!version: $Revision: 1.2 $ !date: $Date: 2009/02/18 00:07:58 $ go/ontology contents documentation Gene Ontology - The Ontologies --------------------------------------------- The GO ontology files are available in both Open Biomedical Ontologies (OBO) and Web Ontology Language (OWL) formats. Various versions are available for download: go-basic.obo This is the basic version of the GO filtered such that the graph is guaranteed to be acyclic, and annotations can be propagated up the graph. The relations included are is_a, part_of, regulates, negatively_regulates and positively_regulates. This version excludes relationships that cross the 3 main GO hierarchies. This is the version that should be used with most GO-based annotation tools. go.obo and go.owl These files contain the core GO ontology in two formats, OBO and OWL-RDF/XML. This view includes relationships not in the filtered version of GO including has_part and occurs_in. The set of relationships used is likely to extend over time. Many of these relationships may not be safe for propagating annotations across, so this version should not be used with legacy GO tools. This version currently excludes relationships to external ontologies. go-plus.owl This version of GO includes cross ontology relationships (axioms) and imports additional required ontologies. This version is only available in OWL. Currently the only external ontology dependency is to CHEBI, but this will change in the future. go-plus-dev.owl This is the development version of the extended GO. It includes dependencies on multiple external ontologies. Not all of the inter-ontology relationships have been vetted. In addition, GO is also available in various legacy formats. These other formats are not recommended for new applications, but as many existing applications rely on these downloads we will continue to support them. For users of the GO-RDF/XML version of the ontology, we recommend the OWL RDF/XML version (see above). For OWL users, we continue to support the legacy obo2owl translation, but users are strongly encouraged to switch to the new translation. See http://beta.geneontology.org/page/download-ontology for more information. For help please contact the GOC at gohelp@geneontology.org