2010 GO camp Meeting Agenda

Day 1 morning session

Introductions and objectives of the meeting

Serenella Ferro Rojas and Pascale Gaudet

GO – Ontology, tools and technical aspects

1. An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax (10-15 min)
2. Latest GO developments. Chris Mungall (30 min)
   1. The extended GO OBO format
3. Annotation Process : General overview (Rama Balakrishnan)
   1. New annotation format – GAF2.0
   2. Annotation extensions (column 16)
4. GO browsers: AmiGO and QuickGO. Rachael Huntley (30 min)

Day 1 afternoon session

Annotation and annotation propagation

Chairs: Alan Bridge and Paul Thomas

• Working group: 2010_GO_camp_working_groups_composition
• Working group notes Annotation propagation rules

1. Introduction to the Reference Genome Project. Pascale Gaudet (20 min)

• Review of the annotation guidelines used by GO, UniProt and other contributing resources(e.g. Ensembl compara), questions/discussions
• PAINT software and examples

---

Day 2 morning session: Focused annotation Session 1

Response to terms

Chairs: Rebecca Foulger and Pascale Gaudet

• Working group: 2010_GO_camp_working_groups_composition
• Working group notes: Response to terms issues

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 2 afternoon session : Focused annotation Session 2

Binding documentation

Chairs: Ruth Lovering and Ursula Hinz

• Working group: 2010_GO_camp_working_groups_composition
• Working group notes: Binding documentation issues

Annotation of complexes

Chairs: Pascale Gaudet and Bernd Roechert

• Working group: 2010_GO_camp_working_groups_composition
• Working group notes: Annotation of complexes issues

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

Day 3 morning session: Focused annotation Session 3:

Use of Regulation

Chairs: Jane Lomax and Kimberly VanAuken

• Working group: 2010_GO_camp_working_groups_composition
• Working group notes: Use of Regulation issues

Day 3 afternoon session: Future plans

Chairs: Suzanna Lewis and Pascale Gaudet

1. Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)
2. Annotation process
3. Annotation infrastructure
4. Co-annotation/verification system
   • Taxon checks
   • Annotation Matrix method (Val Wood)
   • Specific checks based on GO IDs and evidence codes
   • 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')

Closing discussion and summary of meeting

Pascale Gaudet

---

---

Other suggestions for agenda items

1. What is the bottle neck for manual annotations (with experimental evidence)? How can we step up manual curation? (Rama)
2. How are the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)
3. How to define the limits of ISS propagation from phylogenetic studies ? (Manu)
4. How to distinguish between large-scale experiments (LSE) and specific experiments derived GO annotation ? PubMed list of LSE, additional tags ?!? (Manu)
5. How do other groups deal with the issue of not being able to propagate IC GO annotations, leading to inconsistent GO annotation? (Eleanor/Becky).

---

Back to 2010_GO_camp_Meeting_Logistics