Links

Biomedical Ontologies:

Ontologies in OBO Foundry: http://www.obofoundry.org

CARO: Common Anatomy Reference Ontology: https://github.com/obophenotype/caro/

CHEBI: Chemical Entities of Biological Interest: http://chebi.wiki.sourceforge.net/

CL: Cell Type Ontology: https://github.com/obophenotype/cell-ontology

DOID: Human Disease Ontology: http://diseaseontology.sourceforge.net/

ENVO: Environment Ontology: http://environmentontology.org/

GO: Gene Ontology: http://www.geneontology.org

IDO: Infectious Disease Ontology: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology

NCBITaxon: NCBI Taxonomy: http://www.ncbi.nlm.nih.gov/Taxonomy/

MP: Mammalian Phenotype Ontology: http://www.informatics.jax.org/searches/MP_form.shtml

OBI: Ontology for Biomedical Investigations: http://obi-ontology.org

PATO: Phenotypic Quality Ontology: https://github.com/pato-ontology/pato/

PRO: Protein Ontology: http://proconsortium.org/

SO: Sequence Ontology: http://www.sequenceontology.org/

VO: Vaccine Ontology: http://www.violinet.org/vaccineontology

Tools:

Protege ontology editor: http://protege.stanford.edu/

NCBO BioPortal: http://bioportal.bioontology.org/

VO Browser: http://www.ontobee.org/browser/index.php?o=VO (Note: VO uses Ontofox for its own development. For example, ~400 NCBITaxon and ~300 MP terms and their annotations have been imported into VO using Ontofox.)

OWLAPI: http://owlapi.sourceforge.net/

Ontofox Tutorials:

Sivaram's short tutorial on using Ontofox