Principal Scientist, Data Science (Translational Knowledge Engineering)

Scorpion Therapeutics; Raritan (NJ); On-site; USD 150,000 - 190,000; Full time

Benefits offered by this job

Vacation 120 hrs/yr

Sick time 40 hrs/yr

Holiday pay + floating holidays

Parental leave 480 hrs

Job summary

Scorpion Therapeutics seeks a leader to design semantic architecture enabling AI-driven reasoning across discovery, preclinical, clinical, and post-marketing domains. You will drive ontology development, knowledge graph design, and interoperability while ensuring provenance and translational fidelity.

You will collaborate with translational, safety, and data science teams to advance semantic standards and scalable knowledge representations within a cutting-edge drug discovery program.

Qualifications

• PhD or Master’s in Biomedical Informatics/Bioinformatics/Computational Biology/CS/Information Science or related.
• 5+ years in biomedical informatics, semantic technologies, knowledge engineering, or scientific data architecture.
• Experience designing ontology-driven knowledge systems across drug discovery/development phases.
• Expertise: ontology governance, knowledge representation; RDF/OWL/SHACL/SPARQL; semantic web technologies.

Responsibilities

• Design/maintain enterprise knowledge models for discovery biology, toxicology, safety pharmacology, pathology, clinical development, pharmacovigilance, real-world evidence.
• Lead ontology strategy, governance, lifecycle management; ensure semantic consistency and provenance.
• Build RDF-based knowledge graphs; develop mappings, inference rules, and reasoning frameworks; enable GraphRAG, semantic retrieval, AI agents.
• Create semantic bridges across SEND, SDTM, ADaM, MedDRA, HPO, MONDO, SNOMED CT, FHIR, OMOP, Cell/Protein Ontologies.
• Partner with translational, safety, data science, and AI/platform teams to influence semantic standards.

Skills

Biomedical informatics

Ontology-driven systems

RDF/OWL/SPARQL

Semantic web tech

Education

PhD or Master’s in Biomedical Informatics or related field

Tools

SPARQL

SHACL

RDF/OWL

Job description

Position Summary

• Design and implement semantic and knowledge architecture enabling AI-driven reasoning across the drug discovery and development lifecycle.
• Lead ontology development, knowledge graph design, semantic interoperability, and AI-ready knowledge representation.

Mission

• Build the semantic foundation for AI reasoning across discovery, preclinical, clinical, and post-marketing domains while preserving meaning, provenance, and translational fidelity.

Key Responsibilities

1. 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 knowledge models.
2. Ontology Engineering & Governance: Lead ontology strategy, development, governance, lifecycle management; ensure semantic consistency, provenance/traceability, FAIR principles.
3. Knowledge Graph & Reasoning Infrastructure: Build RDF-based knowledge graphs; develop mappings/inference rules/reasoning frameworks; enable GraphRAG, semantic retrieval, AI agents; establish interoperability.
4. Translational Data Harmonization: Create semantic bridges across SEND, SDTM, ADaM, MedDRA, HPO, MONDO, SNOMED CT, FHIR, OMOP, Cell Ontology, Protein Ontology.
5. Scientific & Cross-Functional Leadership: Partner with translational, safety, data science, AI/platform teams; influence semantic strategy and standards communities.

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, or scientific data architecture.
• Experience designing ontology-driven knowledge systems across drug discovery/development phases.
• Expertise: ontology governance, knowledge representation; RDF/OWL/SHACL/SPARQL; semantic web technologies.

Preferred Qualifications

• Experience building semantic foundations for AI/GraphRAG/agentic AI/scientific reasoning; LLM-based retrieval/reasoning.
• Contributions to ontology standards/open-source biomedical ontologies/knowledge graphs.

Benefits (time off)

• Vacation 120 hrs/yr; Sick time 40 hrs/yr (Colorado 48; Washington 56); Holiday pay incl. floating holidays 13 days/yr; Parental leave 480 hrs; plus other listed leave time.