2011 USC Meeting Agenda

Minutes: (By hosts of previous meeting: MGI)

Welcome; Review of schedule and agenda

• Introductions.
• GO PI announcements

Deliverables over the next year

1. Annotation (Rama, Emily, Pascale) Progress and Priorities
   • Outreach to community annotation groups:
     • BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)
     • Texas A&M annotation competition? (CACAO)
     • TAIR GO annotations from submitted publications? (Tanya)
2. Annotation Guidelines
   • Actions resulting from Geneva guidelines
   • Proposed improvements to the Annotation web pages
   • Guide for how external groups should display annotation.
   • Descriptoin of New QC checks
   • Developments to the Taxon GO rules.
     • Should we be restricting taxon from filtered GAF files?
3. How are groups kept up-to-date? Managers discussion March 23rd
4. Evidence Code Ontology
   • ECO presentation. (Marcus)
   • Use of ECO identifiers (Rama)
5. Proposed usage of column 16 and their relationship (Val)
6. Biological focus-group annotations (Emily)
7. Specific annotation team progress.
   • BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth)

Working Group Reports

1. Reference Genomes (Pascale)
   • Timeline: discuss progress and priorities
   • Enhancements to PAINT & DB (Paul T)
   • Incorporating InterPro motifs into PAINT
2. Software (Chris)
   • Timeline: discuss progress and priorities
   • Software status (AmiGO, GOOSE, GOLD, etc. - Seth)
3. Ontology development (David)
   • Timeline: discuss progress and priorities (10mins)
   • recent projects - notes/accomplishments
     • Transcription factors (Karen; available any time Thursday or Friday morning before noon) (15 mins)
     • Signaling (Becky) (15mins)
     • Chemicals (Tanya) (15 mins)
     • Software utilities (Reasoners, QC - Chris)
   • OBO/OWL migration (Chris)
   • Notifications of change.
     • Large-scale changes to the ontology.
       • When a development project is starting up, and when their key changes are released (Becky)
       • Process for discussion and release of proposed term obsoletions.
   • Protein complexes (Harold) (15 mins)
     • The scope of GO relative to that of PRO?
     • Should GO capture gene product specific protein complexes, or species-specific protein complexes?
     • Should protein complexes be defined based on function or component information? (Becky and Peter D'E)
4. Community resources and Dissemination (Emily & Rama)
   • GO Help Rotation. How do share the load. (Rama)
   • InterPro2GO presentation
     • InterPro (Sarah Burge) (40 min presentation, 20 mins discussion)
       • Brief summary of the revised guidelines for the GO mapping of InterPro entries.
       • InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.

Discussion of the Vision defined in the GOC NIH grant application

(This includes presentations of our current efforts and how these will map into the vision. Also what goals are needed to reach the aims stated in the application.)

1. Literature-based annotations (Mike, moderator: Rama)
   • vision (i.e. efficiency, quality and consistency goals)
   • implementation: what will be necessary to accomplish this goal?
   • current status/accomplishments
   • possible metrics
2. Biological focus-group annotations (Judy, moderator: Emily)
   • vision (and entire text-book TOC?)
   • implementation: what will be necessary to accomplish this goal?
   • current status/accomplishments
     • New ontologies terms added at recent meetings?
   • possible metrics/milestones
3. Phylogenetically-based annotations (Paul T)
   • vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
   • implementation: what will be necessary to accomplish this goal?
   • current status/accomplishments
   • possible metrics
4. Common Annotation Framework (Suzi and Paul S)
   • vision
   • implementation: what will be necessary to accomplish this goal?
   • Current Efforts
     • PomBase community annotation tool (Val?)
     • Textpresso, Phenote, PAINT-web, and all the rest...
   • metrics and milestones
5. Ontology development (David)
   • Vision
   • implementation: what will be necessary to accomplish this goal?
   • metrics and milestones
6. Community resources and Dissemination (Mike, moderators: Emily & Rama)
   • vision
   • implementation: what will be necessary to accomplish this goal?
     • Current Efforts in Community GO Annotation (Emily)
       • BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)
       • Texas A&M annotation competition? (CACAO)
       • TAIR GO annotations from submitted publications?
   • Monitoring customer satisfaction

Satellite meetings

1. Cardiac Conduction ontology development workshop (Ruth&David) [1]
   • pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
   • probably straight after main meeting closes on 19th May
   • workshop date not yet set, aiming for Sept-Nov 2011
   • Please let Ruth know if interested in attending workshop/pre-meeting