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Marta Costa edited this page Dec 2, 2015 · 5 revisions

Welcome to the FlyBase miscellaneous ontologies wiki

This repository is a home for the development and release of a number of controlled vocabularies and ontologies developed and used by FlyBase, including the Drosophila phenotype ontology.

These ontologies and CVs have historically been released as a single file (flybase_controlled_vocabulary.obo). This file makes little sense as a single ontology, so, while we will continue to release this combined file for legacy support purposes, this site aims to provide access to separate files for the various underlying ontologies.

Arguably the most important of the component ontologies is the Drosophila Phenotype Ontology (DPO) - which, as of April 2013 had been used to annotate over 160,000 phenotypes by FlyBase. This site provides access to this as a separate ontology for the first time.

Downloads:

  • flybase controlled vocabulary, full OWL version: latest; archive

  • flybase controlled vocabulary, pre-reasoned 'simple' OBO version: latest; archive

  • flybase controlled vocabulary, pre-reasoned flybase 'simple' OBO version (strips all but part_of and conditionality relations): latest

  • Drosophila phenotype ontology, full OWL version: latest; archive

  • Drosophila phenotype ontology, pre-reasoned 'simple' OBO version: latest; archive

  • Drosophila phenotype ontology, pre-reasoned 'simple' OWL version: latest; archive

Publications

  1. Osumi-Sutherland D., Marygold S. J., Millburn G. H., McQuilton P. A., Ponting. L., Stefancsik R., Falls K., Brown N. H., Gkoutos G. V. (2013) The Drosophila phenotype ontology. Journal of Biomedical Semantics 4(30).

Funding

Development of the FlyBase controlled vocabulary has been funded by a series of grants to FlyBase from the National Human Genome Research Institute at the U.S. National Institutes of Health, the most recent of which is #U41 HG000739.