2010 GO camp Meeting Agenda

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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


 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

  • Chairs: Jane Lomax and Kimberly VanAuken
  • Slides:
  1. Introduction and guidelines slides
  2. Regulation example slides
 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

Presentation: File:GO camp 2010 CACAO.pdf

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

Binding group

  • Ursula Hinz and Ruth Lovering

Write up Guidelines and QC agreed in GO Consortium meeting based on binding guidelines

Add to guidelines:

  1. Annotations to the protein binding terms should be maximally informative
  2. Curators should not use the IPI evidence code along with catalytic activity molecular function terms (if SGD annotation review supports this)
  3. Annotation extension (column 16) should only be used for direct target of catalytic activity (using relationship ontology)
  4. Do not use Annotation extension (column 16) for indirect targets
  5. Use ‘with’ column or column 16 only if the GO term definition does not provide information
  6. Has_part to be used to provide links between MF terms and implied substrate binding, existing GO to follow new has_part relationships implying substrate binding eg Transcription factor 'has_part' parent "DNA binding"
  7. Request new Has_part 'binding' parent if this relationship does not exist

Unresolved issues to be discussed by binding group /2010_GO_camp_binding_documentation_issues#Unresolved_issues unresolved issues section:

  1. Annotation of 'NOT' binding a specific protein: new GO term or column 16 (consider IntAct guidelines on this)?
  2. Automate annotation to specific binding term from known functions of protein, eg transcription factor binding, based on evidence that protein is transcription factor, or domain implied? Or not create this type of term?
  3. Transferring cross species information by ISS and inclusion of non-in-vivo targets in column 8 or 16.
  4. How specific to make substrate/product target information?
  5. Will CHEBI IDs in function ontology propagate to process terms?
  6. Existing GO to follow new has_part relationships implying substrate binding

Unresolved issues to be discussed by other groups:

  1. Incorporation of IMEX data being discussed
  2. Col 16 relationship ontology (has_input=substrate)

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
  1. Add to the guidelines: Do not make EXP annotations to MF when only the CC is observed

Downstream Processes group

  • Rachael Huntley and Varsha Khodiyar
  1. What is the process term for a specific transcription factor? (i.e. 'transcription' or 'regulation of transcription'?) ACTION: transcription ontology revision
  2. Define the start and end of signaling processes. ACTION: signaling working group
  3. Is a ligand part of the pathway? Can it also regulate the pathway? Is there a difference between intra- and inter-cellular pathways regarding the ligand?
  4. Some MODs keep legacy annotations (i.e. correct annotations to downstream processes), but some prefer to remove them, is this a problem? ACTION: all
  5. Form a working group to look into phenotype/development/IMP issues. How should we annotate to development terms?
  6. Regarding the survey question 2, whether to annotate ubiquitin ligases to regulation of histone methylation, Val will give reasons why she would like to annotate to regulation of histone methylation. The ontology may need altering to reflect the step-by-step nature of this pathway. ACTION: Val/Sylvain/Ontology editors

Group picture

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