2010 Stanford Meeting Logistics

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GO consortium & SAB meetings March 30-31, April 1, 2010

  1. We wish all attendees to attend from the morning of March 30 through the morning of April 1st. The afternoon of April 1st will be for all GO subcontract PIs, GOC PIs and our SAB. We suggest you arrive the evening of March 29th and leave after noon on the 1st, unless you are a PI or SAB member.


Meetings will be at the Stanford University, Stanford, CA, USA.

The GOC and SAB meeting will take place at the Arrillaga Alumni Center.

Lunches will be at the Arrillaga Center.

There will be a group dinner on March 31st for the GOC and SAB.

We will also facilitate dinners on March 29th and 30th. There are a large variety of restaurants in the area.


Stanford University maps

Meeting will be held at the Arrillaga Alumni Center, 341 Galvez Street, Stanford, CA [1]


Registration will open in early 2010.

  1. Registration Fee. We anticipate a minimal registration fee to cover lunch and a light breakfast. The meeting will be sponsored by the Cherry Lab.

Lodging Information

Four hotels are within a 15-20 minute walk to the Alumni Center. Ordered below by price per night, lowest to highest.

  1. Hotel California $
  2. Cardinal Hotel $
  3. Stanford Terrace Inn $$
  4. Sheraton Palo Alto Hotel $$$$
  5. Westin Palo Alto $$$$


March 30 – Morning - Break

  1. Review Agenda

Communication and Process for the GOC

    1. Changes in Mangers structure; description of roles [Suzi]
    2. Communication about project goals, timetables, shepherds and reporters
      1. Need better definition of process for projects
      2. Need statement of key goals and timeline for each project
      3. Need Shepherd and Reporter for each project; Shepherd to oversee progress and resolve bottlenecks, Reporter to keep all GOC informed as to progress and implications
      4. Use and utility of various mailing lists
    3. MF-BP links, what they are and how they impact annotation (David Hill)
      • what worked, what can work better, in project management; using MF-BP example

March 30 – Morning Break – Lunch

Ref Genome Project and PAINT [Pascale and Kara

  1. current focus on process sets
  2. need for MOD incorporation
  3. Update on PAINT
    • Evidence codes from PAINT and Inferences from MF-BP links
    • Notice of ISMB workshop on Assays, ECO and OBI.

March 30 Afternoon - Break

  1. File Management Issues
      a.  Taxon IDs
      b.  Making ext GO ‘main’
      c.  new column in GAF-Annotation Method
      d.  Mechanics of file dissemination.
    e.  streamlining addition of compositional terms
     f.  GAF2 update
    g.  improved support for OBO/OWL/Protégé intersections

March 30 Afternoon break – Dinner

Update on Cross-Products: the Chebi example (David) OBO-Foundry Report (Jane)

   4.   Update on Cell Type Ontology (Terry)

 March 31 Morning – Break

Action Items Review (Judy)

       a.  from last GOC
       b.   from yesterday, March 30 
    2.  AMIGO updates/report (Seth – 15 min) 
      3.   OBO_EDIT updates/report (Amina – 15 min)

March 31 Morning Break – Lunch

            1.  Annotation [Rama, Emily ]
                   a.  Guidelines for ‘binding’ terms
                  b.  Other Annotation Issues 
                   c.  Geneva GO Annotation Workshop
            2.  Requirements and QC for contributed annotations [Rama]
                      a.  M. tuberculosis example
             3. .  Incorporating IMEX data into GOC? [Emily]

March 31 Afternoon

  1.  Ontology Content Projects 
    a.  bringing the NIF ontologies into GO  (Chris)
    b. GO-Pathway database integration (Chris)
      c.  PRO, MouseCyc, Reactome and GO:  Complexes in PRO and GO  (Harold)

2. Open for further discussion or catch-up reports 3. Open forum on thoughts regarding upcoming competitive renewal applications

Ontology Updates

Cross products (18 slides, David)

    • Internal cross products
      • Cross-products already in place
      • Cross-products "in production"
    • External cross-products

Aligning chemicals (11 slides, David)

MF-BP links (22 slides, David)

Ontology Content Additions

    • Term additions from the ASCB and SDB meeting (6 slides, Tanya)
    • Additions from the kidney and heart development meeting (14 slides, David)
    • PAMGO (Jane)

OBO-Foundry report (Jane)

Ontology files and GAFS

Taxon IDs

I'd like a discussion of taxon IDs and subspecies. --JimHu 17:28, 4 February 2010 (UTC)

Making ext GO 'main'

A suggestion from the OBO Foundry meeting: we make GO ext the main GO file, the one that new users see. The other files continue to exist in the same place, but make it clear they are legacy files. That way anyone new coming to GO will build tools using GO ext. [Jane]

New column in GAF- Annotation Method

Proposal to add a new column to the GAF to indicate if an annotation was reviewed by a curator or no.

Alternative proposal from CJM to extend Evidence codes to support chains of evidence

Evidence codes for PAINT and Inferences from MF-BP links

  • Also need to discuss references for PAINT annotations. Will one generic reference work?

Mechanics of file dissemination

I'd like to discuss the use of ftp rather than CVS for disseminating GAFs, gp2protein and other files (Tony S)

Annotation Issues

Guidelines for 'binding' terms

Discuss guideline documentation, progess and unresolved issues (Emily and Ruth; 12 slides).

proposed guidelines

Unresolved issues:

  • Should we include transporters in these guidelines?
  • Should we capture drug information?
  • Should the guidelines include a statement suggesting that the specific substrate for an enzyme with 'GO:0032451 demethylase activity' can be included in column 16?
  • Should we create terms like ‘ATP binding involved in kinase activity'?
  • What, if any, binding term annotations can be transferred via ISS/ISO?

30th/31st: end of afternoon.

Participants in newly-formed annotation working groups (formed for the June GO Camp) to gather together to begin to discuss issues [2]

Discussion on how ontology development relates to annotations

  • scope of regulation relationship
    • clarifying what 'regulation' terms mean from an annotator/ontology developer perspective (David, 18 slides)
  • scope of has_part relationship





Airport codes: SFO = San Francisco International; SJC = San Jose International Airport

Name Organization Arrival Date/Time to Airport (see codes above) Departure Date/Time from Airport
Mike Cherry GO / SGD walking
Judy Blake GO / MGI March 29 SFO April 2 SFO
Suzi Lewis GO / BBOP Driving
Mary Shimoyama RGD March 29 SFO April 2 SFO
Chris Mungall GO / BBOP CalTrain
Seth Carbon GO / BBOP Driving
Amina Abdulla GO / BBOP Driving
Amelia Ireland GO / BBOP Hitching a ride
Kara Dolinski GO / PPOD TBA TBA
Eva Huala TAIR March 29 April 2
Karen Eilbeck SO (U of Utah) San Jose 29th March San Jose April 1 - evening
Barry Smith SAB (U at Buffalo) March 31 SFO April 1 SFO
Richard Scheuermann SAB (UT Southwestern) March 31 SJC 9:30 am April 1 SJC 6:15 pm
Tanya Berardini TAIR on site on site
Donghui li TAIR on site on site
Larry Hunter SAB (U Colorado) March 31 SFO April 2 SFO
Paul Sternberg WormBase and Caltech San Jose San Jose
Doug Howe ZFIN SFO March 29
Dianna Fisk SGD on site on site
Ben Hitz SGD on site on site
Jane Lomax GO-EBI March 29 SFO April 2 SFO
Pascale Gaudet dictyBase
Harold Drabkin MGI March 29th SFO April TBA
Terry Meehan MGI March 28th SFO April 2
Jim Hu EcoliWiki March 29 SFO 8PM April 2 SFO 1:40PM
David Hill GO/MGI
Stan Laulederkind RGD March 28 SFO 7:47PM April 1 SJC 2:20PM
Monte Westerfield ZFIN April 1 SFO
Selina Dwight SGD on site on site
Kate Dreher TAIR on site on site
Rama Balakrishnan SGD on site on site
Stacia Engel SGD N/A N/A
Ranjana Kishore WormBase SJC 3/29 5.50 PM SJC 4/01 3.00 PM
Kimberly Van Auken WormBase TBD TBD
Petra Fey dictyBase N/A SFO 4/01 1:55 PM
Peter D'Eustachio Reactome / NYUMC SJC 3/29 7:02 PM SJC 4/1 10:25 PM
Serenella Ferro Rojas UniProtKB/Swiss-Prot March 29 SFO April 4 SFO
Eurie Hong SGD on site on site
Emily Dimmer GOA March 29 SFO April 2 SFO
Tony Sawford GOA March 29 SFO April 2 SFO
Karen Christie SGD on site on site
Julie Park SGD on site on site
Ingrid Keseler EcoCyc N/A N/A
Paul Thomas PANTHER/EcoliHub driving

Remote Attendees

Webex and Telephone Conferencing will be provided

Name Organization email (needed to set up your remote access) Attending GOC (March 30-31) Attending SAB (April 1) Calling in alone or in a group (with whom and from where, if known)
Midori Harris EBI GO midori at ebi dot ac dot uk yes yes TBD
Jennifer Deegan GO Editorial Office jdeegan at ebi.ac.uk Yes Yes Probably alone from home.
Ruth Lovering BHF-UCL annotator r.lovering at ucl.ac.uk Yes Yes From home, but will have to miss some parts
Rachael Huntley GOA Curator huntley at ebi.ac.uk Yes Yes From home.
Michelle Giglio IGS, UMD mgiglio at som.umaryland.edu Yes No alone from work/home
Marcus Chibucos IGS, UMD mchibucos at som dot umaryland dot edu Yes No alone from work/home
Alexander Diehl MGI adiehl@informatics.jax.org Yes Yes alone from work/home
Michael Livstone Princeton livstone@genomics.princeton.edu No Yes alone from work/home, can present PAINT families that have been curated via webex if that is on the agenda for the SAB
Lakshmi Pillai AgBase pillai@cvm.msstate.edu Yes No TBD
Susan Tweedie FlyBase sart2 at gen dot cam dot ac dot uk Yes Yes alone from home
Yasmin Alam-Faruque EBI GOA yalam at ebi.ac.uk Yes Yes alone from home
Varsha Khodiyar BHF-UCL annotator v.khodiyar at ucl.ac.uk Yes No alone from home

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