|
|
(22 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
| [[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
| |