Fission Yeast Phenotype Ontology

PomBase curators develop and use the Fission Yeast Phenotype Ontology (FYPO) to annotate phenotypes of mutant alleles and of over- or under-expressing wild type genes.

The contents and structure of FYPO are described on the FYPO page of the PomBase wiki and in the publication:

Harris MA, Lock A, Bähler J, Oliver SG, Wood V. FYPO: The Fission Yeast Phenotype Ontology. Bioinformatics. 2013 July 1;29(13): 1671–1678.
PubMed abstract (PMID:23658422) or Full text (HTML) at Bioinformatics

Browsing FYPO terms

At present, FYPO is included collections such as the National Center for Biomedical Ontology's BioPortal and EBI's Ontology Lookup Service (OLS), both of which allow searching and browsing.

We hope to deploy a browser at PomBase in the not-too-distant future that will include annotations as well as terms.

Finding FYPO terms and annotations in PomBase

FYPO terms are displayed on PomBase gene pages, along with supporting evidence and allele and expression details, as described in the PomBase gene page documentation.

The PomBase advanced search can use either term names or IDs to search FYPO, and returns a list of genes that have alleles annotated to the specified term or any of its descendants. For example, see the FAQ on finding essential genes.

Curating phenotypes with FYPO

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

Submitting Bulk Data

If you have a large set of phenotype data to submit, you may want to do a bulk submission. See the documentation on the recommended file format, and use the Phenotype Data Submission Form.