wiki:FissionYeastPhenotypeOntology

Version 6 (modified by gomidori, 9 years ago) (diff)

--

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 SourceForge:

https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/

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

A selection of OBO format files generated by Oort are archived in date-stamped releases in the releases subdirectory of the SVN repository. The current versions of these files are also available via HTTP at the curation.pombase.org site -- see table below.

OWL files are also generated by Oort, and can be included in the FYPO releases if demand arises.

Available files:

FileDescriptionSVN pathHTTP link
fypo.oboMain FYPO file from Oort; implied links asserted/phenotype_ontology/releases/latest/fypo.obofypo.obo
fypo-merged.oboimplied links not asserted/phenotype_ontology/releases/latest/fypo-merged.obofypo-merged.obo
fypo-simple.obological definitions omitted/phenotype_ontology/releases/latest/fypo-simple.obofypo-simple.obo
fypo-basic.oboincludes only is_a links/phenotype_ontology/releases/latest/fypo-basic.obofypo-basic.obo

Note: We are aware that SourceForge URLs for the 'latest' directory do not work with HTTP access (they do work with command-line svn). If this causes problems, use the curation.pombase.org URLs.

External Ontologies

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

As of 2011-05-17, some relations can be cross-referenced to RO, and others need to be submitted for consideration.

Using FYPO in PomBase

The PomBase online curation tool (Canto) uses FYPO terms for annotation of S. pombe phenotypes. FYPO terms are displayed on PomBase gene pages, along with supporting evidence and allele and expression details.

Phenotype curation documentation is under development.

Tracker

https://sourceforge.net/p/pombase/fission-yeast-phenotype/


Return to main PomBase wiki page