Cambridge GO Consortium & SAB Meeting

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Dates

September 23-25, 2009

Time: 9AM-6PM everyday (subject to update)

Venue

Jesus College, Cambridge, UK

Logistics

See 2009_Cambridge_Meeting_Logistics

Photo of Attendees

Agenda

Tuesday, Sept. 22: Arrival dinner at Restaurant 22 (7:30 PM)

Wednesday 23 September

9:00 AM Status on our grant-authorized and funded specific aims from primary GO grant

(4:00 AM EDT, 1:00 AM PDT)

Watching remote people: Rachael

The following tables and lists were extracted from our original proposal. These goals and tasks are used for our evaluation by funders. We will not discuss these in detail at this point in the meeting, they simply serve as a status check. These will be based on the submitted progress reports.

  • Aim 1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies (Suzi PI chair)
Year Task Status
1 Completing is_a relations Done
1 Completing part_of relations Done
3 Substitution of regulates relationships Done
3 Produce slim versions excluding specified relationship classes Done?
1 Parse implicit Cell terms from GO and resolve In Progress
2 Parse implicit Chemical terms from GO and resolve In Progress
5 Parse implicit Anatomical terms from GO and resolve In Progress
2 OBO-Edit that enables cross-links Done
3 AmiGO that supports cross-links In Process
5 Automate inconsistency checking Ongoing
3 Inclusion of specialized part_of & contained_in relationships in CC Still to do
3 Inclusion of located_in & has_part relationships in BP In Progress
1 Programmable access to retrieve annotations Done
5 Add relationships between BP, MF, and CC In progress
5 Develop tools and protocols to maintain pathways congruency Still to do
3 OBO-Edit support for tracking changes to the ontology Done
5 OBO-Edit interoperability support Done?
5 Implementation of faster querying techniques In progress
  • Aim 2: We will comprehensively annotate reference genomes in as complete detail as possible (Judy PI chair)
Year Task Status
1 Develop breadth of annotation metric utilities Gene Jamborees investigating metric
1 Develop depth of annotation metric utilities Still to do; information theory approach run 1x with Gil Alterovitz group
1 Software for quarterly archival of annotation metrics need to supply annotation versions for computational analysis work
Ongoing Coordinated GO annotation and evaluation at local MOD Most MODs have internal coordination of consistency; still to go: interMOD consistency evaluations
1 Provide proteins sets for ortholog analysis On-going; several sets provided, continuing QC on submitted sets
Ongoing Identification of genes to be annotated On-going: continuing review of process of gene selection
Ongoing Monthly monitoring of annotation of orthologous gene sets and organize annotation quality and consistency camps On-going: consistency of annotation standards still most efficient mechanism because of paucity of annotation and uneven distribution of experimental approaches
Otherwise funded Tool for annotating protein families Beta
    • Aim 3: We will support annotation across all organisms (Michael PI chair)
      • This aim needs to be revisited, as currently we have not made significant progress on most of the stated aims. Examples below
        • What is current status on providing annotated FASTA sequences, with evidence, as a community resource (Ben or Mike?)
        • What sort of documentation are we providing for automated annotation methods? Is it sufficient? (Pascale)
        • Is output from GOA automated annotation pipeline available to public for individual genomes?
      • Talk about Quest for orthologs?
      • Gold set for groups to test annotations tools
    • Aim 4: We will provide our annotations and tools to the research community (Mike PI chair)
      • All of these were listed in the grant as on-going tasks
Task Status
Usability studies of user GOC user interfaces Still to do
Make gateway to Web Interface request tracker easily available Done?
Configure and maintain Web Interface request archives Done (Google analytics)
Daily updates of ontology downloads, in all formats Ongoing
Create monthly archives Ongoing
Respond to user e-mail queries Ongoing
Maintain and enhance AmiGO Ongoing
Incorporate user community feedback on annotations Still to do
Organize GO software development camps Still to do
Organize annual "tiger" teams to critique usability of GO for users Still to do
Develop curriculum and hold tutorials on GO usage Still to do
Maintain the GO database Ongoing (schema update needed)

10:30 AM Break

11:00 AM Community Interactions and Outreach

(6:00 AM EDT; 3:00 AM PDT)

Watching remote people: Ruth

  • Report from the GO review from the OBO Foundry meeting in June. (Jane)
  • Community annotation report (5 mins - Val Wood?)
  • Web stats (with Google Analytics) - Mike & Seth?
    • Quick demo of news pages and how it all works [Jane]
  • AmiGO status (Seth)
  • Soliciting community input for new GO initiatives - Suzi


12:30 PM Lunch

2:00 PM Reference Genomes: Part 1, Software

(9:00 AM EDT; 6:00 AM PDT)

Watching remote people: Midori

  • Pascale: Progress report: annotation metrics and QC
    • measuring progress
    • Addressing NIH priorities (human biology)
  • Brenley: GONUTS update
  • Suzi: PAINT Demo

3:30 PM Break

4:00 PM Reference Genomes: Part 2, Biocuration

(11:00 AM EDT, 8:00 AM PDT)

Watching remote people: Jane

  • Paul: PAINT annotation example and possible future directions
  • Bio-curation Issues
    • Pascale: Work flow optimization, identifying bottlenecks so we can finish in our lifetime.
    • Dan: The primary protein sets, follow-up from the Quest for Orthologs meeting

(Informal logo-brainstorm session for interested members of web-presence WG immediately following meeting in Jesus College bar.)

6:30 PM Dinner at Jesus College

Thursday 24 September

9:00 AM Summary of Previous day and Infrastructure

(4:00 AM EDT, 1:00 AM PDT)

Watching remote people: Varsha

Summary/Review of Wednesday

  • Brief feedback on annotation jamborees action items.
  • Action Items

Infrastructure

  • Mirrors - Suzi and Seth (at EBI, Berkeley, Princeton and Northwestern)
  • Timely GAF submissions
  • GAF 2.0 Transition - Chris
    • Isoforms
  • Should we stop creating the GO-FULL database - Mike

Currently this flavor of the GO database is created once a month. This database includes all annotations including IEAs from all GAFs. This database does not include sequences. This database is only for download and is not used by AmiGO. Because of various software issues this database we have not been able to always creat it every month. For sometime we have been pointing users to the GO-Lite database and those that ask are happy for GO-Lite. The GO-Lite database includes sequence for all annotations loaded. GO-Lite includes IEA from all GAFs except GOA UniProt, and GO-Lite is made available weekly. The usage of GO-Full is thus low and a bit of a pain considering it is not used by the GOC. We thus wish to stop creating this database.

  • Reduce the frequency of GO-Lite creation - Mike

GO-Lite is created three times a week. GO-Lite is used by AmiGO. GO-Lite is made available via the FTP site once a week. GAFs are updated once a week at most. Each build has to be watched as there are typically one problem or another. Decreasing the build frequency would only impact the AmiGO data. The annotations shown by AmiGO would essentially be the same while the ontology updates would decrease. Additions to the ontology would not have annotations for a week or so until curators update their files. The main effect is on obsoleted terms, and the GAFs are processed once a week (Saturday) to remove all obsolete terms. Decreasing GO-Lite builds to once a week would be good.

10:30 AM Break

11:00 AM Ontology Structure/Logic/Engineering/etc.

(6:00 AM EDT; 3:00 AM PDT)

Watching remote people: Ben

  • Annotation relationships - example:
    • cellular component vs cellular location. CC contains terms that are cellular components and whose instances have mass e.g. nucleus, and things that are cellular locations e.g. anchored to membrane. We have four possible courses of action (see Chris's email). (Chris)
    • Virus terms [Jane]
GO & internal cross-products
  • Current usage for QC (David) Slides
  • Release plans (Midori) Slides
Function-process links

12:30 PM Lunch

2:00 PM UniPathway

(9:00 AM EDT; 6:00 AM PDT)

Watching remote people: Rachael

2:30 PM Ontology Content

Binding

3:30 PM Break

4:00 PM GO & external ontologies

(11:00 AM EDT, 8:00 AM PDT)

Watching remote people: Jen

  • ChEBI overview - presentation by ChEBI curators. This will give us a better understanding of ChEBI's content and structure, which could help a lot wherever GO uses ChEBI - in cross-products, reasoning to infer links, etc. (Chris, Jane, Midori, ChEBI curator(s))
  • If we are planning to use small external ontologies in GO should we import them whole and keep their different (non-GO) ids, or make references from GO and keep the small ontologies entirely external? e.g. MeGO ontology phage terms. (Jane)
  • GO Cellular component and the NIF-Subcellular ontology (Chris)

4:30 PM Ontology Content—continued

Display issues

GO Slims

  • Can we decide on a policy regarding which ones we should maintain e.g. generic, multicellular org, prok org, euk org etc., and who should maintain them. Also GO slims v/s GO subsets. Accepted guidelines for making GO slims. See GO_slim_overhaul. (Jane, Val)

Change Management

  • A discussion of ontology structural changes - Mike

We need a discussion on policies associated with changes such as the recent has_part relationship implementation. The new relationship has_part was added for very good reasons. The ontology was changed to put this new relationship in place by changing the directional relationship of nodes. An example, note there is no issue with the biology of this change. The distribution of the change is at issue. The example below shows the changes in the "cell envelope" term. The old is_a relationship with "envelope" indicated that "cell envelope" is a child of "envelope", as all relationship they define the children of a term. The has_part relation implemented for "cell envelope" indicates "cell envelope" has the parent "plasma membrane". The relationship has_part indicates the parent of a term.

[Term]
id: GO:0030313
name: cell envelope
namespace: cellular_component
is_a: GO:0030312 ! external encapsulating structure
is_a: GO:0031975 ! envelope

[Term]
id: GO:0030313
name: cell envelope
namespace: cellular_component
is_a: GO:0031975 ! envelope
relationship: has_part GO:0005886 ! plasma membrane

This change would likely have a significant affect on software used to display this new relationship. This must be true as this new relationship is not displayed with AmiGO. It is also not dealt with by TermFinder or Mapper. It was decided that the new relationship would not be distributed to our user community and is stripped fromall OBO files, except of the gene_ontology_ext.obo.

Another important component of any ontology change is the use of thenew features by the GOC curation staff. The has_part makes the true path rule difficult.

These are all growing pains that are part of enhancing the ontologies. We need to give the external use, application use and curation with the new changes an appropriate level of importance.

5:30 PM OBO-Edit updates

(12:30 PM EDT, 9:30 AM PDT)

Watching remote people: Jane

  • OBO-Edit cross-products (CJM)
  • OBO-Edit term generation (Thomas)

7:30 PM Dinner at River Bar & Kitchen

Friday 25 September GO-top will confab in the morning

9:30 AM GO clinic to work on SourceForge requests (Jane, Midori, David, Tanya)

(4:30 AM EDT, 1:30 AM PDT)

Watching remote people: TBD if needed

Emphasis on items from Val relevant to GO slims

SF items:

12:00 LUNCH for all registered participants

1:00 PM Content Meetings and Taxon Constraints

(8:00 AM EDT, 5:00 AM PDT)

Watching remote people: Varsha, Debby

Content meetings

  • Signaling proposal presented. For comment only. The terms are not ready to be made live. (Jennifer).
  • Report on heart development meeting (Varsha)
  • ASCB meeting requires summary report on method
  • Ontology Development Direct Meeting ($4,000 )

Taxon Constraints

  • Report on automated detection of (potential)annotation/ontology inconsistencies using taxon constraints (Jen) Slides

2:30 Wrap up

9:30 AM EDT, 6:30 AM PDT)

Watching remote people: Ruth

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