2010 GO camp Meeting Agenda: Difference between revisions

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# Annotation Process  
# Annotation Process  
#* 9:30 General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan (15 min)
#* 9:30 General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan (15 min)
#* 9:45 General overview SwissProt. Serenella (15 min)
#* 9:45 General overview UniProtKB/SwissProt manual annotation. Serenella (15 min)


   Break
   Break

Revision as of 11:23, 7 June 2010

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 An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax (10-15 min)
  2. Annotation Process
    • 9:30 General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan (15 min)
    • 9:45 General overview UniProtKB/SwissProt manual annotation. Serenella (15 min)
 Break

Binding documentation

Day 1 afternoon session

Annotation and annotation propagation

  • Chairs: Alan Bridge and Paul Thomas
  • Minutes:
  1. Compara (remote presentation). Javier ~ 20 min
  2. Automated Inferencing methods. Alan Bridge ~ 20 min
    • HAMAP inferencing
  3. PAINT phylogenetic inferencing.
    • Introduction to the Reference Genome Project and to PAINT. Paul ~ 20 min
    • Rules and guidelines for inferencing
    • PAINT demo and examples. Mike ~ 20 min
  4. Comparison of tools. Pascale ~ 10 min

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)


 Break

Response to terms


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)

Annotation of HTP data: reviewing the guidelines

  • Rama : SGD practices
  • Swiss-Prot practices

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)

New evidence codes proposal

Rama 


 Break


Annotation of complexes

Day 2 afternoon session

 Explore Geneva
 Group dinner

Day 3 morning session

Use of Regulation

 Break

How is a downstream effect defined

  • Chairs: Rachael Huntley and Varsha Khodiyar
  • *Minutes:

Day 3 afternoon session: Future plans

  • Chairs: Suzanna Lewis and Pascale Gaudet
  • Minutes:

Quality control checks

Summary from all working groups

  • Taxon checks
  • Specific checks based on GO IDs and evidence codes: 5515, IEP, etc (Rama) - see wiki page
  • Annotation Matrix method (Val Wood)
    • interontology links: could not only be used to infer new GO annotations, but could also be useful to indicate where GO terms should not be co-annotated (e.g. if you know that protein X is directly involved in process Y - then you should not consider annotating to 'regulation of process Y')

Communication within the GO consortium

Communication flow to ensure that the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)

Proposing annotation projects to the reference genome

see Strategy_for_establishing_RefG_annotation_priorities

Closing discussion and summary of meeting

Pascale Gaudet




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