2011 UCL Meeting Agenda: Difference between revisions
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** opportunities for integration with QuickGO ~~ Tony, Chris | ** opportunities for integration with QuickGO ~~ Tony, Chris | ||
* [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta GOLD beta] | * [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta GOLD beta] | ||
** GAF services | |||
*** Annotation file QC | |||
*** Inference of new annotations | |||
**** Use of logical definitions to suggest deeper annotations | |||
**** Cross-ontology inference using [[part_of]] and [[occurs_in]] | |||
* OBO-Edit ~~ Heiko/Chris | * OBO-Edit ~~ Heiko/Chris | ||
** 2.1 Release | ** 2.1 Release |
Revision as of 19:40, 1 October 2011
back to meeting logistics page
Agenda
Coffee from 9.00am Morning session to start at 9:30am End of sessions: 6pm Monday and Tuesday, 2pm on Wednesday GOC dinner Monday 6:30pm
Software
- Presentation on GOMine (Stanford group)
- Migration of GO to SVN (Proposal) Chris
Milestones Report
- Overview of software group activities and Roadmap ~~ Chris
- New architecture
- AmiGO 2 alpha ~~ Seth
- amigo2 walkthrough demo
- overview of architecture, use of Solr
- opportunities for integration with QuickGO ~~ Tony, Chris
- GOLD beta
- OBO-Edit ~~ Heiko/Chris
- 2.1 Release
- 2.2 Plans : mostly maintenance, a few key features, integration of obo2owl code
- Beyond 2.2. - should there be a 3.0? Proteg4 plugin? Web-based tool? Lego?
- TermGenie 1 beta ~~ Heiko
- Retiring TG0
- Extensions - additional templates
- Integration with ontology roadmap
- obo2owl roundtripping ~~ Heiko/Shahid
- OORT
- GPAD specification and tools ~~ Amelia
- GO Galaxy ~~ Amelia
- http://galaxy.berkeleybop.org:8080/
- Use by Phenoscape for obo-diffs
- Wrapping multiple term enrichment tools
- Use case - miRNA pipeline
Ontology
- MIREOTing subsets of external ontologies into editors version ~~ Chris
- Ontology Release Files Proposal ~~ Chris
Annotation Working Group (Emily, Rama)
- Progress Report
- Column 16 usage and development by groups
- Annotation Proposals and Discussions
- IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
- The annotation of the stoichiometry of binding by GO groups. Under the spotlight: protein homodimerization, protein tetramerization etc.
- IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
- Annotation to Protein Complex objects: a suggested annotation format. see wiki page.
- Use of the new relationship Ontology to describe relationships between entities in an annotation, and for the generation of detailed, composite GO terms
- specific use for column 16 (annotation extension field
- specific use proposed for explicitly defining a gp to GO term relationship. see wiki
- Use of the new relationship Ontology to describe relationships between entities in an annotation, and for the generation of detailed, composite GO terms
Software Group: Annotation Display and Support activities?
- presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters? - presentation on AmiGO2 and column 16 display intentions?