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
- OBO Foundry : Open Biomedical Ontologies
- 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)