Software meeting 2014-02-26
GO Meeting Prep
Anything the berkeley team needs to coordinate with others before the meeting?
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
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)