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| [[Category:Meetings]]
| | #REDIRECT[[Talk:2010_GO_camp_Meeting_Agenda]] |
| =Day 1 morning session=
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| ===9:00 Introductions and objectives of the meeting===
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| # Introductions & Logistics: Serenella Ferro Rojas | |
| * Poll for Thursday lunch reservations, depending on weather.
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| * Dinner at [http://www.resto.ch/labourse/ Brasserie la Bourse] on the Carouge
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| ** ~ 1.9 km from meeting site
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| Friday
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| Reception at noon for Amos Bairoch celebration of the Otto Naegeli prize.
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| Introductions
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| ==== Goals: Pascale Gaudet ====
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| ===GO – Ontology, annotation, tools and technical aspects===
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| '''Chairs: Serenella Ferro Rojas and Pascale Gaudet'''
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| ==== GO overview ====
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| An introduction to the GO ontology : terms, definitions, synonyms, relationships, cross-products. Jane Lomax
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| * Inter-ontology links
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| ** Most tools don't make inferences across the ontoogies. Make redundant annotations.
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| ** Cross products
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| *** between GO ontologies
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| *** external ontologies (cell ontology; CHEBI)
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| * Ontology development
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| ** large scale targeted projects
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| ** logical consistency
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| ** small scale requests (Sourceforge tracker; future via Amigo)
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| Q/A: classical relationships (e.g. part_of within an ontology) are subset of cross-products.
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| ==== Annotation Process ====
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| ===== General overview of the annotation guidelines used by GO, and contributing resources. Rama Balakrishnan =====
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| ** Annotation guidelines
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| Goal:say as much as possible about a gene product. Be useful to bench and computational biologists.
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| * GO annotation: Gene product association with GO terms and other info.
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| ** Core
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| *** gene product identifiers
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| *** GO term
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| *** Reference
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| *** Evidence code
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| ** Additional info
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| *** qualifiers
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| *** with/from
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| *** Annotation detail (16)
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| *** Isoform
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| * Sources
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| ** Manual
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| ** Automated
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| ** PAINT (new)
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| *** inter-ontology inferences (new)
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| Differences between previous GO camps and this one. This one more internal and focused on strengthening guidelines.
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| * Challenges ...
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| * Avoiding redundancy.
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| ** Authoritative sources
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| *** no MOD - UniProt-GOA.
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| ===== General overview UniProtKB/SwissProt manual annotation. Serenella =====
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| * protein selected for manual annotation based on priorities
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| ** Recent papers chosen for high impact
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| ** Curation of specific processes (e.g ubiquitin-like conjugation)
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| ** User requests
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| Flow
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| * sequence curation
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| ** One record for all different products for the same gene
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| * Sequence analysis. - automated. manual checking. domains, ptms, etc.
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| * Literature curation. Species, protein names, gene names, journals, tissues, plasmids
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| ** Store as comment lines free text with controlled tags(?)
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| ** Sequence annotation of features (relation to SO?)
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| ** GO annotation 50 curators, Automated: spkw2go, mappings2GO, etc.
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| * Family-based curation
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| * Attribution
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| * QA and integration
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| ** e.g. throw error when nucleus kw for bacterial protein
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| Q: Isoforms?
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| A: linked to parent ID - ACCESSION_#
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| Q: Connection between references and items.
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| A: Findable in the XML. This is being retrofitted to older entries.
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| Q: What is the unit of annotation - Genes, isoforms?
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| A: Isoforms yes. Not yet things like cleavage products, but should be in the future.
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| ==10: 30 Binding documentation ==
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| * '''Chairs: Ruth Lovering and Ursula Hinz '''
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| *'''Minutes: Jim Hu - Damien Lieberherr
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| * '''Working group''': [[2010_GO_camp_working_groups_composition]]
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| * '''Working group notes''':[[2010_GO_camp_binding documentation issues| Binding documentation issues]]
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| 12:30 Lunch
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