Principal Scientist, Data Science (Translational Knowledge Engineering)

Scorpion Therapeutics; Cambridge (MA); On-site; USD 150,000 - 230,000; Full time

Benefits offered by this job

Vacation time

Sick leave

Parental leave

Bereavement leave

Volunteer leave

Military spouse leave

Job summary

Scorpion Therapeutics in Cambridge, MA, seeks a senior Biomedical Informatics Architect to establish semantic foundations for AI-driven reasoning across discovery, preclinical, and clinical development.

You will lead ontology governance, build RDF-based knowledge graphs, and harmonize translational data (SEND, SDTM, ADaM, MedDRA, FHIR) while partnering with research and engineering teams.

Qualifications

• PhD or Master’s in Biomedical Informatics, Bioinformatics, Computational Biology, Computer Science, Information Science, Knowledge Engineering, or related.
• 5+ years in biomedical informatics/semantic technologies/knowledge engineering/scientific data architecture.
• Experience designing ontology-driven systems in life sciences/healthcare/pharma R&D; across multiple drug discovery/development phases.

Responsibilities

• Semantic Architecture & Knowledge Modeling: design/maintain enterprise knowledge models across discovery biology, toxicology, safety pharmacology, pathology, clinical development, pharmacovigilance, real-world evidence.
• Ontology Engineering & Governance: lead ontology strategy, development, governance, lifecycle management; curate/extend biomedical ontologies; ensure provenance/traceability and FAIR principles.
• Knowledge Graph & Reasoning Infrastructure: build RDF-based knowledge graph architectures; develop semantic mappings/inference rules/reasoning frameworks; enable GraphRAG, semantic retrieval, AI agents, reasoning.
• Translational Data Harmonization: create semantic bridges across SEND, SDTM, ADaM, MedDRA, HPO, MONDO, SNOMED CT, FHIR, OMOP, Cell Ontology, Protein Ontology.
• Cross-Functional Leadership: partner with stakeholders and engineering/platform teams; influence enterprise semantic strategy.

Skills

Biomedical informatics

Ontology engineering

Knowledge graphs

RDF/OWL/SPARQL

FAIR data principles

Education

PhD or Master’s in Biomedical Informatics

Tools

SHACL

RDF graph architectures

Job description

Position Summary

Design and implement semantic/knowledge architecture enabling AI-driven reasoning across the drug discovery and development lifecycle.

Mission

Build the semantic foundation for AI systems to reason across discovery, preclinical, clinical, and post-marketing domains while preserving scientific meaning, provenance, and translational fidelity.

Key Responsibilities

• Semantic Architecture & Knowledge Modeling: Design/maintain enterprise knowledge models (discovery biology, toxicology, safety pharmacology, pathology, clinical development, pharmacovigilance, real-world evidence); create conceptual/logical/physical models for AI-enabled discovery.
• Ontology Engineering & Governance: Lead ontology strategy, development, governance, lifecycle management; curate/extend biomedical ontologies; establish governance/quality/semantic review; ensure consistency, provenance/traceability, and FAIR principles.
• Knowledge Graph & Reasoning Infrastructure: Build RDF-based knowledge graph architectures; develop semantic mappings/inference rules/reasoning frameworks; enable GraphRAG, semantic retrieval, AI agents, reasoning; ensure semantic interoperability.
• Translational Data Harmonization: Create semantic bridges across SEND, SDTM, ADaM, MedDRA, HPO, MONDO, SNOMED CT, FHIR, OMOP, Cell Ontology, Protein Ontology.
• Cross-Functional Leadership: Partner with stakeholders and engineering/platform teams; influence enterprise semantic strategy.

Required Qualifications

• PhD or Master’s in Biomedical Informatics, Bioinformatics, Computational Biology, Computer Science, Information Science, Knowledge Engineering, or related.
• 5+ years in biomedical informatics/semantic technologies/knowledge engineering/scientific data architecture.
• Experience designing ontology-driven systems in life sciences/healthcare/pharma R&D; across multiple drug discovery/development phases.
• Technical: ontology development/governance; knowledge representation; RDF/OWL/SHACL/SPARQL; semantic web technologies; enterprise ontology platforms; RDF graph architectures; semantic APIs; FAIR.
• Domain: familiarity with translational science/toxicology/safety pharmacology/clinical development/pharmacovigilance/regulatory standards; experience with SEND/SDTM/ADaM/MedDRA/HPO/MONDO/FHIR/OMOP.

Preferred Qualifications

• Experience building semantic foundations for AI/GraphRAG/agentic AI/scientific reasoning; LLM-based retrieval/reasoning; translational safety/efficacy/biomarker/mechanistic reasoning use cases; contributions to ontology standards/open-source ontologies/knowledge graph initiatives.

Benefits (time off)

• Vacation: 120 hours/year
• Sick time: 40 hours/year (CO: 48; WA: 56)
• Holiday pay including floating holidays: 13 days/year
• Work/Personal/Family time: up to 40 hours/year
• Parental leave: 480 hours
• Bereavement leave
• Caregiver leave
• Volunteer leave
• Military spouse time-off