2015 Washington DC GOC Meeting Agenda: Difference between revisions
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(Helen offered to chair this discussion) | (Helen offered to chair this discussion) | ||
* General issues (Sandra) | * General issues (Sandra) | ||
** ID co-ordination between GO, | ** ID co-ordination between GO, Intact, and PRO [Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD] | ||
* Annotation guidance (Rama) | * Annotation guidance (Rama) | ||
* Ontology issues (David OS?) | * Ontology issues (David OS?) |
Revision as of 14:05, 14 August 2015
Please plan to join us this fall from August 30th through September 2nd for the next meeting of the Gene Ontology Consortium. We will host the meeting at the Marvin Conference Center, George Washington University, at the heart of Washington, DC.
- The GOC meeting will be held on August 30-31, 2015.
- A GOC Symposium day will be held on September 1, 2015. (Details will be posted here: http://wiki.geneontology.org/index.php?title=2015_Washington_DC_GOC_Symposium_Agenda)
- The GOC SAB will convene on September 2, 2015. (Details will be posted here: http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Scientific_Advisory_Board_Meeting_Agenda)
Details to follow soon.
Daily schedule
- Start: ??
- Morning coffee break: ??
- Lunch: ??
- Afternoon session: ??
- Afternoon coffee break: ??
Minutes
http://wiki.geneontology.org/index.php?title=2015_Washington_DC_GOC_Meeting_Minutes
Agenda for the main GOC meeting (August 30-31 2015)
Please ensure that all outstanding items from the trello board are covered here in the agenda under the appropriate heading.
User support and interaction
- GO survey and user experience
- GO enrichment analysis
- GO website and FAQs
- AmiGO
- GO helpdesk
- GO Facebook page
- Protein2GO: 15 min - demo/new features + 5 min discussion (ECO codes) - Aleksandra Shypitsyna
- PSIQUIC GO annotations (5 min) - Ruth
Phylogenetic Annotation
Literature Annotation
Annotation issues
- Guidelines for annotation to x-catabolism to capture the product of a reaction rather than the end product of a pathway (Pascale)
Proteome sets
- Resolving ID issues (what is in the ref_proteome, what is a gene centric proteome reference proteome, TrEMBL, SwissProt etc) (see e.g. http://jira.geneontology.org/browse/GO-820)
- https://github.com/geneontology/touchup/issues/14 - how to remedy the change in PAINT files format (we expect uniprot accessions in column 2 and those have been replaced by ensembl IDs)
Traceability of annotations
- When one annotation is derived from another (manually or logically) it would be useful to have an easy way to point back to the existing annotation. Tony Sawford
Annotating complexes to GO
(Helen offered to chair this discussion)
- General issues (Sandra)
- ID co-ordination between GO, Intact, and PRO [Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD]
- Annotation guidance (Rama)
- Ontology issues (David OS?)
Compounding Evidence codes
- Is it possible to do this and is it appropriate? An example of this would be capturing the evidence when a direct enzymatic assay is used to test the loss of function in a mutant enzyme (IDA or IMP) - Rama?
- Continuing discussion of IGI example from May annotation call - Rama
Annotation extension relationship progress
Usefulness of annotation extensions, intelligent querying (5 min) - David OS?
Survey how many groups who are actively annotating are using or are capable of using annotation extensions (5 min) - Rama?
Dealing with annotation extension inconsistencies (30 min) - Ruth/Rachael (e.g. dependent_on https://github.com/geneontology/annotation_extensions/issues/17)
Progress on documentation (10 min) - David OS/Rama
MicroRNA guideline summary
Brief overview (15 min) - Rachael Huntley
Resolution on chromatin binding
chromatin binding vs localization to chromatin (15 min) - Ruth, Karen, others?
Software, Database and API
- New architecture (Chris)
- GAF/GPAD version and file naming (Tony S)
Making use of annotation extensions
Very few tools consume annotation extensions usefully. For example, an annotation to 'cytosol' part of 'postsynapse' will NOT be grouped under postsynapse by the vast majority of tools. How can we fix this!?
Can we provide 'folded' temp terms for at least some AE relationships: @ a minimum, part_of + occurs_in.
Common Curation Environment and LEGO annotations
- Noctua update (Seth, Chris)
- Combined GO/Phenotype annotation (Chris)
Ontology Production and R&D
Molecular Function refactoring
David OS/Paul T?
Deepening annotations - develop ontology patterns e.g. protein binding
(David H/Chris/Paul T) https://trello.com/c/J9jFm8Ex/95-deepening-annotations-develop-ontology-patterns-e-g-protein-binding
Update on focused projects (vesicles, autophagy…)
Vesicles (Paola)
Biochemical pathways (David H)
Autophagy (David H)
Synapse project (David OS)
Cilia (Paola/Karen)
Other ontology issues
Protein production https://github.com/geneontology/go-ontology/issues/10787 (Pascale)
Ontology stats
Moving to GitHub (Chris)
A brief introduction to GitHub- getting accounts, submitting and updating tickets etc. With a focus on ontology requests.