2013 Cambridge GOC Meeting Agenda

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The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following Biocuration 2013.

Action Iterms

  1. On table Suzi to organize a working group on Phenotype to Process question. They will report recommendations at the April GO meeting.
  2. in progress (bug Seth) Goal is to figure out what should be on the public website (relevant to all kinds of users).
  3. in progress [Seth] move current content to the Drupal system, set up a beta site and give external users access to this. will use this time to do some spring cleaning as well.
  4. in progress [Seth] Set up a working group what will make the landing page.
  5. done (as in we have no recollection--if important will come up again) [Seth] Provide Solr frontend/widgets to external groups. Specifically ZFIN and the plant ontology group. Maybe sometime with WikiGenes/Andrew Su
  6. in progress [Seth] Seth and Paul S will work out what is useful on a stats page (via AmiGO 2).
  7. discussion had [Tony, Seth, Chris] Tony and Seth/Chris will coordinate development on the use of the Solr indices in QuickGO & AmiGO. Might have a Solr interest group f2f meeting. MGI folks (Joel Richardson and Jim Kaden) are also interested.
  8. [Mike] Mike will send around the link so that anyone who is interested can vote on the new GO Logo. Mike will make the final call on who gets the $300.
  9. DONE Help Desk 10 week rotation works, answers can appear on our drupal main page, start sending answers out to forum, eliminate separate rota for software questions by merging into a single list.
  10. DONE - TAIR group now hosting and managing GOhelp JIRAGOhelp staff, others compile gripe list, give to Rama, so we can come up with a better solution for managing emails, reports, etc.
  11. carried forward We should draft a survey and have the SAB critque the survey.
  12. in progress [Seth, Chris] Seth and Chris will work with go-managers on plan for Drupal transition. Defined action items.
  13. Add meetings that people are attending to the central GO Calendar (Google Cal)
  14. in progress (but we've booted pub pages?) Once Drupal is set up then everyone (as part of the Drupal training) will update their publication
  15. done (suggested by Paul T) Come up with a Tag Line for GOC to add to the new logo. Decide this by end of the meeting. Add your ideas here!
  16. in progress (will go with new site) [Seth] Implement CC BY as our licensing on new site
  17. in progress Heiko will proceed with incorporating OE user features into Protege. He’s already added the graph viewer. No timeline for completion of new version
  18. in progress For terms that don’t have a template, Heiko can add a button (or some ui manipulable) to termgenie so that curators can easily submit the term request on the spot.
  19. in progress Work with CHEBI on providing reciprocal links from CHEBI interface (Alan Bridge’s mass spec use case)
  20. done Publish ChEBI paper
  21. done Suzi- The group who are now exercising the model (Kimberley, David and Tanya) are also looking at the curation policy and provide recommendations on to what degree ‘model’ information should be included by the curator.
  22. done[Jane] Jane will ensure that GPAD 1.1. spec are finalized
  23. in progress[Chris] Chris needs to convert existing annotation data into GPAD format that is conformant with the spec… so that protein2go will still work. Current scripts very old and need to be reviewed. Chris will make sure this is synchronized with Tony once 1.1 is defined. Make sure the ECO mappings are incorporated.
  24. [Rama] Rama to write the announcement, waiting for more information.
  25. done complete round-tripping of GO annotations from WB curators via protein2go into UniProt and back to WormBase.
  26. done make sure ontologies are available to support col16 curation
  27. Judy looking at this, We need a automated workflow to measure what happens (can be done with Jenkins and/or Galaxy)
  28. in progress Each group (SGD, mouse, zfin, fly, worm, human) should put together some gene sets for this exercise. Mike and PaulS will shepherd this effort
  29. done Group of curators (names?) will attend an on-line training session to begin PAINT annotation.
  30. Add to Jenkins pipeline Use that GOOSE query to identify and remove ISS annotations for which the supporting exp annotation don’t exist or is now contradictory. A rule for detecting transitivity errors that creep in over time..
  31. move forward [David] group to come up with a plan for handling chains of evidence codes and inter-ontology links.
  32. done [Heiko] Allow TermGenie to create a Temp ID for non-template mediated term requests
  33. include in Paul's discussion on Scope Ontology editors will write down global areas of biology that needs to be developed (cleaned up). Also, we need areas that we are missing completely.
  34. include in Paul's discussion on Scope[PIs] set global priorities by surveying whole scope
  35. done USE JIRA
  36. force 11 focus on publishing Request journal editors to require GO related data to have version # /date for when GO annotations/ontology were retrieved. What is the minimum data they need to include (PIs).

Thursday (starts at 8:45)

2013_04_11_through_04_13 Meeting minutes on Google Docs


GOAL:Provide community with ability to obtain and use GO resources

Coffee break (10:30-11)

Comparative and Phylogenetic Annotations

  • PAINT progress, including overview of SOPs
    • PAINT progress overview (Paul T.) (11-11:15)
    • SOP overview plus example (Donghui) (11:15-11:45)
    • Examples of annotation issues in PAINT, plus discussion (11:45-12:30) (Paul T, Pascale)

Lunch (12:30-1:30)

    • Update on JsPAINT (Chris/Suzi) (1:30-1:45)
  • Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:45-2)
  • ECO update (Chris) (2-2:15)
  • New rules for ISO mouse/human/rat when M:N gene sets (Judy) (2:15-2:35)

Literature Annotation

Coffee break (3:30-4)

  • Curation tools: transition to Protein-GO, prospects for text-mining integratrion (4-5)

Biological Knowledge

  • Interaction between ontology development and annotation (5:30-6)
    • Current mechanisms: tracker, TG, Jira (Jane)
    • Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) Media:TGreview_Cambridge_April13.pdf
    • TermGenie freeform demo (Jane)

Dinner at Moller Centre (7pm)

Friday afternoon breakout sessions

1. Annotation Extension 1.30-2.30pm

Interested in attending: Jane, Rachael, Susan, Petra, Mary, David, Midori, Chris, Kimberly, Ruth, Donghui, Tanya, Val, Harold,
Rama, SGD curators, Rebecca, Li, Prudence, Doug

2. Cell cycle 2.30-3.30pm

  • WG to work through outstanding issues
Interested in attending: Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence

3. PAINT Meeting - Huaiyu 3.30-4.30pm

  • including ontology developers
  • Look at annotation consistency
Interested in attending: Jane, Susan, Ruth, Donghui,Val, Rama, Li, Petra


GO help emails and Multiple tracker systems (Rama)

  • GO Help in JIRA
  • Sourceforge, JIRA for certain projects, reminder emails from TermGenie, github for AmiGO2, Jenkins for checking errors (too many places to keep track of). Can we consolidate?

Biological Knowledge (continued)

  • Cross-product status, inc cell type (David) (8:30-9)
  • Cell cycle report (Val) (9-9:30)
  • Annotation expressivity
    • LEGO
      • Test example: Wnt signaling (David) (9:30-10)
      • Implementation plan (Chris) (10-10:30)

Coffee break (10:30-11)

      • Mapping to community representations, e.g. BioPAX, SBGN (Huaiyu) (11-11:15)
    • Annotation extensions (Rachael) (11:15-11:45)
      • Annotation relations
    • GPAD status (Chris) (11:45-11:55)

Meeting wrap up and action item review (11:55-12:30)

Action Item Review and Reports

Caltech meeting minutes meeting minutes as a Google Doc

See also

Group Photo

GOC Cambridge 2013.jpg