2010 GO camp Geneva minutes: Difference between revisions

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[[Category:Meetings]]
#REDIRECT[[Talk:2010_GO_camp_Meeting_Agenda]]
=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 [http://www.resto.ch/labourse/ 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 ==
* '''Chairs: Ruth Lovering and Ursula Hinz '''
*'''Minutes: Jim Hu - Damien Lieberherr
* '''Working group''': [[2010_GO_camp_working_groups_composition]]
* '''Working group notes''':[[2010_GO_camp_binding documentation issues| 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. 
 
Paul: Annotations for the target must exist somewhere.  Does this create redundancy to annotate binding to proteins of function X where target has function X?
 
Jane: Won't always be function terms.  e.g. LIM binding domain binding.
 
Ruth: GOC still needs more discussion.
 
Judy: no inconsistency in what SGD does and what Ruth does.  Annotations are consistent but SGD chooses different annotations to make.
 
 
 
 
 
  12:30 Lunch
 
=== Summary of ontology development ===
Chris not available until after lunch

Latest revision as of 05:07, 17 June 2010