Phenotype ontologies on googlecode

For the PATO project we’ve set up a repository on googlecode to collect phenotype ontologies and various bridging axioms:

This aggregates together the main phenotype ontologies, together with logical definitions bridging ontologies, as defined in

Mungall, C. J., Gkoutos, G. V., Smith, C. L., Haendel, M. A., Lewis, S. E., and Ashburner, M. (2010). Integrating phenotype ontologies across multiple species. Genome Biology 11, R2. Available at:

You can access the aggregated ontology via this PURL:

It may be slow to open this via the web. If you have the phenotype-ontologies repository checked out, you can open the file from the filesystem – external ontologies will be obtained via svn:externals.

I recommend using Elk as the reasoner, others will be too slow with the combination of HP, MP, FMA, MA, PATO, etc. Unfortunately Elk doesn’t yet allow DL queries or explanations of inferences.

The above ontology uses a slightly modified version of the definitions described in the Genome Biology paper – instead of modeling each phenotype as a single quality (e.g. redness of nose), we now model them as aggregates of phenotypes. This tends to work better for HPO, which has many composite phenotypes.

Note also that we’re using a hacked version of the uberon bridging axioms to ZFA, MA and FMA – we treat these as precise equivalents rather than taxonomic equivalents. This is necessary as we mix uberon in with the species ontologies in the logical definitions.

About Chris Mungall
Computer Research Scientist at Berkeley Lab. Interests: AI / Ontologies / Bioinformatics. Projects: GO, Monarch, Alliance, OBOFoundry, NMDC

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