Difference between revisions of "HCLSIG/Pharmacogenomics/Data Sources"

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==Linked Open Data==
 
==Linked Open Data==
 
* [http://download.bio2rdf.org/release/2/release.html Bio2RDF] : PharmGKB, OMIM, DrugBank, NCBI Gene, PubMed
 
* [http://download.bio2rdf.org/release/2/release.html Bio2RDF] : PharmGKB, OMIM, DrugBank, NCBI Gene, PubMed
* Structured Product Label (SPL)
+
* DailyMed - Structured Product Label (SPL)
 +
* PGx labelled FDA approved drugs
  
 
==Gene and Gene Variation==
 
==Gene and Gene Variation==

Revision as of 14:46, 17 April 2013

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

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