2010 GO camp Meeting Agenda
Day 1 morning session
8:30 Registration
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 UniProtKB/SwissProt manual annotation. Serenella (15 min)File:Serenella-Swiss-Prot Intro.pdf
10: 15 Break
10: 30 Binding documentation
- Chairs: Ruth Lovering and Ursula Hinz
- File:Bindingannotationsurvey-Ruth-Ursula.pdf
- Minutes: Jim Hu - Damien Lieberherr
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Binding documentation issues
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
- 1:30 Compara (remote presentation). Javier ~ 20 min
- 1:50 Automated Inferencing methods. Alan Bridge ~ 20 min
- HAMAP inferencing
- 2:15 Reference genome: GO's approach to annotation propagation
- Introduction to the Reference Genome Project Pascale ~ 10 min
- Phylogenic tree-based homology annotation- Paul ~ 20 min
- PAINT demo and examples. Mike ~ 20 min
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
3:15 Break
3:30 Response to terms
File:WG-Response-to-Becky-Pascale.pdf
- Chairs: Rebecca Foulger and Pascale Gaudet
- Minutes: Michele Magrane - Shyamala Sundaram
- 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)
10:00 Annotation of HTP data: reviewing the guidelines
- Chairs: Rama Balakrishnan and TBA from Swiss-Prot
- Minutes: Cecilia
- 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)
10:20 New evidence codes proposal
Rama
10:30 Break
10:45 Annotation of complexes
- Chairs: Pascale Gaudet and Bernd Roechert
- File:WG-Protein-complexes-Pascale-Bernd.pdf
- Minutes: MikeL - Kristian Axelsen
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Annotation of complexes issues
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
- Minutes: Susan T
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Use of Regulation issues
10:30 Break
10:45 How is a downstream effect defined
- Chairs: Rachael Huntley and Varsha Khodiyar
- *Minutes: Yasmin, Ursula
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes Downstream effect issues
12:00 lunch
2:00 Day 3 afternoon session: Future plans
- Chairs: Suzanna Lewis and Pascale Gaudet
- Minutes: Jane and Val
2:00 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')
2:30 Community involvement in annotation
- Jim Hu: students project CACAO
- dictyBase, pomBase: involving the community
3:00 Break
3:15 Proposing annotation projects to the reference genome
see Strategy_for_establishing_RefG_annotation_priorities
3:30 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)
Closing discussion and summary of meeting
Pascale Gaudet