GONUTS:About
From GONUTS
This Gene Ontology Normal Usage Tracking System (GONUTS) is a wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms .
The Gene Ontology project provides a valuable mechanism for standardization of annotation of gene products from different organisms. This is important for making annotation computable, and for facilitating data mining across different genomes. The rationale for Gene Ontology is well described at geneontology.org. The rationale for this wiki is based on helping new users of the ontology understand and use it.
Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker (see also Submitting suggestions to GO using SourceForge on the GO website). However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages.
Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology.
The GONUTS wiki is not an official product of the the Gene Ontology consortium.
The GO consortium has a public wiki at their website.
GONUTS technology
GONUTS relies on the structural similarity between ontologies like GO and the Category system in MediaWiki. Both are Directed Acyclic Graphs (DAG). Thus, GONUTS creates a Category page for each GO term. Each term is a subcategory of its parent terms and has subcategories that represent its child terms. A second DAG is used for taxonomy. Articles in GONUTS contain information about individual genes that have been annotated to specific GO terms. Each gene is also attached to the taxonomy through the source organism.
Wiki version and extensions are listed in Special:Version. Mediawiki extensions written or modified for GONUTS are available through the usual open source free licensing:
Acknowledgements
Thanks to the members of the Gene Ontology consortium for input and tips on how to do things. Special thanks to Emily Dimmer and EBI for allowing us to hotlink image files for GO terms.
The GONUTS wiki is part of the EcoliHub model organism data resource, which is funded by NIGMS grant 1U24 GM077905-01 subaward 511-1960-01 and and U24 GM088849
Versions
January 2007 - renamed to avoid confusion with the official GO wiki
Fall 2006 Automated updating
Updates from the geneontology.org files are logged in the GONUTS:Update log
Version 0.2 July 2006
Version 0.1 September 2005. See the main page for links to more information, and the Help page for help with using this system.
