2010 GO camp Meeting Agenda: Difference between revisions

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# Introduction to the Reference Genome Project. Pascale Gaudet (20 min)
# Introduction to the Reference Genome Project. Pascale Gaudet (20 min)
# Automated Inferencing methods. Alan Bridge. (20 min)
# Automated Inferencing methods. Alan Bridge. (20 min)
#* Ensembl compara pipeline.
#* HAMAP inferencing
#* HAMAP inferencing
# PAINT phylogenetic inferencing. Paul Thomas (30 min)
# PAINT phylogenetic inferencing. Paul Thomas (30 min)
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   Break
   Break


==Response to terms==
==Response to terms==

Revision as of 04:10, 1 June 2010

Day 1 morning session

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 SwissProt. Serenella (15 min)
 Break

Binding documentation

Chairs: Ruth Lovering and Ursula Hinz


Day 1 afternoon session

Annotation and annotation propagation

Chairs: Alan Bridge and Paul Thomas

  1. Introduction to the Reference Genome Project. Pascale Gaudet (20 min)
  2. Automated Inferencing methods. Alan Bridge. (20 min)
    • HAMAP inferencing
  3. PAINT phylogenetic inferencing. Paul Thomas (30 min)
    • Rules and guidelines for inferencing
    • PAINT software and examples

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

Chairs: Rebecca Foulger and Pascale Gaudet



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

Chairs: Rama Balakrishnan and TBA from Swiss-Prot

  • 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

Chairs: Pascale Gaudet and Bernd Roechert


Day 2 afternoon session

 Explore Geneva
 Group dinner

Day 3 morning session

Use of Regulation

Chairs: Jane Lomax and Kimberly VanAuken

 Break


How is a downstream effect defined

Chairs: Rachael Huntley and Varsha Khodiyar

Day 3 afternoon session: Future plans

Chairs: Suzanna Lewis and Pascale Gaudet

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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