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


  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

  1. 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
  • 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.


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

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.
 12:30 Lunch

Summary of ontology development

Chris not available until after lunch