":"Pytest","optional":true},{"name":"Python","optional":true},{"name":"RAG","optional":true}],"status":"live","first_seen_at":"2026-10-08T17:21:29Z","employer_posted_date":"2026-10-08","last_verified_at":"2026-11-15T01:54:28Z","board_verified":true,"closed_at":null,"days_open":37,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":37},"description":"Our Mission\nOur mission is to restore cell health and resilience through cell rejuvenation to reverse disease, injury, and the disabilities that can occur throughout life.\nFor more information, see our website at altoslabs.com.\nOur Value\nOur Single Altos Value: Everyone Owns Achieving Our Inspiring Mission.\nDiversity at Altos\nAltos Labs has been named one of the Top 3 Biotech Companies and ranked for the second year on the Forbes 2026 Best Startups in America list. At Altos, exceptional scientists and industry leaders from around the world work together to advance a shared mission. Our intentional focus is on Belonging, so that all employees know that they are valued for their unique perspectives. We are all accountable for sustaining a diverse and inclusive environment.\nWhat You Will Contribute To Altos\nAs a contract Senior Knowledge Engineer, Ontology and Data Standards, you will drive how our team represents biological knowledge At Altos\nWe have built the machinery: a large canonical LinkML/Biolink schema including REST/MCP/CLI service layer; specification packages covering multiple prior-knowledge sources; and an agentic / human-in-the-loop curation framework. What it lacks is a technical owner-someone to govern and administer the content.\nYou are the scientific translation layer between biological discovery and AI platform engineering. You will elicit implicit models from bench and computational scientists, encode them rigorously, and utilize the agentic workflows that scale curation beyond what manual review can reach.\nThis role carries explicit decision rights: review authority on canonical schema change, ownership of the curation conventions that data atlas and engineering teams follow.\nKey Responsibilities\nKnowledge 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.\nOwn mapping and alignment as a discipline: cross-ontology mappings with recorded justification and provenance, and upstream term requests as appropriate.\nServe as reviewer of record for schema change, holding the line that reuse precedes coining anything new.\n\nAgentic & 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.\nStandardize tool definitions (FastMCP), prompt templates, and LLM-driven workflows that extract, normalize, and validate metadata from prior-knowledge sources and experimental assets.\n\nBiological Data Harmonization:Define mapping patterns and metadata conventions for diverse experimental modalities (genomics, single-cell, screening data) to conform to the canonical schema.\nEstablish standardized conventions that allow both external prior-knowledge sources and internal experimental datasets to cleanly map into the LinkML graph architecture.\n\nQuality, 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.\nMeasure whether the knowledge is correct, not merely reproducible: gold-standard sets, inter-curator agreement, and precision/recall on automated extraction.\n\nWho You Are\nEducation & 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.\nBiological Data Lifecycle: Direct experience turning messy, real-world exploratory datasets (genomics, single-cell, screening, imaging) into structured metadata. \nOntology & 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.\nPython & 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.\nSoftware & Data Management: Familiarity with Git, GitHub Actions, graph/relational databases, and cloud storage (e.g., AWS S3).\nThe salary range for Redwood City, CA:\nSenior Engineer: $105/hr to $123/hr\nExact compensation may vary based on skills, experience, and location.\nFor UK applicants, before submitting your application:\n- Please click here to read the Altos Labs EU and UK Applicant Privacy Notice (bit.ly/eu_uk_privacy_notice)\n- This Privacy Notice is not a contract, express or implied and it does not set terms or conditions of employment.\nEqual Opportunity Employment\nWe value collaboration and scientific excellence.\nWe believe that a culture of belonging are foundational to scientific innovation and inquiry. At Altos Labs, exceptional scientists and industry leaders from around the world work together to advance a shared mission. Our intentional focus is on Belonging, so that all employees know that they are valued for their unique perspectives. We are all accountable for sustaining an inclusive environment.\nAltos Labs provides equal employment opportunities to all employees and applicants for employment, without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws. Altos prohibits unlawful discrimination and harassment. This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation and training.\nThank you for your interest in Altos Labs where we strive for a culture of scientific excellence, learning, and belonging.\nNote: Altos Labs will not ask you to download a messaging app for an interview or outlay your own money to get started as an employee. If this sounds like your interaction with people claiming to be with Altos, it is not legitimate and has nothing to do with Altos. 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