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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README.md

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).

Ontologies that GenEpiO draws upon

APOLLO SV, CHEBI, CHMO, DOID, EFO, ENVO, EO, ERO, FOODON, GAZ, GEO, HP, IDO, NCBITaxon, NCIT, OBI, PATO, PTO, 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.

Note that GenEpiO is under development (many terms have a curation status of "requires discussion") and its existing content requires a few more editing passes for proper description of terms.