Develop a FAIR-compliant cell phenotype semantic schema based on OBO Foundry ontologies and related standards and an extraction, translation, and loading (ETL) protocol for translating processed single cell transcriptomic assay results and experiment metadata from sc/snRNA-seq datasets into standardized semantically-structured assertions about cell phenotypes for loading into the C2DKB graph knowledgebase; collaborate with other project team members to integrate these C2DKB cell phenotypes with disease, drug, and other complementary information from external public graph knowledgebases (e.g., SPOKE) to facilitate the core mechanistic, diagnostic, and therapeutic discovery use cases.
• PhD and/or MD degree in a biomedical science, computer science or related field.
• Experience managing taxonomies, ontologies, and controlled vocabularies, including OBO Foundry ontologies, especially the Cell Ontology, Ontology of Biomedical Investigation, and UMLS/MeSH.
• Strong working knowledge of data and metadata standards and application of metadata in a biomedical repository setting, commonly used ontology and terminology development tools (e.g., Protégé, Ontology Lookup Service, Ontology Development Kit), Semantic Web technologies (RDF/s, OWL), query languages (SPARQL) and validation/reasoning approaches and standards.
Candidates should send the following application materials directly to Dr. Richard H. Scheuermann at rscheuermann@jcvi.org :
• Current curriculum vitae
• Cover letter/statement of research interest
• Contact information for three references