Scientific knowledge bases

Literature

Surveys

  • Bodenreider & Stevens, 2006: Bio-ontologies: current trends and future directions (doi, pdf)
  • Blake & Bult, 2006: Beyond the data deluge: data integration and bio-ontologies (doi)
  • Goble & Stevens, 2008: State of the nation in data integration for bioinformatics (doi)

Books

  • Robinson & Bauer, 2011: Introduction to bio-ontologies
  • Arp, Smith, Spear, 2015: Building ontologies with Basic Formal Ontology

Knowledge bases

Biology

  • BioSharing
    • Repository of biology databases and standards (some of which are ontologies)
    • McQuilton et al, 2016: BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences (doi, PubMed )
  • OBO Foundry : Open Biomedical Ontologies
    • Standards for bio-ontologies based on Basic Formal Ontology (BFO)
    • Used by Gene Ontology, Sequence Ontology and others
    • Smith et al, 2007: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration (doi, PubMed )
  • Gene Ontology
    • Early, influential ontology in biology
    • Ashburner et al, 2000: Gene ontology: tool for the unification of biology (doi)
  • Sequence Ontology
    • Ashburner et al, 2005: Sequence ontology: tool for the unification of genome annotations (doi)

Biomedicine

  • BioPortal
    • Repository of biomedical ontologies created by Stanford’s Mark Musen
    • Noy et al, 2009: BioPortal: ontologies and integrated data resources at the click of a mouse (doi)
  • CEDAR : Center for Expanded Data Annotation and Retrieval
    • Metadata standards backed by ontologies, also created by Musen
    • Musen et al, 2015: The center for expanded data annotation and retrieval (doi)
  • PharmGKB
    • Created by Stanford’s Russ Altman (a16z podcast )
    • Klein et al, 2001: Integrating genotype and phenotype information: an overview of the PharmGKB project (doi)