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) | ||
#* 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
- Introductions & Logistics: Serenella Ferro Rojas
- Goals: Pascale Gaudet
GO – Ontology, annotation, tools and technical aspects
Chairs: Serenella Ferro Rojas and Pascale Gaudet
- 9:15 An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax (10-15 min)
- 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
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Binding documentation issues
Day 1 afternoon session
Annotation and annotation propagation
Chairs: Alan Bridge and Paul Thomas
- Introduction to the Reference Genome Project. Pascale Gaudet (20 min)
- Automated Inferencing methods. Alan Bridge. (20 min)
- HAMAP inferencing
- PAINT phylogenetic inferencing. Paul Thomas (30 min)
- Rules and guidelines for inferencing
- PAINT software and examples
Questions from participants
- How do other groups deal with the issue of not being able to propagate IC GO annotations, leading to inconsistent GO annotation? (Eleanor/Becky).
- How to define the limits of ISS propagation from phylogenetic studies ? (Manu)
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes Annotation propagation rules
Break
Response to terms
Chairs: Rebecca Foulger and Pascale Gaudet
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Response to terms issues
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
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Annotation of HTP data
- Rama : SGD practices
- Swiss-Prot practices
Questions from the users
- 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
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Annotation of complexes issues
Day 2 afternoon session
Explore Geneva Group dinner
Day 3 morning session
Use of Regulation
Chairs: Jane Lomax and Kimberly VanAuken
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Use of Regulation issues
Break
How is a downstream effect defined
Chairs: Rachael Huntley and Varsha Khodiyar
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes Downstream effect issues
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