Fission Yeast Phenotype Ontology (FYPO) - pombase/fypo GitHub Wiki

Summary

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

FYPO is developed to support the comprehensive and detailed representation of phenotypes in the comprehensive online fission yeast resources PomBase and JaponicusDB. 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 released under the CC-BY license, and is maintained in a 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 ODK to manage the FYPO release process.

Files generated by ODK in OBO and OWL formats are available in the /release/ directory of the GitHub repository (the FYPO file currently loaded for Canto and website usage by PomBase and JaponicusDB is copied to the curation.pombase.org site, and is available via HTTP). Released files are archived by tagging in the GitHub repository.

FYPO is in the OBO Foundry ontology collection.

Content and Structure

FYPO content and structure documentation is on its own wiki page.

External Ontologies

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

• PATO
• Gene Ontology (GO)
• ChEBI
• Cell Ontology (CL)
• Sequence Ontology (SO)
• Protein Ontology (PRO)

Some relations used in FYPO are cross-referenced to RO, others are borrowed from GO, and a few are local to FYPO. All will eventually be incorporated into RO (or updated to RO relations); this work is ongoing.

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 gene, genotype, and publication pages in PomBase and JaponicusDB, 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