2010 GO camp Meeting Agenda: Difference between revisions
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*'''Chairs: Jane Lomax and Kimberly VanAuken''' | *'''Chairs: Jane Lomax and Kimberly VanAuken''' | ||
*'''Slides:''' | *'''Slides:''' | ||
;# [[Regulation slides.pdf| introduction and guidelines slides]] | ;# [[Media:Regulation slides.pdf| introduction and guidelines slides]] | ||
;# [[Regulation example.pdf| regulation example slides]] | ;# [[Regulation example.pdf| regulation example slides]] | ||
*'''Minutes: Susan Tweedie and Andrea Auchincloss''' | *'''Minutes: Susan Tweedie and Andrea Auchincloss''' |
Revision as of 08:13, 9 July 2010
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
- Introductions & Logistics: Serenella Ferro Rojas
- Goals: Pascale Gaudet
GO – Ontology, annotation, tools and technical aspects
Chairs: Serenella Ferro Rojas and Pascale Gaudet
- 9:15 Presentation: 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) Presentation: File:Rama-intro-to-annotation.pdf
- 9:45 General overview UniProtKB/SwissProt manual annotation. Serenella (15 min)Presentation: File:Serenella-Swiss-Prot Intro.pdf
10: 15 Break
10: 30 Binding documentation
- Chairs: Ruth Lovering and Ursula Hinz
- File:BindingUrsula-Ruth.pdf
- 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 Presentation: File:EnsemblCompara annotation propagation-2010.06.16.pdf
- 1:50 Automated Inferencing methods. Alan Bridge ~ 20 min Presentation: File:Alan-Propagation-UniProtKB.pdf
- HAMAP inferencing
- 2:15 Reference genome: GO's approach to annotation propagation
- Introduction to the Reference Genome Project Pascale ~ 10 min Presentation: File:Pascale-2010-reference-genome-intro.pdf
- Phylogenic tree-based homology annotation- Paul ~ 20 min
- PAINT demo and examples. Mike ~ 20 min Presentation: File:Mike-Annotation-using PAINT.pdf
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
Presentation: 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)
- Presentation: File:Rachael-GO Browser Talk.pdf
10:00 Annotation of HTP data: reviewing the guidelines
- Chairs: Rama Balakrishnan and TBA from Swiss-Prot
- Minutes: Cecilia Arighi , Silvia Jimenez and Anne Estreicher
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Annotation of HTP data
- Rama : SGD practices | Presentation: File:Geneva HTP.pdf
- Swiss-Prot practices | Presentation : File:Manu-SP-HTP.pdf
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: Mike Livstone - 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
- Slides:
- Minutes: Susan Tweedie and Andrea Auchincloss
- 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 Alam-Faruque and Ursula Hinz
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes Downstream effect issues
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
- Annotation Matrix method (Val Wood) Presentation: File:Val-Matrix-QC.pdf
- Taxon checks
- Specific checks based on GO IDs and evidence codes: 5515, IEP, etc (Rama) - File:Annotation QCs rb.pdf
- Summary from all working groups File:QC-complexes-response.pdf File:BindingSummary.pdf Downstream Process Summary slides
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:
- Annotations to the protein binding terms should be maximally informative
- Curators should not use the IPI evidence code along with catalytic activity molecular function terms (if SGD annotation review supports this)
- Annotation extension (column 16) should only be used for direct target of catalytic activity (using relationship ontology)
- Do not use Annotation extension (column 16) for indirect targets
- Use ‘with’ column or column 16 only if the GO term definition does not provide information
- 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"
- 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:
- Annotation of 'NOT' binding a specific protein: new GO term or column 16 (consider IntAct guidelines on this)?
- 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?
- Transferring cross species information by ISS and inclusion of non-in-vivo targets in column 8 or 16.
- How specific to make substrate/product target information?
- Will CHEBI IDs in function ontology propagate to process terms?
- Existing GO to follow new has_part relationships implying substrate binding
Unresolved issues to be discussed by other groups:
- Incorporation of IMEX data being discussed
- Col 16 relationship ontology (has_input=substrate)
Response to group
- Pascale Gaudet and Rebecca Foulger
- Update definition of response to terms to indicate that we are capturing mediators (wording needs to be worked out)
- Quality control check: High level ‘response to’ terms should not directly be used for annotation
- Update guidelines: Encourage the use of granular terms for ‘responses’
- Update guidelines: Expression experiments should not be annotated to response to terms
Protein complexes group
- Pascale Gaudet and Bernd Roechert
- Long term goal is to annotate complexes; details and requirements need to be clarified.
- Guidelines + Quality control check: Avoid annotations to GO: MF by IPI (except for ‘protein binding’ and children)
- Error reports will be generated
- 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
- What is the process term for a specific transcription factor? (i.e. 'transcription' or 'regulation of transcription'?) ACTION: transcription ontology revision
- Define the start and end of signaling processes. ACTION: signaling working group
- 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?
- Some MODs keep legacy annotations (i.e. correct annotations to downstream processes), but some prefer to remove them, is this a problem? ACTION: all
- Form a working group to look into phenotype/development/IMP issues. How should we annotate to development terms?
- 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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