Software meeting 2014-02-26

GO Meeting Prep

Anything the berkeley team needs to coordinate with others before the meeting?

• http://wiki.geneontology.org/index.php/2014_College_Station_GOC_Meeting_Agenda

Ontology Update

A brief update on changes in ontology editing and publishing pipeline, some may affect quickgo or protein2go

• editors file now contains imports and external-pointing axioms - https://www.ebi.ac.uk/panda/jira/browse/GO-223
• go-plus reflects editors file - http://beta.geneontology.org/page/download-ontology
• new axioms can be used in AmiGO 2 and QuickGO. E.g. search by chemical entity, cell type
• taxon_go_triggers - will be deprecated but supported, as constraints go into main file
• we would like to obsolete gene_ontology_ext

GAF/GPAD

• notification: change to GPAD for inter-species interactions
• conversion scripts - perl & java (owltools) - make more prominent.

GO Website

• Enrichment environment update - https://www.ebi.ac.uk/panda/jira/browse/GO-155

Annotation Tools

http://wiki.geneontology.org/index.php/2014_College_Station_GOC_Meeting_Agenda#Sunday_16_March_-_Community_relations_and_Annotation_Production

How do we better share components and manage interaction points

• protein2go
• (js)PAINT
• molecular modeling environment
• canto
• gonuts
• TG
• textpresso

Molecular Modeling Environment demo (chris):

MM architecture: http://geneontology.org//experimental/lego/docs/lego-architecture.png

Action Items from call

• [2/26/14 8:10:53 AM] Chris Mungall: todo: check if go-plus contains everything in go (heiko)
• [2/26/14 8:13:07 AM] Chris Mungall: todo: make a gpad-1.2 (cjm, tony)
• [2/26/14 8:13:45 AM] Chris Mungall: todo: revisit gpi, namespace should be separate column
• [2/26/14 8:14:32 AM] Chris Mungall: todo: add examples for complexes in GPI (cjm, tony)
• [2/26/14 8:15:41 AM] Chris Mungall: todo: add agenda for college station (cjm)
• [2/26/14 8:17:59 AM] Chris Mungall: todo: get parsers into java/owltools (heiko, cjm)
• [2/26/14 8:25:10 AM] Chris Mungall: todo: get panther loaded weekly (for TE) (anushya)
• [2/26/14 8:31:32 AM] Chris Mungall: todo: get documentation on urls from anushya (aunshya)
• [2/26/14 8:32:01 AM] Chris Mungall: todo: replacement for go xref abbs at college station meeting (cjm to add to agenda)
• [2/26/14 8:32:52 AM] Chris Mungall: different entity types within an ID space
• [2/26/14 8:37:33 AM] Chris Mungall: todo: solve the MGI:MGI problem - devise a plan at college station (cjm)
• [2/26/14 8:39:14 AM] Chris Mungall: todo: follow up with anushya on entry in go xref abbs for PANTHER (anushya, seth)