HCLSIG/Pharmacogenomics/Data Sources

Linked Open Data

• Bio2RDF : PharmGKB, OMIM, DrugBank, NCBI Gene, PubMed
• DailyMed - Structured Product Label (SPL)
• PGx labelled FDA approved drugs

Gene and Gene Variation

• dbSNP - Single Nucleotide Polymorphism database
• NCBI Gene - Integrative resource for genes, variants and phenotypes
• HVP - Human Variome Project
• LOVD Leiden Open Variation Database
• COSMIC - Catalogue of Somatic Mutations in Cancer
• clinvar

Drug-Gene

• DrugBank - DrugBank (drugs, formulations, targets, interactions)
• CTD - Comparative Toxicogenomics Database (genes, chemicals, diseases, phenotypes)

Gene-Phenotype

• dbGaP- Database of Genotypes and Phenotypes
• PhenGenI - Phenotype-Genotype Integrator (PheGenI), merges NHGRI genome-wide association study (GWAS) catalog data with Gene, dbGaP, OMIM, GTEx and dbSNP
• OMIM - Online Mendelian Inheritance in Man
• PhenCode - human genotype and phenotype
• Model Organisms - mouse, rat, worm, fly, yeast, slime mold

Drug-Phenotype

• SIDER - Drug side effects + frequency
• RxNORM

Drug-Drug

• DrugBank
• AERS signal detection

ontologies

• Variation Ontology (VariO)
• Mutation Impact Ontology (MIO)
• Sequence Ontology (SO)
• Semanticscience Integrated Ontology (SIO)
• Clinical Decision Support (CDS) ontology