2011 USC Meeting Agenda

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Minutes: (By hosts of previous meeting: MGI)

Meeting action items

Thursday May 19, Cardinal & Gold Room

8:30 Registration

9:00 Welcome; Review of schedule and agenda

  • Introductions.
  • GOC PI announcements

9:15 - 5:30 Working Group Reports, plans through 2011, discussion of priorities

9:15 Annotation

(Rama, Emily, Pascale) Progress and Priorities

To encompass:

  1. Annotation Outreach efforts (30 min)
  2. Development of Annotation Guidelines (Geneva, Evidence codes). Suggestions for further guidelines.
  3. Draft on how external groups should display annotation.
  4. Focused annotation efforts by GO Consortium members (Emily)
  5. Proposed improvements to the Annotation web pages
  6. has_part relationship (Chris)
  7. Automated annotation support (QCs, Taxon GO, inferred annotations)
    1. XML encoding of QC checks: http://geneontology.org/GO.annotation_qc.shtml
    2. Demo of web-based GAF validator: http://ladle.lbl.gov:8888/gaftools.html (Amelia)

AAC Discussion Questions

File:AAandC presentation.pdf

10:15 Community resources and Dissemination (Emily & Rama)

  1. GO Help Rotation. (Rama) File:ECOtoGO.pdf

10:30 Break

11:30 Evidence Code Ontology presentation

  1. Marcus (25 minutes)
  2. Discussion on the appropriate usage of ECO identifiers in annotation (Rama)

12:00 Annotation deliverables

  1. Discussion of the distinction between annotations distributed by the GOC and those from the MODs. (Mike, 15 min)
  2. Discussion on changing the policy on restricting taxon to specific GAF files. (Mike, 15 min)

12:30 Lunch

1:30 Overview of the outreach efforts

  1. Overview of the outreach efforts to specific scientific communities for community annotation by the BHF-UCL File:BHF UCL CommunityAnnotation.pdf and TAIR teams as well as the CACAO (Community Assessment of Community Annotation with Ontologies; File:CACAO2011.pdf) course by EcoliWiki (Ruth, Tanya and Jim; 10 mins each and 15 mins discussion)
  2. RACE-PRO community submission/annotation tool for the Protein Ontology has a section for adding GO annotation. http://pir.georgetown.edu/cgi-bin/pro/race_pro

2:30 InterPro2GO presentation

(Sarah Burge) (40 min presentation, 10 mins discussion)

  1. Brief summary of the revised guidelines for the GO mapping of InterPro entries.
  2. 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.

3:20 Break

3:30 Ontology development


  1. Timeline: discuss progress and priorities (10 mins)
  2. Recent projects - notes/accomplishments
    • Transcription factors (Karen; available any time Thursday or Friday morning before noon) (15 mins)
    • Signaling (Becky) (15 mins) [1]
    • Chemicals (Tanya) (15 mins)

Dinner on your own

Friday May 20, Alumni Room

8:15-12:30 Working Group Reports (cont), plans through 2011, discussion of priorities

8:15 ontology group (cont'd)

  1. Protein complexes (Harold) (15 mins, File:Complexes in GO and PRO.pdf)
    • 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)
    • Notifications of change (Becky) (15-20 mins).
    • Large-scale changes to the ontology.
      • When a development project is starting up, and when their key changes are released
      • Process for discussion and release of proposed term obsoletions.

9:00 Reference Genomes

  1. Report from the Reference Genomes project (Pascale) File:2011-05-USC-RefGenome-Report-Pascale.pdf
  2. Timeline: discuss progress and priorities 20 min
  3. PanTree website for tree annotations and evidence trail for inferred annotations from PAINT (Paul T) 15 min

10:00 Break

10:30 annotation

  1. BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth; 15 mins) File:BHF UCL FocusedAnnotation.pdf

10:45 Software

  1. Report from the Working Group (Chris)
    • Software utilities (Reasoners, QC - Chris; TG - Heiko)
  2. OBO/OWL migration (Chris)
  3. Timeline: discuss progress and priorities
  4. Software status (AmiGO, GOOSE, GOLD, etc. - Seth) File:GoSW-USC-CM.pdf

11:30 Annotation Extension information

  1. Annotation Extension information (Column 16) (MGI / Chris / Val/Emily 30 min)

Other related slides:(File:Annotation extension tableVal.pdf, File:UniProtKB col16.pdf, File:MGI GO Notes demo.pdf)

12:00 Review Action items from Bar Harbor meeting

see 2010 Bar Harbor Action items

12:30 Lunch

1:30-5:30 Discussion of the Vision defined in the GOC NIH grant application

(Friday afternoon, Saturday Morning) (This includes presentations of our current efforts and how this vision can become a reality. Also what goals are needed to reach the aims stated in the application.)

1:30 Literature-based annotations (Mike)

(chair of session Rama)

  1. Vision (i.e. efficiency, quality and consistency goals)
  2. Implementation: what will be necessary to accomplish this goal?
    • Prioritization of which organisms and genes to be curated
  3. Current status/accomplishments
  4. Possible metrics

2:00 Biological focus-group annotations (Judy)

(chair of session Emily)

  1. vision (and entire text-book TOC)
  2. Implementation: what will be necessary to accomplish this goal?
  3. Current status/accomplishments
    • New ontologies terms added at recent meetings.
  4. Possible metrics/milestones

2:45 Phylogenetically-based annotations (Paul T)

  1. Vision (comprehensive annotations)
  2. Implementation (scalability)
  3. Pilot project, including possible metrics

3:30 Break

3:45 Common Annotation Framework (Paul S)

  1. Vision
    • Goals:
      • More efficient curation
      • Support annotation by volunteers
    • Plan:
      • Specify Requirements 2011 including minimal functional system and common GOC database
      • Make it so 2012 onwards
    • Pieces: Curation Form (ontology viewer, autocomplete with synonyms, multi-value fields, QC checks [GAF validator], etc.)
      • Paper Viewer (view markup on HTML, XML, PDF;)
      • NLP modules (run algorithms, see results on Paper (entity recognition; and auto-fill into Curation Form).
      • PAINT (web) [interPro etc. window] PAINT viewer? with pictures of organisms…
      • Term Genie
      • Control Panel
  1. implementation: what will be necessary to accomplish this goal?
  2. Current Efforts
    • PomBase community annotation tool (Val; File:Curation tool.pdf)
    • Textpresso, Phenote, PAINT-web, and all the rest...
      • Introduction to GO Curation using Textpresso (Kimberly, 10-15 mins.)
  3. metrics and milestones

Group dinner at Rosa Mexicano at LA Live (Downtown LA) at 6pm

Saturday May 21, Davidson Center, Board Room

9:00-10:45 Discussion of the Vision defined in the GOC NIH grant application

9:00 group photo

9:05 Annotation File Format proposals

Proposal for annotation submission in GPAD and GPI formats - see Annotation File Format Proposal

9:15 Ontology development (David)

  1. Vision
  2. Implementation: what will be necessary to accomplish this goal.
  3. Metrics and milestones

10:00 Community resources and Dissemination (Mike, co-chairs: Emily & Rama)

  1. Vision
  2. Implementation: what will be necessary to accomplish this goal.
  3. Monitoring customer satisfaction

10:45 Coffee break

11 to 11:45 Wrap up, action items

11:45 fresh air break

12:00 lunch and departures or Satellite meeting

Satellite meetings

  1. Cardiac Conduction ontology development workshop (Ruth & David) [2]
    • 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