Software and Utilities

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The purpose of the Software and Utilities group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics and computer-science related matters. In addition, this group will help drive the GOC through the research and provision of new computational technologies and methodologies relating to ontologies and ontology-based data analysis. This group is responsible for creating, clarifying and extending the common model that underpins all of GO. Ontology development tools are necessary for the Ontology Development group to perform its function. In addition, the Annotation Outreach group and wider community need means of exploring and utilizing GO and existing annotations. This group complements all the other groups.

Software and Utilities group summary

Meetings

See Category:SWUG-TCons for all new meetings

  • Visualisation meeting, 2007-08-16. No notes, demo only
  • March 14 2007 -

Past Meetings:

Forthcoming meetings:

Schedule to be decided

Reports

Mail List

There is no public mailing list for this group.

Resources

Documentation

Trackers

People

Principles

Wiki

All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)

Projects

Galaxy

Everything you need to know about GO Galaxy

OBO-Edit

AmiGO

General Interest

Internal interest

RefGenome

TreeCurationTool

Collaboration with PantherDB


GO database and go-perl

Main page: http://www.geneontology.org/GO.database.shtml

  • gp2protein report This is a script run "peridically" to cross-check gp2protein files submitted by mods.

SO

Main page: http://www.sequenceontology.org

MiSO

CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO

browser http://song.sf.net/SO_view/index.html

Cross-products in SO

SO contains cross-product definitions of many composite terms. See SO Cross Products for the methodology.

Obol

http://www.berkeleybop.org/obol

Reference Genome Software Prototype

Sohel Merchant has created a prototype as support for the Reference Genome Annotation Project. Currently the project data is managed by means of a google spreadsheet that is difficult to use. The new database and interface will allow the administrator to enter new target genes and for the model organism curators to call their orthologs and to track curation progress of each gene. (For more on the Reference Genome Annotation Project: http://gocwiki.geneontology.org/index.php/Reference_Genome_Annotation_Project )

To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000