2010 GO camp Geneva minutes: Difference between revisions
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Q/A: classical relationships (e.g. part_of within an ontology) are subset of cross-products. | Q/A: classical relationships (e.g. part_of within an ontology) are subset of cross-products. | ||
==== Annotation Process ==== | ==== Annotation Process ==== | ||
===== General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan ===== | |||
** Annotation guidelines | ** Annotation guidelines | ||
Goal:say as much as possible about a gene product. Be useful to bench and computational biologists. | Goal:say as much as possible about a gene product. Be useful to bench and computational biologists. | ||
Line 56: | Line 56: | ||
===== General overview UniProtKB/SwissProt manual annotation. Serenella ===== | |||
* protein selected for manual annotation based on priorities | |||
** Recent papers chosen for high impact | |||
** Curation of specific processes (e.g ubiquitin-like conjugation) | |||
** User requests | |||
Flow | |||
* sequence curation | |||
** One record for all different products for the same gene | |||
* Sequence analysis. - automated. manual checking. domains, ptms, etc. | |||
* Literature curation. Species, protein names, gene names, journals, tissues, plasmids | |||
** Store as comment lines free text with controlled tags(?) | |||
** Sequence annotation of features (relation to SO?) | |||
** GO annotation 50 curators, Automated: spkw2go, mappings2GO, etc. | |||
* Family-based curation | |||
* Attribution | |||
* QA and integration | |||
** e.g. throw error when nucleus kw for bacterial protein | |||
==10: 30 Binding documentation == | ==10: 30 Binding documentation == |
Revision as of 04:14, 16 June 2010
Day 1 morning session
9:00 Introductions and objectives of the meeting
- Introductions & Logistics: Serenella Ferro Rojas
- Poll for Thursday lunch reservations, depending on weather.
- Dinner at Brasserie la Bourse on the Carouge
- ~ 1.9 km from meeting site
Friday Reception at noon for Amos Bairoch celebration of the Otto Naegeli prize.
Introductions
Goals: Pascale Gaudet
GO – Ontology, annotation, tools and technical aspects
Chairs: Serenella Ferro Rojas and Pascale Gaudet
GO overview
An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax
- Inter-ontology links
- Most tools don't make inferences across the ontoogies. Make redundant annotations.
- Cross products
- between GO ontologies
- external ontologies (cell ontology; CHEBI)
- Ontology development
- large scale targeted projects
- logical consistency
- small scale requests (Sourceforge tracker; future via Amigo)
Q/A: classical relationships (e.g. part_of within an ontology) are subset of cross-products.
Annotation Process
General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan
- Annotation guidelines
Goal:say as much as possible about a gene product. Be useful to bench and computational biologists.
- GO annotation: Gene product association with GO terms and other info.
- Core
- gene product identifiers
- GO term
- Reference
- Evidence code
- Additional info
- qualifiers
- with/from
- Annotation detail (16)
- Isoform
- Core
- Sources
- Manual
- Automated
- PAINT (new)
- inter-ontology inferences (new)
Differences between previous GO camps and this one. This one more internal and focused on strengthening guidelines.
- Challenges ...
- Avoiding redundancy.
- Authoritative sources
- no MOD - UniProt-GOA.
- Authoritative sources
General overview UniProtKB/SwissProt manual annotation. Serenella
- protein selected for manual annotation based on priorities
- Recent papers chosen for high impact
- Curation of specific processes (e.g ubiquitin-like conjugation)
- User requests
Flow
- sequence curation
- One record for all different products for the same gene
- Sequence analysis. - automated. manual checking. domains, ptms, etc.
- Literature curation. Species, protein names, gene names, journals, tissues, plasmids
- Store as comment lines free text with controlled tags(?)
- Sequence annotation of features (relation to SO?)
- GO annotation 50 curators, Automated: spkw2go, mappings2GO, etc.
- Family-based curation
- Attribution
- QA and integration
- e.g. throw error when nucleus kw for bacterial protein
10: 30 Binding documentation
- Chairs: Ruth Lovering and Ursula Hinz
- Minutes: Jim Hu - Damien Lieberherr
- Working group: 2010_GO_camp_working_groups_composition
- Working group notes: Binding documentation issues
12:30 Lunch