FYPO: the fission yeast phenotype ontology

Abstract

Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast.

Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species.

Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/).

Fig. 1.

Several specific types of mitotic catastrophe have been defined based on whether cell size or shape is affected, and whether the cells undergo septation despite the failure of chromosome segregation (‘cut’ phenotype). As the different specific mitotic catastrophe phenotypes support different interpretations of the underlying biology, the distinctions among these related phenotypes are valuable for downstream applications of phenotype annotations. (A) Graphical view of terms and is_a relationships, which classify the terms. More specific terms build on less specific terms by addition of differentiating features. A complex phenotype such as ‘mitotic catastrophe with cut, elongated cells’ has multiple paths to the root (most general term) of the ontology via different parents, allowing annotations at any level of specificity. Also note that the paths in FYPO parallel the paths describing mitosis and the cell cycle in GO as well as those in the cell morphology area of FYPO. (B) OBO stanza defining FYPO:0001054 ‘mitotic catastrophe with cut, elongated cells’. Note that the two is_a relationships shown are manually asserted. The logical definition is specified by the intersection_of lines, and the def line provides a human-readable definition

Fig. 2.

Representation of FYPO:0000161, ‘abnormal actomyosin contractile ring assembly’, and its logical definition. (A) Manchester syntax. (B) OBO format