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GenEpiO / genepio

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
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The Genomic Epidemiology Ontology

Build Status

This is the GitHub repository for the Genomic Epidemiology Ontology, an application ontology that belongs to the OBOFoundry family of ontologies. For more information on the project itself, including consortium working group details and GenEpiO ontology design information, please go to http://genepio.org. To view the consortium's new email list, go to https://groups.google.com/forum/#!forum/genepio. To join the list, visit https://groups.google.com/forum/#!forum/genepio/join (you don't need a Google account for this).

The Issues tab dives deep into particular GenEpiO design and implementation questions being resolved. You can make new term requests here too.

A handy way to view this ontology's content is via a web service like the EBI Ontology Lookup Service or Ontobee service.

Many terms have been collected in the main file, genepio.owl, which imports terms from over 25 OBOFoundry.org ontologies (as listed in the /imports/ folder).

Key ontologies that GenEpiO draws upon

CHEBI, CHMO, DOID, EFO, ENVO, FOODON, HP, IDO, NCBITaxon, NCIT, OBI, PATO, RO, SO, STATO, UBERON, UO

Much of GenEpiO's content is geared towards fulfilling sequence repository standards. We are developing a Genomic Epidemiology Ontology Mart (GEEM) portal to enable users to browse GenEpiO content via web forms that detail fields for these standards. It currently displays all of the GenEpiO "Data Representational model" data standard / data standard component / draft data standard entities found within GenEpiO.

Build notes

Genepio owl products are generated using the Ontology Development Kit (ODK) linux Makefile command at command line, such as "> sh run.sh make" in the /src/ontology/ folder to generate the suite of owl and obo products from genepio-edit.owl; and , "sh run.sh make refresh-general"" to update one particular import file. Using/installing of ODK requires install of Docker as well, see https://oboacademy.github.io/obook/tutorial/odk-tutorial-2/ as a starting point for ODK familiarity.

If when running make or when running "robot" directly you encounter obscure robot OWLAPI errors such as "java.lang.IllegalArgumentException: URI is not absolute", install Apache jena and use the "riot" command to validate an owl/xml version of genepio-edit.owl. (For Mac users, to install riot, use "> brew install jena"). In Protege, save a copy of genepio-edit.owl (which is not in owl/xml syntax) to an owl/xml syntax as genepio-validate.owl :

riot -v --validate genepio-validate.owl

After a successful make build, you can test that robot is able to read genepio correctly via:

robot convert -i genepio-merged.owl -o genepio.json