SWUG:Report 200901

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  • Ben has been preparing an 1.6 Amigo release on Dev machines.
  • Another pass on ref genome information for AmiGO 1.6
  • AmiGO 1.6 release clean-up: fixes for installation and documentation
  • Developed a testing guide Web_Presence_Working_Group:_Testing_Guide
  • Some work on new graph display

This month we've been doing a lot of work with the WPWG on an overhaul of the GO News system


The SGD/Production group and Berkeley/AmiGO group have started having monthly F2F meetings to go over AmiGO installation, database issues and general development discussion.

This month we had Tanya and David join us to discuss future database requirements based on ontology and annotation changes. We drew up a timeline that proposes when new additions to ontology and GAF files are introduced:

As a first step, Mike and Chris have coordinated on the publication of gene_ontology_ext.obo -- see Ontology_publishing_pipeline_2009

  • firefighting for obo2obo pipeline - ongoing
  • Preparing database for removal of fake 'all' root node

OBO-Edit and ontology support

Chris met with Tanya and David at Carnegie. Chris extended the OBO-Edit semantic parser to capture more XP links. Demonstrated use of OE2 reasoner to automatically maintain links - we agreed that this will make future work much simpler

We continue to have weekly OE meetings.

  • Beta53 release. Two week beta release cycle January 09 onwards.
  • Intensive testing period January 15th - January 31st.
  • Public release date set for March 09.


  • Ongoing development on Panther/paint tool