Difference between revisions of "2010 Stanford Meeting Logistics"

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(Ref Genome Project and PAINT [Pascale and Kara])
(AmiGO and GO database updates/report (Seth and Chris))
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# New search features
# New search features
# PAINT-style displays in AmiGO and family-based annotation reports
# PAINT-style displays in AmiGO and family-based annotation reports
# Improved tree view
# Improved tree view [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=term_details&term=GO:0022008]
# loading the database with full gene product sets for reference genome groups
# loading the database with full gene product sets for reference genome groups
# plans for displaying col 16
# plans for displaying col 16

Revision as of 09:47, 30 March 2010


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

Agenda for GOC meeting March 30 and March 31

Tuesday, March 30 – Morning [Start - Break]

  1. Review Agenda; intro new people, grant info [Judy]
  2. who is taking minutes?
  3. who is tracking the teleconferencers?

Communication and Process for the GOC [Suzi]

  1. GO vision
  2. Changes in Managers structure

(add slides)

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.
    • References for PAINT annotations: One reference is available for each family's annotation.
  3. Inferences from MF-BP links
  4. Need for MOD incorporation

Tuesday, March 30 Afternoon [After lunch - Break]

AmiGO and GO database updates/report (Seth and Chris)

  1. New search features
  2. PAINT-style displays in AmiGO and family-based annotation reports
  3. Improved tree view [2]
  4. loading the database with full gene product sets for reference genome groups
  5. plans for displaying col 16
  6. using reasoner as part of loading

Evidence Codes

  1. to what purpose evidence codes?
  • needs of computational biologists to distinguish predicted vs. experimental annotations
  • why to curators want to track NOT, ISS and RCA variants?
  • why would we compute on evidence codes? why would others?
  • What is role of ECO vs OBI?
  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
  2. Disentangling evidence codes (Kara/Chris). Annotation_method (Kara) Extending_evidence_codes (Chris)
  3. Position of ISM
  4. RCA usage and documentation
  5. Notice of ISMB workshop on Assays, ECO and OBI [Judy]

Tuesday, March 30 Afternoon [Break – Dinner]

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

Annotation 1: Binding (Rama, Emily)

  1. Guidelines for 'binding' terms'

Wednesday, March 31 Morning – Break

Action Items Review (Judy)

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

Annotation 2 (Rama, Emily)

  1. 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'?
  2. Discussion of taxon IDs and subspecies [Jim Hu]
  3. Requirements and QC for contributed annotations [Rama]
    • M. tuberculosis example
  4. Ideas for incorporating IMEX data into GOC? [Emily]
  5. Plans for Geneva GO Annotation Workshop [Pascale]

Wednesday, March 31 Morning [Break – Lunch]

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/multi-organism process update (Jane)
  4. Generic GO slim (2 slides, Jane)
  5. Cross products (18 slides, David)
    • Internal cross products
    • Cross-products already in place
    • Cross-products "in production"
    • External cross-products
  6. Aligning chemicals (11 slides, David)

Cell Ontology (Terry)

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

Ontology Content Projects

  1. Bringing the NIF ontologies into GO. Allowing other groups write access to parts of GO (Jane)
  2. GO-Pathway database integration (Chris)
  3. PRO, MouseCyc, Reactome and GO: Complexes in PRO and GO (Harold)

Wednesday, March 31 Afternoon [Lunch - Break]

GOC website redesign (Rama)

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 for new gene product data file format for submitting gene/protein data independently of annotations
  3. Proposal for new annotation file format containing only annotation data (complementary to the GP data file format above)
  4. 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]

Renewal, SAB and AOB

  1. OBO-Foundry Report (Jane)
  2. Parking lot item discussions or catch-up reports
  3. Strawman proposal for upcoming competitive renewal (Suzi, Chris, & Paul)
  4. Preparation for SAB next day

Agenda GO SAB Meeting April 1 2010


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 (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


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]


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 Public
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
Rex Chisholm dictyBase driving SFO

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 miss wed 10am-4pm
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
Dmitry Sitnikov MGI dmitrys@informatics.jax.org Yes No 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. Available 9AM-5PM EDT, 6AM-2PM PDT.
Lakshmi Pillai AgBase pillai@cvm.msstate.edu Yes No group call from work
Fiona McCarthy AgBase fmccarthy@cvm.msstate.edu Yes No group call from work
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 No alone from home
Varsha Khodiyar BHF-UCL annotator v.khodiyar at ucl.ac.uk Yes No alone from home
Valerie Wood PomBase! val at sanger.ac.uk Yes Yes Probably alone from home.
Rebecca Foulger EBI UniProt/GO office rfoulger at ebi.ac.uk Yes No Probably alone from home.
Daniel Renfro EcoliWiki / EcoliHub bluecurio@gmail.com yes yes From the Hu lab, probably alone.
Peter Good NHGRI Program Staff goodp at mail.nih.gov maybe as much as possible Alone where ever I can
Mary Dolan MGI mdolan@informatics.jax.org Yes Yes alone from home
Amelia Ireland BBOP / GO EBI see above Tues only; in person Weds No alone from the office

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