2010 GO camp Geneva minutes: Difference between revisions
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=== Annotation extension discussion === | === Annotation extension discussion === | ||
Ruth | |||
* Annotation extension = column 16 | |||
* Should only be used for direct targets. | |||
* Examples | |||
** Co-IP. Lnx-I and Boz. Use two txn factor binding annotations with IPI and with for partner. | |||
**:Q: Do we need exp evidence that (e.g.) Boz is a txn factor? | |||
**:A: curator judgement at present. Rama: SGD would read the paper and make check other annotations of Boz, not just based on assertion in the paper. Same paper does not have to show Boz is a txn factor. Ruth: in humans, would use sequence analysis, e.g. domains. Actually SGD doesn't annotate protein binding. | |||
12:30 Lunch | |||
=== Summary of ontology development === | === Summary of ontology development === | ||
Chris not available until after lunch | Chris not available until after lunch |
Revision as of 05:14, 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
Q: Isoforms?
A: linked to parent ID - ACCESSION_#
Q: Connection between references and items.
A: Findable in the XML. This is being retrofitted to older entries.
Q: What is the unit of annotation - Genes, isoforms?
A: Isoforms yes. Not yet things like cleavage products, but should be in the future.
Break
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
Binding has been discussed at three consortium meetings.
Current guidelines
Ursula:
- Binding biological entity (not today)
Macromolecules (proteins)
- specific proteins vs. protein classes vs. protein domains
- GO:0005505 must be with IPI and reciprocal annotation should be made.
- Use child terms
- Evidence
- IPI for specific proteins
- IDA for clases of protein
- Propagation
- GO0005515 should not be propagated via ISS.
- propagation of child term annotations is OK
- Do not use NOT with GO:0005515
- NOT with chilld terms is OK.
Small molecules
- avoid redundant annotation of substrates, including transporter substrates
- e.g. ATP binding for ATPases (exceptions where hydrolysis not shown)
- Example DNA demethylase/dioxygenase
- are annotations to alkylated DNA binding, O2 binding etc. redundant.
Discussion
Q: protein binding - evidence that it does not bind a specific protein. Need a new GO term?
A: No. Use column 16 or create new GO term. Still in discussion. GO terms if the proteins can be put into groups. Don't want specific protein terms.
Q: What is wrong with having 25K GO terms?
A: Does it matter? May be able to do all PRO classes. Instantiate as needed.
Comment: NOT terms.. IntAct only annotates negative interactions for isoforms where a different isoform has a positive isoform. Negatives are not exported to GO.
Judy summary: discussion of are we going to instantiate lots of protein binding terms. PRO families could be used for terms. Column 16 could be used for NOT and specific isoforms.
Emily: some things are not well captured by GO.
Annotation extension discussion
Ruth
- Annotation extension = column 16
- Should only be used for direct targets.
- Examples
- Co-IP. Lnx-I and Boz. Use two txn factor binding annotations with IPI and with for partner.
- Q: Do we need exp evidence that (e.g.) Boz is a txn factor?
- A: curator judgement at present. Rama: SGD would read the paper and make check other annotations of Boz, not just based on assertion in the paper. Same paper does not have to show Boz is a txn factor. Ruth: in humans, would use sequence analysis, e.g. domains. Actually SGD doesn't annotate protein binding.
- Co-IP. Lnx-I and Boz. Use two txn factor binding annotations with IPI and with for partner.
12:30 Lunch
Summary of ontology development
Chris not available until after lunch