2015 Washington DC GOC Meeting Agenda

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: 8:30AM
• Morning coffee break: 10:30AM
• Lunch: 12:30PM
• Afternoon session: 2:00PM
• Afternoon coffee break: 4:00PM
• Close of day: 6:00PM

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.

Operations Update

• GitHub update (Chris)
  • This should come first as it pertains to other business on agenda
  • A brief introduction to GitHub, with a focus on ontology requests
    • getting accounts
    • submitting and updating tickets etc.
    • permissions and pull requests (editing metadata, and the general github workflow)
  • https://docs.google.com/document/d/1iyVY8kDBJIEydoWFLG9j5BoO4VmdIXES95fVhIkFXfk/edit#
  • How to be more effective in organizing and prioritizing issues
  • Proposed migration of ontologies from SVN
• New architecture (Chris)

Usability: are we delivering?

• AmiGO 2.3 (Seth)
• GO survey and user experience (Paola)
• GO enrichment analysis
• GO website and FAQs
• GO helpdesk
• GO Facebook page
• GO tools registry
• GO for non-GOC members: how can non-MODs most effectively use GO?

Common Curation Environment and LEGO annotations

• Noctua update (Seth, Chris)
• Walkthrough (TBA: we will send a paper out in advance of the meeting)
• Combined GO/Phenotype annotation (Chris)
• Scaling up and next steps (Chris)
  • 2015-12 milestone
  • Bootcamp/Jamboree? Where?

Ontology

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

Standardizing protein production classes

See: https://github.com/geneontology/go-ontology/issues/10787 (Pascale)

Annotation

Annotating complexes to GO (last session on first day as Sandra as to leave on day 2)

• Annotation guidance (Rama)
• Ontology issues (David OS)
• ID co-ordination between GO, Intact, and PRO (Sandra)
  • Contacts: Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD

Guidelines for curators: Lessons from PAINTing

• PAINT curation progress update (Huaiyu)
• Guidelines for annotation to x-catabolism to capture the product of a reaction rather than the end product of a pathway (Pascale)
• Guidelines for annotation of ligands (Pascale) - see email exchange dates Aug 7, 2015

Making use of annotation extensions

• 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)
• Downstream, very few tools can 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.
• Progress on documentation (10 min) - David OS/Rama

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) - Tony S.

Evidence codes

• When are we deprecating the 3 letters codes? (Also pertains to the GAF/GPAD discussion below)
• Is it possible to compose evidence codes 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

GAF/GPAD

• Standardizing GAF Names
  • Proposal to standardize GAF names - 5-10 min. proposal + discussion time (Kimberly)
    • Generic file name: lower case submitting group abbreviation from GO.xrf_abbs_NCBI taxon id_NCBI taxon id name.gaf.gz
    • NCBI taxon id name would be the corresponding taxonomic name or lower case genus species name abbreviated as: gspecies
  • Examples:
    • wb_6239_celegans.gaf.gz
    • wb_6157_platyhelminthes.gaf.gz
  • Does this work for everyone?
  • Other information currently in file names, such as 'ref' and 'noieas'. Will this information stay?
  • Related issue: How many varieties of GAF files should GO offer for download, i.e. gene-centric, transcript-centric, proteome-centric?

• GAF/GPAD version and file naming (Tony S)

gp2protein Files

• 5-10 min. + discussion (Kimberly)
  • How are they currently used?
  • Are they still needed?
  • What other options are available, and currently used, for mapping IDs across databases?
  • How should responsibility/workflow for ID synchronization be managed?
  • If we continue to provide them, standardize file names, as well, e.g. wb_gp2protein_6239_celegans.tab.gz?

Update on focused projects

• PSIQUIC GO annotations (5 min) - Ruth
• Synapse and Roche projects (David OS, Huaiyu)
• Improving the assistance we provide to external groups offering to annotate (Moni, Melanie, Rama)
• Strategies and templates for independent funding of targeted projects ? (e.g. eye, Ruth)
• Internal: Vesicles (Paola), Biochemical pathways (David H), Autophagy (David H), Cilia (Paola/Karen)

Protein2GO

• Protein2GO: 15 min - demo/new features + 5 min discussion (ECO codes) - Aleksandra Shypitsyna

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 (and not just a gene product). Tony Sawford

MicroRNA guideline summary

• Brief overview (15 min) - Rachael Huntley

Reactome Annotations

• Reactome Annotations: TAS or EXP? (Harold; Peter)
  • Brought up in 2007 (http://gocwiki.geneontology.org/index.php/2007_GOC_Action_Items). Thought resolved here: http://gocwiki.geneontology.org/index.php/GO_18th_Consortium_Meeting_Action_Items (2009)

Resolution on chromatin binding

• chromatin binding vs localization to chromatin (15 min) - Ruth, Karen, others?

Breakout thoughts

1. OBO-Edit to Protege transition
   • Rama, David H, Chris, David OS
2. Shedding server services from Stanford (move to Amazon)
   • Chris, Seth, Mike, Rama
3. Review SAB slides