2011 UCL Meeting Agenda: Difference between revisions
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=Wednesday= | =Wednesday= | ||
*Meeting Wrap-Up | |||
** Action Items | |||
** Dates for next meeting | |||
* Ontology editors discussion with ChEBI group (separate room booked) | |||
* Annotation Discussion: | |||
** Progress and Direction of the Reference Genome Project (Pascale) | |||
** Ways in which PAINT annotation can be carried out to quickly generate annotations as a first draft annotation set (raised on the annotation call 25/10/2011) | |||
** suitable projects to engage all groups | |||
Revision as of 07:53, 3 November 2011
back to meeting logistics page
Venue
Main meeting Monday to Wednesday
Wilkins Haldane Room ([1])
GO managers and PIs
Tuesday 1pm to 2:30pm Wilkins JBR Meeting Room ([2])
GO curators and ChEBI
Wednesday 10:30am to 1:30pm Cruciform Foyer Seminar Room 3 ([3])
Monday
Morning Coffee from 9.00am
Morning session to start at 9:30am
Philippa Talmud to welcome the GO Consortium to UCL.
PIs to kick off meeting...?
Software (requested: 3 hours)
- Overview of software group activities and Roadmap [Chris]
- Personnel Updates [Chris]
- Migration of GO to SVN (Proposal) Chris (15 mins)
- New architecture (30 mins)
- 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
- OBO-Edit ~~ Heiko/Chris (20 mins)
- 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 (25 mins)
- Retiring TG0
- Extensions - additional templates
- Integration with ontology roadmap
- Use of TG as SF replacement ("freeform" term creation)
- obo2owl roundtripping ~~ Heiko/Chris (20 mins)
- Using OORT to produce releases ~~ Chris (!keep this item here - Jane)
- GO Galaxy ~~ Amelia (10 mins)
- http://galaxy.berkeleybop.org:8080/
- Use by Phenoscape for obo-diffs
- Wrapping multiple term enrichment tools
- Use case - miRNA pipeline
- Presentation on GOMine (Stanford group) (Rama)
- New tool from Stanford group, accessing GO data like GOOSE
Annotation Software
- Annotation Tools
- PAINT report ~~ Suzi, PaulT
GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html
Tuesday
Separate lunchtime meeting for GO managers and PIs. Wilkins JBR Meeting Room 1pm to 2:30pm
Annotation (requested: 5 hours)
Software and Annotation Group: Annotation Display and Support activities?
- Annotation Roadmap overview (Rama)
- Annotation Progress Report [Rama and Emily]
to include:
- GO Consortium outreach activities and integration of external data sources into primary species GAFs.
- Development of GO annotation guidelines,
- Community Annotation Tool
- ECO codes
- Annotation QCs, including taxon constraints.
- Progress of CACAO biocurator training on GONUTS [4]
[Jim 10 mins]
- Annotation Extension Field (column 16)
- Development of the column 16 format (Val)
- Discussion:
- Rules for transferring column 16 via ISS and via F->P inferences.
- specific use proposed for explicitly defining a gp to GO term relationship. see wiki
- GPAD specification and tools ~~ Amelia
- GOLD beta ~~ Chris - on behalf of Shahid
- LEGO_Model_Draft_Specification ~~ Amelia, Chris, PaulT
[15mins talk + 20min discussion]
- Common Annotation Framework ((Aim 4 of the Grant) - a centralized curation system to help curators efficiently capture annotations from the literature
- Brainstorming session on GO curation tool features - what features are essential, what features would be great to have, what do curators not want
Ontology (requested: 3 hours)
- Roadmap/project overview [Jane/David]
- Ontology editing workflow
- Dual mode Obo-Edit and Protege editing ~~ Chris
- Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
- MIREOTing subsets of external ontologies into editors version ~~ Chris
- Report on how the GO editors are using SourceForge: triage, jamborees etc ~~ Jane
- Cross-products
- Roadmap for new logical definitions and relationships - Category:Cross_Products
- Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
- Aligning with external ontologies
- Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
- Integration with Uberon
- Use in FANTOM5
- Neuro-cell work
- Update on GOCHE ~~ David
- Behaviour alignment and NBO - a proposal [Jane]
- Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
- Content Projects
- Update on signaling ~~ Rebecca
- Update on viruses ~~ Jane
- Update on transcription ~~ Karen (please make this a late time slot so Karen can call in: 3pm UK time at the earliest)
- Update on GO apoptosis project (Paola and Pablo)
- Update on generic GO slim (was this done at LA?) [Val]
- Processes and components
- Functions
- Protein Binding (covering both ontology and annotation issues)
- Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
- Level of detail required under GO:0005515 protein binding (Jane)
- Relations
- Update on RO and BFO ~~ Chris
- GO subset of RO
- Coordinating between annotation group and ontology group on GO subset of new RO
Wednesday
- Meeting Wrap-Up
- Action Items
- Dates for next meeting
- Ontology editors discussion with ChEBI group (separate room booked)
- Annotation Discussion:
- Progress and Direction of the Reference Genome Project (Pascale)
- Ways in which PAINT annotation can be carried out to quickly generate annotations as a first draft annotation set (raised on the annotation call 25/10/2011)
- suitable projects to engage all groups
Project Management
- Overall project management under new grant goals
- Manage documentation
- Manage staff
- Discussion on appropriate software tools to help manage and report progress on individual project milestones
- Jira demo [Tony]
- Discussion on a replacement for the Webex screen sharing tool. - Communication between managers projects.