It is now the 1st OPEN Period for CACAO Fall 2017! It will end on Sunday September 24, 2017 at 11:59 pm CDT
This is your chance to make annotations OR challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.

Have any questions? Please email us at ecoliwiki@gmail.com

GONUTS:About

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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.

Until February 2014, GONUTS used a photo of some pistachios as its logo. At a Phenotype RCN workshop at BioSphere 2, it was pointed out that while pistachios are nuts in the culinary sense, they are botanically not true nuts. Jim Hu created a new logo that illustrates how the idea of nuts has multiple meanings. The logo includes:

  • a Hazelnut, which is a true botanical nut
  • Nut, the Egyptian goddess of the night, who has been invoked in explaining the N-utilization (nut) site of bacteriophage lambda
  • A hardware nut

The parts that compose this logo were modified from images found at Wikimedia Commons.

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 PortEco model organism data resource, which was funded by NIGMS grant 1U24 GM077905-01 subaward 511-1960-01 and U24 GM088849.

Versions

  • Feb 2014: New logo
  • Jan 2014: updated to MW 1.21
  • Jan 2013: updated to MW 1.19
  • … updates not logged
  • 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.

References