Topic map conversion of Gene Ontology
Gene Ontology is a controlled vocabulary to describe gene and gene product attributes in any organism. Gene Ontology is an ongoing developed of The GO Consortium. Topic map conversion is based on OBO flat file version (dated 17:01:2008 14:47) of the Gene Ontology hosted by the OBO Foundry. Gene Ontology was converted with Wandora's OBO Import feature.
Download topic map conversion of Gene Ontology
There are two versions available:
- Wandora project file (8 MB). This version is targeted to Wandora users. Project file contains two separate topic map layers: Gene Ontology and Wandora's base topic map. Wandora requires at least 1 GB of memory (use wandora_large.bat or wandora_huge.bat) to open topic map version of GO.
- Single XTM dump (8 MB, unzipped 148 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.
History
- 2008-01-21 Initial release. Gene Ontology dated 17:01:2008 14:47.
Metrics
- Number of topics: 99767
- Number of associations: 186626
- Number of topic base names: 98719
- Number of subject identifiers: 99772
- Number of subject locators: 0
- Number of occurrences: 71962
- Number of distinct topic classes: 17
- Number of distinct types of associations: 12
- Number of distinct roles in associations: 20
- Number of distinct players in associations: 99734
Conversion details
Topic map conversion of Gene Ontology contains special grouping topics that are not actually part of original ontology. These grouping topics are
- Wandora class connects all grouping topics to the root topic of Wandora.
- gene_ontology is a superclass root of Gene Ontology terms. It collects all superclass roots of Gene Ontology and serves as a starting point for ontology browsing.
- obo (biological_process) collects meta-topics of namespace biological_process.
- obo (cellular_component) collects meta-topics of namespace cellular_component.
- obo (molecular_function) collects meta-topics of namespace molecular_function.
- obo (gene_ontology) collects meta-tags of Gene Ontology's default namespace gene_ontology.
- obo-schema is used to collect all association types, roles, and occurrence types used in Gene Ontology. It also contains player topics considered static constants.
License
Gene Ontology is a collaborative and ongoing effort of the GO consortium (Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29).
The Gene Ontology database and vocabularies are in the public domain [1]
Wandora authors and the actual converter (Aki Kivelä) set the topic map conversion of Gene Ontology (dated 17:01:2008 14:47) also in the public domain. Gene Ontology's usage policy applies also to the topic map version.
