2011 UCL Meeting Agenda: Difference between revisions
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** Use in FANTOM5 | ** Use in FANTOM5 | ||
** Neuro-cell work | ** Neuro-cell work | ||
* [[Cellular_component_disjoint_classes#Spatial_disjointness:_Disconnected_from|Proposal to introduce new disjointness axioms into GO CC]] ~~ Chris | |||
* Update on GOCHE | * Update on GOCHE | ||
* [[Ontology Release Files Proposal]] ~~ Chris | * [[Ontology Release Files Proposal]] ~~ Chris | ||
* Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]] | * Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]] | ||
* Update on RO and BFO ~~ Chris | * Relations | ||
** Update on RO and BFO ~~ Chris | |||
** GO subset of RO | ** GO subset of RO | ||
** Coordinating between annotation group and ontology group on GO subset of new RO | ** Coordinating between annotation group and ontology group on GO subset of new RO |
Revision as of 13:36, 6 October 2011
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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
- Example queries using c16
- CL examples (mouse annotations)
- POMBE examples
- Treatment of evidence types
- overview of architecture, use of Solr. Demo of Solr API
- 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
- Use of TG as SF replacement ("freeform" term creation)
- obo2owl roundtripping ~~ Heiko
- 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
- LEGO_Model_Draft_Specification ~~ Amelia, Chris, PaulT
- PAINT report ~~ Suzi, PaulT
Ontology
- Ontology editing workflow ~~ Chris
- Dual mode Obo-Edit and Protege editing
- Introduction to fast OWL reasoners, what they can do for the ontology group
- MIREOTing subsets of external ontologies into editors version
- Using OORT to produce releases
- Greater use of ontology constraints (disjointness, taxonomic constraints)
- Update on cell ontology ~~ Chris
- Integration with Uberon
- Use in FANTOM5
- Neuro-cell work
- Proposal to introduce new disjointness axioms into GO CC ~~ Chris
- Update on GOCHE
- Ontology Release Files Proposal ~~ Chris
- Roadmap for new logical definitions and relationships - Category:Cross_Products
- Relations
- Update on RO and BFO ~~ Chris
- GO subset of RO
- Coordinating between annotation group and ontology group on GO subset of new RO
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?
General Discussions
- Discussion on appropriate software tools to help manage and report progress on individual project milestones