2009-09 Cambridge GO Consortium & SAB Meeting

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

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)

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

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

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.)

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.

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

• Presentation on progress so far and plans (David)Slides
• Report on automated inference of BP annotations from MF annotations + inter-ontology part_of links (Chris/David/Tanya)

2:00 PM UniPathway

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

Watching remote people: Rachael

• Presentation of (http://www.grenoble.prabi.fr/obiwarehouse/unipathway) - possible source of new terms to add to the GO biological processes and molecular functions (Anne Morgat (SIB), via email from Serenella Ferro Rojas)

2:30 PM Ontology Content

Binding

• Report by binding terms working group and discussion (Ruth)
  • draft proposal Slides Summary Slides

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

• General discussion about graph visualization for AmiGO and OBO-Edit wrt new relations that have a different parent-child structure e.g. has_part [perhaps as part of AmiGO report?]

  Examples where the has_part relationship is used:

  • in component, relationships between spliceosomal snRNPs and spliceosomal complexes

    Graph Editor view of "U5 snRNP"

    Ontology Tree Editor view of "U5 snRNP"

  • in process, relationships relating to mRNA surveillance

    Graph Editor view of "mRNA surveillance"

    Ontology Tree Editor view of "mRNA surveillance"

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)

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:

• SF 2678878 - regulation usage query
• SF 2844431 - cell growth/cell size
• SF 2854395 - biogenesis and organization; see also SF 2520134 - ATP synthase ...
• SF 2136864 - chaperone activity

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).
  • Minutes of discussion so far
  • Branch file
  • Slides
• 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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