Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Phenotype analyses, e.g. investigating metabolic processes, tissue formation,
or organism behavior, are an important element of most biological and medical
research activities. Biomedical researchers are making increased use of
ontological standards and methods to capture the results of such analyses, with
one focus being the comparison and analysis of phenotype information
between species.
We have generated a cross-species phenotype ontology for human, mouse
and zebrafish that contains classes from the Human Phenotype Ontology,
Mammalian Phenotype Ontology, and generated classes for zebrafish
phenotypes. We also provide up-to-date annotation data connecting human
genes to phenotype classes from the generated ontology. We have included
the data generation pipeline into our continuous integration system ensuring
stable and up-to-date releases.
This article describes the data generation process and is intended to help
interested researchers access both the phenotype annotation data and the
associated cross-species phenotype ontology. The resource described here
can be used in sophisticated semantic similarity and gene set enrichment
analyses for phenotype data across species. The stable releases of this
resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.