GO 18th Consortium Meeting

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Sept 23-24th, 2007 Princeton, New Jersey

Meeting Location
Prospect House - Presidential Dining Room
 Prospect House ]] 
 Washington St
 Princeton, NJ 08544
 (609) 258-3455
Dinner on Sunday (9/23) @ 5.00 PM - Winbere's in Palmer Sq
Dinner on Monday (9/24) @ 6.00 PM - Triump Brewery on Nassau St
Nassau Inn
 Nassau Inn
 10 Palmer Sq E
 Princeton, NJ 08542
 (609) 921-7500



GOC2007 Princeton2.jpg

Draft Schedule

Sunday morning, September 23, 2007


  1. Introductions, especially new people
  2. Quick review of any outstanding 2007 GOC Action Items from Jan 2007GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort

Progress Reports

2007 Progress Report for NHGRI due Jan. 1, 2008

These reports will review accomplishments to date.
We are using the itemized list of sub-aims from the grant to organize these
 Aim1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
 Aim2: We will comprehensively annotate reference genomes in as complete detail as possible.
 Aim3: We will support annotation across all organisms.
 Aim4: We will provide our annotations and tools to the research community.
Aim 1- Ontology Development

Suzi Lewis - Moderator/PI Lead.

  1. Ontology Development - Biological Content:::Midori Harris and David Hill reporting
  2. Ontology_Structure :::Chris Mungall reporting
  3. Ontology_Development wiki site.
  4. SO progress :::Karen Eilbeck reporting
Aim 2- Reference Genome Project

Judy Blake - Moderator/PI lead.

  1. Reference Genome Project :: Rex Chisholm and Pascale Gaudet reporting
  2. Reference Genome Annotation Project wiki site.
Aim 3- Annotation across all organisms

Michael Ashburner - Moderator/PI lead.

  1. Annotation Outreach:: Jen Deegan reporting
  2. OBO-Edit working group::John Day-Richter reporting
Aim 4- Providing annotations and tools to Users

Mike Cherry - Moderator/PI lead.

  1. User Advocacy::Eurie Hong reporting
  2. Production Systems :: Ben Hitz? reporting
  3. AmiGO and Web presence (Hub) working groups :: Amelia Ireland and Chris Mungall reporting.
  4. Report on SWUG:Database_changes_2007
  5. Reference_Genome_Database_Requirements_Discussion
  6. SWUG:AmiGO_Architecture_Roadmap
  7. AmiGO:_Prototypes

Afternoon, Sunday, Sept 23, 2007

Discuss protein complexes and the intersection with Reactome annotations

Peter D'Eustachio (Reactome) will be able to join us only for the afternoon.

These are some other topics that Ewan Birney brought up at the Interactome meeting:

  • Reactome has a lot of function annotations with the connections to the complex that has the function. These are for very small complexes like homodimers. He says can we accept these? Also he says that he understands that this is a bit granular for us and that we have a lot of similar information for larger complexes. He suggests that there might be better way to store all the data for the functions of all sizes of complexes if we pooled out data and thought of a good system to make it available.
  • Ewan Birney and the people at the Interactome meeting felt strongly that the more complicated annotations such as those with a NOT or colocalizes_with qualifier, and those with annotations to the root should be in a separate file from the straightforward annotations. The users felt that many people do not know about these more complicated annotations and it would be better to make them an added extra that people must specifically go to download. They were particularly concerned that users may not know that it is important to parse the qualifier column and so may miss vital information.
  • Reactome would like to have a new evidence code to show where an IEA has been transferred from a known orthologue. Such transfers tend to produce more granular annotations. (This has been discussed before but Ewan asked me to bring it up while Peter is there to back the proposal.)

Topics related to Ontology Development

Updates and next steps
  1. Update on 'regulates' terms and relationships in GO (David)
  2. Plan for adding 'regulation of' relationship to GO (Chris)
    1. Will we maintain two copies of GO live at once?
    2. How will will notify users of timing and consequences of this (and other) changes?
  3. Completing is_a relations in the GO (Chris demo)
  4. Update on revamp of 'Sensu' terms. (David)

Background: Cross_Product_Guide

  1. Collaboration and cross-products with Cell Ontology
  2. Taxon-GO links
  3. The intersection of SO and CC (Chris and Karen E)
  1. Incorporation or synchronization with the SAO (sub-cellular anatomical ontology)
  2. How can we confer micro-credit to experts who contribute to the content?
  3. Creating Complex terms in the component ontology-when do two interacting proteins become a complex? How long should the interaction last for it to be called a complex? (Rama)
  4. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  5. The scope of 'binding' terms in the function ontology:
    1. How granular should terms be?
    2. Should there be terms for substrate origin (e.g. "viral protein binding")? See SF 1674020.
  6. Discuss whether GO can add a has_part relationship (mah, krc)

Morning, Monday, September 24, 2007

Topics related to Annotation

  1. Annotation of protein complexes
  2. Finalizing the format for cross-product information for the new column 16 of the gene association file - could this column also include information on the 'target' of a protein's activity?
  3. Issue with taxon/dual taxon usage to capture strains and cultivars etc, for which taxon IDs do not exist in NCBI.
  4. Ontology versioning proposal for keeping annotations up-to-date (John and Chris)

Annotation Evidence Codes

  1. Evidence code proposals from Evidence Code Committee
    1. Finalizing Proposed evidence code documentation (need someone to oversee completion of final details; see also summary email and Proposed evidence code documentation)
    2. Boundary between ISS & RCA and scope of RCA evidence code (Michelle and Rama (filling in for KarenC); see Evidence Code Committee discussion on ISS vs RCA and Email sum up on RCA (contains link to RCA example papers)).
    3. Use of with column for ISS, pending decision on ISS vs RCA boundary (?; see summary of ISS with (blank) proposal (contains link to ISS with '____' sample papers) and some further comments on filling with field for ISS).
    4. Boundary between IMP and IGI (Val; Email synopsis and further comment)
    5. Use of with column for NAS evidence code (David; see summary Email thread on NAS).
    6. Annotations to root nodes (Rama; see Email sum up on ND and probable conclusion of use of ND for root annotations).
    7. Thoughts from MGI See this document and some responses to MGI from Karen
    8. Karen's draft of an Evidence Code Decision tree (and John's html implementation)
  2. Use cases for evidence codes
  3. "use" of IPI protein binding to track physical interactions

Gene Association file

(Rama and MikeC)

  • We have previously discussed the interest of some groups in having two gene association files. This will allow users to easily download a subset of the annotations. The GO database will load all annotations files. We propose a discussion on the naming convention that should be used for these second (or third) files. The HTML table would have all GA files listed. This proposal comes from SGD as we have now incorporated all S. cerevisiae annotations from the GOA UniProt file. The manual annotations from this file are included in our gene_association.sgd file with UniProt (or MGI) as source. We would like to use a second file for the IEA annotations. This is to allow users to easily use the curated annotations or the computationally predicted set. The worry is that many do not look inside the file before they use it for analysis or as a training set. If developers include the computationally predicted annotations within their training sets the overall quality of there annotations will suffer.

Afternoon, Monday, September 24, 2007

Our Public Face

  1. AmiGO Architecture
  2. ORB and AmiGO
  3. GOOSE
  4. Changes to AmiGO to improve visualization when there are multiple relationships linking terms
And the rest
  1. Wiki
  2. Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.

GOC and Staff issues (this is largely go-top stuff, perhaps a breakfast?)

  • Considering sending in a proposal to ESF Research Conferences 2007 RFA
  • The PIs should consider options for the future of the GO Editorial Office (GOEO). Affiliation with EBI has numerous advantages (for both GO and EBI), but all four GOEO staff will reach the 9-year limit by the end of the current NIH grant period.
(added at Michael's request)
  • Currently we have several working groups including:
    1. Ontology content - to work on the content of the ontology
    2. Annotation-Outreach - to encourage new groups to start annotating
    3. User Advocacy - to help users to learn how to use the GO and to represent user's need to the consortium.
    4. Reference Genomes - to choose genes lists for everyone to work on.

So the questions are:

    1. Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common?
    2. Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group. The main annotation group could have two annotators to chair, or perhaps a rolling chair.