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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 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.
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:
| File | Description | OBO format | OWL |
| fypo.* | Main FYPO file from Oort; implied links asserted | fypo.obo | fypo.owl |
| fypo-merged.* | implied links not asserted | fypo-merged.obo | fypo-merged.owl |
| fypo-simple.* | logical definitions omitted | fypo-simple.owl | fypo-simple.obo |
| fypo-basic.obo | includes only is_a links | fypo-basic.obo | N/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:
- PATO
- Gene Ontology (GO)
- ChEBI
- Cell Ontology (CL)
- Sequence Ontology (SO)
- BRENDA Tissue Ontology (BTO)
- Protein Ontology (PRO)
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. 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://sourceforge.net/p/pombase/fission-yeast-phenotype/
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
