2010 Stanford Meeting Logistics

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Dates

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.

Venue

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.

Maps

Stanford University maps

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

Registration

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 $$
  4. Sheraton Palo Alto Hotel $$$$
  5. Westin Palo Alto $$$$

Agenda for GOC meeting March 30 and March 31

Tuesday, March 30 – Morning [Start - Break]

  1. Review Agenda; intro new people
  2. who is taking minutes?
  3. who is tracking the teleconferencers?

Communication and Process for the GOC [Suzi]

  1. Changes in Managers structure
  2. Description of integrated team approach to annotation
  3. Increasing our efficiency in completing projects (using MF-BP and RefGenome as examples)
    1. Clear problem statement, what will the end result look like: Fuzziness = Failure
    2. Identify -a- project manager to oversee progress
    3. Establish project priority with respect to all other GOC projects
    4. Talk to all affected parties, revisit these groups as each new milestone is reached
      • Effective use of wiki and mailing lists
    5. Establish milestones and dependencies

Tuesday, March 30 – Morning [Break – Lunch]

Ref Genome Project and PAINT [Pascale and Kara]

  1. Current focus on process sets
  2. Update on Annotation
    • Curation: About eleven protein families have been done with beta version of PAINT, primarily by Mike Livstone in Kara's group at Princeton. slides.
    • References for PAINT annotations: One reference is available for each family's annotation.
  3. PAINT Software [Ed]
  4. Inferences from MF-BP links
  5. Need for MOD incorporation

Tuesday, March 30 Afternoon [After lunch - Break]

AMIGO updates/report (Seth)

  1. New search features
  2. PAINT-style displays in AmiGO
  3. Improved tree view

Ontology Updates

  1. Term additions from the ASCB and SDB meeting (6 slides, Tanya)
  2. Additions from the kidney and heart development meeting (14 slides, David)
  3. PAMGO (Jane)
  4. Cross products (18 slides, David)
    • Internal cross products
    • Cross-products already in place
    • Cross-products "in production"
    • External cross-products
  5. Aligning chemicals (11 slides, David)

Tuesday, March 30 Afternoon [Break – Dinner]

Cell Ontology (Terry)

  1. Content update (Terry)
  2. Improved support for OBO/OWL/Protégé intersections (Chris)
  3. OBO_EDIT updates/report (Amina)
  4. streamlining addition of compositional terms [Chris]

Ontology Content Projects

  1. Bringing the NIF ontologies into GO (Chris)
  2. GO-Pathway database integration (Chris)
  3. PRO, MouseCyc, Reactome and GO: Complexes in PRO and GO (Harold)

Wednesday, March 31 Morning – Break

Action Items Review (Judy)

  1. from last GOC
  2. from yesterday, Tuesday, March 30

Impact of recent ontology changes from an annotator/ontology developer perspective [David]

  1. MF-BP links, what they are and how they impact annotation
  2. Scope of regulation relationship
  3. Scope of has_part relationship

Evidence Codes

  1. NOT evidence codes
    1. "IMR" -> "Inferred from missing residues“ lacking domains, etc
    2. "IRD" -> "Inferred from rapid divergence“ sequences have rapidly diverged (e.g., paralogs)
    3. "IDS" -> "Inferred from descendant sequence(s)“ lack of function is annotated due to existing protein that have been previously annotated with lacking this function
  1. Proposal from CJM to extend Evidence codes to support chains of evidence
  2. Position of ISM
  3. RCA usage and documentation
  4. Notice of ISMB workshop on Assays, ECO and OBI [Judy]

Wednesday, March 31 Morning [Break – Lunch]

Annotation (Rama, Emily)

  1. Guidelines for 'binding' terms
  2. Discuss guideline documentation, progress and unresolved issues (Emily and Ruth; 12 slides).
    • 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'?
  3. Discussion of taxon IDs and subspecies [Jim Hu]
  4. Requirements and QC for contributed annotations [Rama]
    • M. tuberculosis example
  5. Ideas for incorporating IMEX data into GOC? [Emily]
  6. Plans for Geneva GO Annotation Workshop [Pascal]

Wednesday, March 31 Afternoon [Lunch - Break]

File Issues

  1. 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.
  2. Ease of file dissemination

GAF file

  1. GAF2 update
  2. Proposal to add a new column to the GAF to indicate if an annotation was reviewed by a curator or not.

Wednesday, March 31 Afternoon [Break - end of day]

  1. OBO-Foundry Report (Jane)
  2. Parking lot item discussions or catch-up reports
  3. Open forum on thoughts regarding upcoming competitive renewal applications
  4. Preparation for SAB next day

Agenda GO SAB Meeting April 1 2010

Morning

8:30: Welcome, Agenda Review
9:00am - 9:20 Grant news: 5 year Aims, Structure with Subcontracts, Metrics of Ontology and Annotation Success [Judy]
9:20 – 10:00 Management structure and Project process (Suzi)
10:00- 10:20 AmiGO and GO usage stats (Mike)
10:20 – 10:45 Break
10:45 – 11:00 Vision and Questions for Competitive Renewal/Future of GO (Michael)
11:00 – 12:00 Discussion of Aims and Objectives for Competitive Renewal (Suzi: Judy and others note-taking)
12:00 – 1:00 pm working lunch, open discussion

Afternoon

1:00 – 2:00 SAB executive session
2:00 – 3:00 SAB and PIs
3:00 – 3:30 Break
3:30 – 4:30 Summary [open to all GOC still round]

Attendees

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, Tuesday, and wed afternoon session only
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
Li Ni MGI ln@informatics.jax.org Yes Yes alone from 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. Available 9AM-5PM EDT, 6AM-2PM PDT.
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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