2015 Washington DC GOC Meeting Agenda

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Please plan to join us this fall on 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 Marvin Conference Center is located at 800 21st St NW Washington, DC 20052.

The 2015 GO meeting will include an all-day symposium + workshops day, open to the research community. During the GO Symposium + Workshops day we will host two talks about research projects that highlight the use of our resources, and offer workshops on annotation and term enrichment using the GO. More details are available on the Agenda Pages for the GOC2015 Meeting. We will also count with the participation of our Scientific Advisory Board.

Planned Schedule for the Week of the Meeting

  • Sunday August 30 and Monday August 31 - GOC Meeting:
  • Tuesday September 1 - GO Symposium + Workshops:
  • Wednesday September 2 - Scientific Advisory Board Meeting:


Daily Schedule for the GOC Meeting

  • Plan to arrive on Sunday and Monday morning at 8:30AM.
  • Breakfast will be served from 8:30AM - 9:00 AM
  • Morning coffee break: 10:30AM
  • Lunch: 12:30 - 2:00 PM
  • Afternoon session: 2:00 PM
  • Afternoon coffee break: 3:30 PM
  • Close of day: 5:00 PM


GOC2015 Meeting Dinner

Circa

We have a reservation at Circa At Foggy Bottom on Monday 31-August-2015 at 6:30 PM. Circa is located at 2221 I St NW Washington, DC 20037, within walking distance of both the Meeting Venue and the Hotel. Please see the map to the right to review its location. Please be courteous and respectful of everyone's time. Our reservation is at 6:30 PM, so please plan to be there 5 minutes in advance. Thank you!

Minutes

The Minutes of the GOC2015 Meeting are recorded in this Google Document.


Agenda

Please ensure that all outstanding items from the Trello board are covered here and under the appropriate heading.


Breakout Groups - Fit in however possible

  1. OBO-Edit to Protege transition
    • Rama, David OS, Chris
  2. SF/ cell cycle ticket resolution
    • David H, Val
  3. Shedding server services from Stanford (move to Amazon)
    • Chris, Seth, Mike, Rama
  4. GO Handbook Chapters - coordination and reconciliation of contents.
    • Paul T, Suzi, Chris, Claire, Rachael, Ruth, Pascale, moni.
  5. UniProt & Ensembl: how to remedy the change in PAINT files format (we expect uniprot accessions in column 2 and those have been replaced by ensembl IDs). - See GitHub Issue here.
    • Tony S, Paul T, Suzi.
  6. Review SAB slides
  7. Revise GO user survey
    • Paola, Mike



Day 1

1. Operations Update

  • GitHub update (Chris) (20 minutes)
    • 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)


2. Usability: are we delivering?

  • GO HelpDesk - (moni, Rama) Rota checkup, Stats on open/closed topics, efficiency.
  • GO Facebook page - (moni)
  • GO for everyone; GOC and non-GOC members:
  • how can non-MODs most effectively use GO? (moni).
  • Contributing to GO
  • Documentation (moni)
  • Improving the assistance we provide to external groups offering to annotate (Moni, Melanie, Rama)
  • Deposit GAF2.0 on GitHub (Seth - for the future)
  • Updated naming conventions (Kimberly).
  • GO tools registry (Paola, 10')


3. Common Curation Environment and LEGO annotations

  • Noctua update (Seth, Chris) (45 mins)
  • Refresher on LEGO concepts (Paul, Chris)
  • Walkthrough (TBA: we will send a paper out in advance of the meeting) (Rama)
  • Combined GO/Phenotype annotation (Chris)
  • Scaling up and next steps (Chris) (15 minutes)


4. Ontology

Molecular Function refactoring

David OS/Paul T?

  • detailed discussion in breakout, main summary at meeting

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


5. Annotation

Annotating complexes to GO

(Claire will be chairing the discussion)

  • 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


Day 2

5. Annotation (Continued)

Standardizing protein production classes

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

Guidelines for curators: Lessons from PAINTing (30 min)

  • PAINT curation progress update (Huaiyu) Slides
  • 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

Update on focused projects (20 min)

gp2protein Files & Proteome sets (20 min)

  • Update on what the ref_proteome is, what a gene centric proteome reference proteome is, TrEMBL, SwissProt etc. See UniProt-in-GO Glossary document here and the related JIRA ticket here.
  • 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?

GAF/GPAD (30 min)

  • Standardizing GAF/GPAD Names and Versions (Tony S)
    • 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?

Evidence codes (20 min)

  • Set timelines for deprecation of the 3 letters codes in GAF and replacing with ECO identifiers
  • 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

Making use of annotation extensions (45 min)

  • 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) - File:AnnotationExtensionGOC2015 RH.pptx 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.
    • Demo of how this works in Jenkins inference pipeline (Heiko)
  • Progress on documentation (10 min) - David OS/Rama

Protein2GO (15 min)

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

Reactome Annotations (30 min)

Traceability of annotations (15 min)

  • 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 (15 min)

Annotation guidelines (30 min)

  • Resolution on chromatin binding: chromatin binding vs localization to chromatin (15 min) - Ruth, Karen, others? Presentation slides
  • Resolution on regulation of activity: Would you annotate a protein involved in localisation (or regulation of localisation) of X to ‘regulation of X activity’ ?

Parked Items

  • GO on Wikipedia/Wikidata (melanie, davidOS, chris) (5 minutes)
  • displaying all PANTHER species in GO website enrichment tool (see http://jira.geneontology.org/browse/GO-888) (suggested by Paola).
  • Internal: Vesicles (Paola, 5'), Biochemical pathways (David H, 5'), Autophagy (David H, 5'), Cilia (Paola/Karen, 5')

Wrap-up

  • Review action items

Group Photo

2015 GOC Group Photo at George Washington University