Topic map conversion of Gene Ontology

Gene Ontology is a controlled vocabulary used 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 2011-08-22) of the Gene Ontology hosted by the OBO Foundry. Gene Ontology was converted to topic map with Wandora's OBO Import feature.

Download topic map conversion of Gene Ontology

There are two versions available:

• Wandora project file (13.7 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_huge.bat) to open topic map version of GO.

• Single XTM dump (15.1 MB, unzipped 154 MB). This version is a general topic map file usable in any topic map application supporting XTM file format.

Note: Gene Ontology hosted at OBO Foundry is updated frequently. Topic Map version provided here may be out of date. To get the latest version of Gene Ontology Topic Map we suggest you download latest OBO version of the Gene Ontology from OBO Foundry and convert it to a Topic Map with Wandora's OBO Import feature.

History

• 2011-08-22 Synchronizing the topic map conversion with original OBO flat file ontology.
• 2009-10-27 Synchronizing the topic map conversion with original OBO flat file ontology.
• 2008-09-15 Synchronizing the topic map conversion with original OBO flat file ontology.
• 2008-03-04 Added SI base http://www.wandora.org to Wandora schema topics. Added LTM version of Gene Ontology topic map.
• 2008-01-21 Initial release. Gene Ontology dated 17:01:2008 14:47.

Wandora is also capable to view topic maps as scalable graph presentations. Example graph below views small fragment of GO's topic map conversion. Graph contains super-subclass associations (is_a relations of GO). Also, the graph contains only cellular_component (GO:0005575) and it's neighbors to depth 2. All other relations and terms have been filtered out. Photoshop was used to add blue arrows and texts.

Metrics

Metrics were measured on layer gene ontology of Wandora project file.

• Number of topics: 177301
• Number of associations: 280198
• Number of topic base names: 175814
• Number of subject identifiers: 177309
• Number of subject locators: 0
• Number of occurrences: 148057
• Number of distinct topic classes: 15
• Number of distinct types of associations: 16
• Number of distinct roles in associations: 20
• Number of distinct players in associations: 177265

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.

For more conversion details see Conversion details chapter at OBO flat file import page.

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 public domain [1]

Wandora Team gives the topic map conversion of Gene Ontology (2011-08-22) to the public domain. Gene Ontology's usage policy applies also to the topic map version.