wiki:FissionYeastPhenotypeOntology

Version 15 (modified by mah79, 5 years ago) (diff)

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Fission Yeast Phenotype Ontology (FYPO)

Summary

The Fission Yeast Phenotype Ontology (FYPO) is a formal ontology of phenotypes observed in fission yeast.

FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.

Availability

FYPO is maintained in a Subversion repository hosted at GitHub:

https://github.com/pombase/fypo

The main phenotype_ontology directory contains the editors' working file (fypo_edit.obo). FYPO curators use Oort to manage the FYPO release process.

Files generated by Oort in OBO and OWL formats are archived in date-stamped releases in the releases subdirectory of the SVN repository. The current versions of these files are also available in the /releases/latest/ directory (and via HTTP at the curation.pombase.org site).

Available files:

FileDescriptionOBO formatOWL
fypo.*Main FYPO file from Oort; implied links assertedfypo.obofypo.owl
fypo-merged.*implied links not assertedfypo-merged.obofypo-merged.owl
fypo-simple.*logical definitions omittedfypo-simple.obofypo-simple.owl
fypo-basic.oboincludes only is_a linksfypo-basic.oboN/A

Content and Structure

FYPO Content and Structure documentation

External Ontologies

Most FYPO terms have logical definitions (aka equivalence axioms, computable definitions, cross-product definitions) following the entity-quality (EQ) model. FYPO uses these OBO ontologies in its logical definitions:

Some relations used in FYPO are cross-referenced to RO, and others are borrowed from GO (so presumably eventually will refer to RO).

Using FYPO in PomBase

The PomBase online curation tool (Canto) uses FYPO terms for annotation of S. pombe phenotypes. Phenotype curation documentation is available via Canto.

FYPO terms are displayed on PomBase gene pages, along with supporting evidence and allele and expression details. PomBase documentation describes the display.

Tracker

https://github.com/pombase/fypo/issues

Citation

Harris MA, Lock A, Bähler J, Oliver SG, Wood V. FYPO: The Fission Yeast Phenotype Ontology.
Bioinformatics. 2013 Jul 1;29(13):1671-8. doi: 10.1093/bioinformatics/btt266. Epub 2013 May 8. PMID:23658422


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