2010 GO camp Meeting Agenda: Difference between revisions

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* Pascale Gaudet and Rebecca Foulger
* Pascale Gaudet and Rebecca Foulger
# Update definition of response to terms to indicate that we are capturing mediators (wording needs to be worked out)
# Update definition of response to terms to indicate that we are capturing mediators (wording needs to be worked out)
# Quality control check: �High level ‘response to’ terms should not directly be used for annotation  
# Quality control check: High level ‘response to’ terms should not directly be used for annotation  
# Update guidelines: �Encourage the use of granular terms for ‘responses’
# Update guidelines: Encourage the use of granular terms for ‘responses’
# Update guidelines: �Expression experiments should not be annotated to response to terms�
# Update guidelines: Expression experiments should not be annotated to response to terms
 


==Protein complexes group==
==Protein complexes group==

Revision as of 10:25, 22 June 2010

Minutes are on the Discussion area for this page - please add/edit.

Day 1 morning session

8:30 Registration

9:00 Introductions and objectives of the meeting

  1. Introductions & Logistics: Serenella Ferro Rojas
  2. Goals: Pascale Gaudet

GO – Ontology, annotation, tools and technical aspects

Chairs: Serenella Ferro Rojas and Pascale Gaudet

  1. 9:15 Presentation: An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax (10-15 min)
  2. Annotation Process
 10: 15 Break

10: 30 Binding documentation

 12:30 Lunch

Day 1 afternoon session

1:30 Annotation and annotation propagation

  • Chairs: Alan Bridge and Paul Thomas
  • Minutes: Rachael Huntley and Ivo Pedruzzi
  1. 1:30 Compara (remote presentation). Javier ~ 20 min Presentation: File:EnsemblCompara annotation propagation-2010.06.16.pdf
  2. 1:50 Automated Inferencing methods. Alan Bridge ~ 20 min Presentation: File:Alan-Propagation-UniProtKB.pdf
    • HAMAP inferencing
  3. 2:15 Reference genome: GO's approach to annotation propagation


Questions from participants

  1. How do other groups deal with the issue of not being able to propagate IC GO annotations, leading to inconsistent GO annotation? (Eleanor/Becky).
  2. How to define the limits of ISS propagation from phylogenetic studies ? (Manu)


 3:15 Break

3:30 Response to terms

Presentation: File:WG-Response-to-Becky-Pascale.pdf



Day 2 morning session

9:00 Latest GO development

Chris Mungall (30 min)

    • The extended GO OBO format
    • New annotation format – GAF2.0
    • Annotation extensions (column 16)

9:30 GO browsers: AmiGO and QuickGO

Rachael Huntley (30 min)

10:00 Annotation of HTP data: reviewing the guidelines

Questions from the users

  1. How to distinguish between large-scale experiments (LSE) and specific experiments derived GO annotation ? PubMed list of LSE, additional tags ?!? (Manu)

10:20 New evidence codes proposal

Rama


 10:30 Break

10:45 Annotation of complexes

Day 2 afternoon session

 12:30 Lunch  
 Afternoon: Explore Geneva


 7 PM Group dinner

Day 3 morning session

9:00 Use of Regulation

 10:30 Break

10:45 How is a downstream effect defined

  • Chairs: Rachael Huntley and Varsha Khodiyar
  • *Minutes: Yasmin Alam-Faruque and Ursula Hinz

Downstream Process slides

 12:00 lunch

1:00 Day 3 afternoon session: Future plans

  • Chairs: Suzanna Lewis and Pascale Gaudet
  • Minutes: Jane Lomax - Kimberly Van Auken

1:00 Quality control checks

2:00 Community involvement in annotation

  • Jim Hu: students project CACAO
  • dictyBase, pomBase: involving the community

2:20 Proposing annotation projects to the reference genome

Pascale: Presentation : File:Pascale-RefGenome-Process.pdf see Strategy_for_establishing_RefG_annotation_priorities

Closing discussion and summary of meeting

Pascale Gaudet

4:00 World Cup Soccer

Slovenia vs. United States


ACTION ITEMS from working groups

Response to group

  • Pascale Gaudet and Rebecca Foulger
  1. Update definition of response to terms to indicate that we are capturing mediators (wording needs to be worked out)
  2. Quality control check: High level ‘response to’ terms should not directly be used for annotation
  3. Update guidelines: Encourage the use of granular terms for ‘responses’
  4. Update guidelines: Expression experiments should not be annotated to response to terms

Protein complexes group

  • Pascale Gaudet and Bernd Roechert
  1. Long term goal is to annotate complexes; details and requirements need to be clarified. �
  2. Guidelines + Quality control check: �Avoid annotations to GO: MF by IPI (except for ‘protein binding’ and children)�* Error reports will be generated �
  3. Add to the guidelines: �Do not make EXP annotations to MF when only the CC is observed

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