2010 GO camp Geneva minutes

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

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

• 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.

Annotation extension discussion

 12:30 Lunch

Summary of ontology development

Chris not available until after lunch