GO 18th Consortium Meeting Minutes Day 1

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GO Consortium Meeting Minutes

Sunday morning, September 23, 2007

Introductions chronologically:

2007 dimitri seth carbon bop 2006 jim hu ecoli, susan tweedie, trudi pamgo Donghue tair 2005 ben sgd, 2004 doug zfin, ruth ucl, victori rgd 2003 jen Emily, alex deihl mgi, mary dolan mgi, Karen eilbeck, petra fey, ranjana Caltech, pascale ddb, Kimberley, 2002 jdr bop, eurie sgd, Tanya Amelia 2001 rama sgd, mgwin tigr, Harold mgi, 2000 rolf ebi, rex ddb, cm bop, 1999 midori, kara dolinski PU, david hill mgi, 1998 suzi lewis bop, MA, mike cherry, judy


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.


2.1.2.1 Ontology development (Midori, David) Midori: All content changes and ??? Documented on Ontology Development Wiki http://gocwiki.geneontology.org/index.php/Ontology_Development is_a complete was almost finished last meeting, but is now done and a system is in place to make sure it remains so.

Three high level terms need to be disjoint – cellular process, multicellular organism process and ??? – <<add wiki link>>. Topics also overviewed High priority revisions <<wiki>> Content meetings and their documented changes <<wiki>>

Question IMG/FIG mapping. How much hanging now Jane gone on maternity? Not fixed!

JB/SL wiki can get muddled sometimes – managers should keep track Alex – if you add new large section you should send out a general email. ACTION ITEM – tutorial on wiki discipline (assigned to Who?). Rex – wiki help contact group.

David: i) Taxon and sensu: “Sensu” confused users, curators and editors became lazy in its implementation and use. Sensu terms have been renamed, merged or obsoleted (how many?) in collaboration with domain experts. 60 left to differentiate.

ii) Regulation. New relationship – ‘regulates’ <<add wiki link>> `regulates will not be a part_of process terms, but will have a new relationship type ‘regulates’

“Regulation of “ terms were evaluated and fell into 3 categories

i) regulates a molecular function (activity) ii) regulation of a biological process iii) regulation of a quality (membrane potential/ blood pressure) (some will be is_a some part_of, didn’t catch this)


Three types of violations were identified:

i) regulation of a process which did not exist. ii) regulation terms that are more specific than existing parents (Possibly missing processes, but may be not necessary to add) eg. Transcription involved in forebrain patterning? Regulation of transcription involved in forebrain patterning Part of forebrain patterning (check) Part of regulation of transcription (check) Transcription of forebrain patterning is not necessary





Chris went through ontology and told them were things did not make sense. All analyses in CVS in /go/scratch directory regulation-of-non-process.txt and on the wiki they have been split into 3 distinct categories detailed here:

http://gocwiki.geneontology.org/index.php/Regulation_Worksheet

Part 2:

How are we going to relate these terms to the rest of the ontology?

Action Item: need to trash through regulation.

Part 3 are problem cases. Including typos! Search on this page for ‘?’ for proposals by David where he needs resolution. Going through this list created links between function and process ☺

Negative and positive regulation question – were subtypes. Blood pressure it made no sense. Thought better to be part_of relationships. Keep it as subtypes for BP.

Collaboration with MIT/Harvard group.

Terms in wrong place? Shown through with their content analysis tool. Information Content Analysis. Can we place these terms in a better place – most of the time the answer was, yes. For example, pilus retraction moved further down.

Possible to put this analysis into GOC tools? CM – analysis already in database – check with Chris what he means.

Ontology Structure – CJM

Wiki should be merged with Ontology Development

http://gocwiki.geneontology.org/index.php/Ontology_Structure

Mining Reactome links to link process to function – more after lunch.

Internal cross products can start to be created and maintained in the ontology. OBO-Edit 2.0 will make it easier to maintain these cross products. Features ontology repair tool for links that don’t exist or are broken. Need consistent rules for regulation terms where the regulated stand in part_of relations.

New cross product guide on wiki. Links to ongoing work on BP – CP cross products;

http://gocwiki.geneontology.org/index.php/Cell_cross-products


Karen Eilbeck SO progress

Development : March – august joined J Thornton group - Gabi reeves for Biosapiens project. 96 new terms to SO.

Mark Hathon (with Barry)– ongoing work.

Content meeting in June, HLA immunology community – looking for terms to describe variants. New terms, rearranging of SO – very productive.

Collaboration with phyGo.

Working on synonyms with Colin Batchelor.

Release SO every 2 months.

Karen dropping down to 60%.


COFFEE BREAK


Aim2: We will comprehensively annotate reference genomes in as complete detail as possible.

Reference Genome Project

Rex/Pascale

Provide comprehensive annotation for 12 genomes. MOD, genome DB, curators. Complete means breadth and depth. Breadth – every gene. Depth – to the highest possible knowledge. If small amount of papers then read all. If extensive then summary of reviews. Metrics. GET REX’s PRESENTATION.

250 genes identified for curation. Gene when mutated should contribute to a disease (OMIM).

Per MOD – curators responsible for identifying orthologs using the commonly available tools.

S/W – Google spreadsheets – erratic. Not robust. Anxious to work with the SW group to develop a database – requirements have been written up. Merchant (left in July) wrote prototype. A new member of staff is starting at the end of September to continue development.

Annotation Progress – see slide.

Display approaches – comparing annotations to generic GOSlim branches.

Number of sourceforge requests from reference genome group in the hundreds over 16 months. Average of 10-12 requests per month. GO editorial group doing a good job at keeping up with these. Existing requests are problematic. 411 terms.


Aim3: We will support annotation across all organisms.

Annotation Outreach – Jen Deegan

Keeping track of new groups annotating and writing documentation.

ASK JEN FOR HER SLIDES.

People going to meeting – report back gossip from willing people to Jen.

The SOPs have been tricky but are now on the public GOC website:

http://www.geneontology.org/GO.annotation.SOP.shtml

Michelle created nice ISS guideline SOP.

Action Jen: A reference to these pages should go in next newsletter.

There has been much progress on grants.

Attending many regular conferences.

Less cold calling, it wasn’t very successful. More luck tracking down the right person at conferences. Responding to invitations.


Eurie - User Advocacy

Focusing on lines of communication, newsletter and mailing list. Rota of mailing list monitors.

Newsletters archived. Future news items page on wiki. Michael A wants ISSN for the newsletter. Action Michael! Michael sent URL to Eurie – Action Eurie!

Users meetings, we have a page of potential meetings on wiki.

Tools standards.

Production Systems – Ben Hitz

Deployed 4 nesw linux machines 1 for loading, 2 for amigo poduction, 1 amigo development.

ASK BEN FOR SLIDES

Production Amigo now more fault resistant.

Go Database loading speeded up and now in testing.

Godb sequences – using gp2protein files. If possible do all sequences in your DB, not just annotated.

Assocdb fasta file – Header line massive – can be slimmed down?

Association file cleaning – All IEAs must have a with field.

Amigo – Amelia ASK AMELIA FOR SLIDES

Term enrichment.

Go slimmer.


LUNCH BREAK

Action Items Review

Items In progress or marked as done are not re-listed here.


10. NOT DONE. Action Item for John: Add a term creation date to the .obo file. It didn't get added to the feature request tracker so it was overlooked. Now added:

-> JDR added to tracker on plane on the way here. NOW DONE


13. NOT DONE: Action item for AmiGO Working Group (from 4): The AmiGO Working Group will implement a strategy to incorporate and display the contents of the GO references. Request is on the AmiGO tracker (thanks Jane) http://sourceforge.net/tracker/index.php?func=detail&aid=1667315&group_id=36855&atid=494390

-> Done in next release. Amelia. On the tracker still.

15. Action Item for GOA (from 1): Talk to Reactome about getting non-TAS evidence. TAS is no longer considered a useful evidence code and will not be used in any consistency measures of reference genome annotation. Since part of the idea of the reference genomes is to provide a source of IEA annotations for other groups, we strongly encourage reference genome annotators to not use TAS, and instead use experimental evidence codes whenever possible. The GO documentation should also state this in a clear fashion. [annotation camp participants]

-> IN PROGESS NEXT ON AGENDA

16. Action Item for Judy, Harold, Amelia, Eurie, John Day-Richter (from 3,4,5): Resolve communication issues around obsoletes.

-> Midori to look into but probably done – tags applied to obsolete terms in OBO edit file.

17. NOT DONE (more discussion required) Action Item for Chris and Jane (Revisit 7): Remove the word 'activity' from the molecular function terms, and consider renaming the molecular function ontology. [note that later on in the meeting after action item 73 notes state that more discussion on this proposal is needed]

-> Strike activity from the function terms? Some people very opposed. DH.

18. [In Progress] Action Item for Jen & Chris (from 8): Assign priorities for contents changes needed to implement sensu plan. Discuss the different aspects of changes to our use of sensu, write documentation on this, and implement the new strategy. This change will then be announced to the community. Comment: There is more discussion to be had on this and a slot has been assigned for this in the meeting.

-> Jen to update on sensu later in meeting. See action items under Taxon/Sensu.


21. Action Item for Eurie (Revisit 12): No conclusion about how to distinguish large- vs small-scale experiments was reached. People are encouraged to keep thinking about this issue, which clearly needs more discussion.

-> To be discussed at this meeting.

28. Action item (Suzi, Tanya): Continue developing [protein family-based annotation] tool.

-> Put aside for the moment. Need to revisit. EVOLVING

29. Action item (Midori and Rex): Do it [i.e., new column in annotation files], add the column and document the formalism. It's not at all clear why this has my name (and I don't remember); it seems more for the software group and annotators. [mah]

-> TO BE DISCUSSED. Column 16. Structured Notes Field AKA SLOTS ☺

31. Action Item (Jane): Keep researching CARO integration.

-> Jane.

32. Action Item (AWG): Explore whether this [Mary's graphs] would be a useful addition to AmiGO 2.0.

-> STILL EXPLORING. Use logs? More discussion.

33. Action Item (AWG): There should be more tracking of what users are doing in the next AmiGO; explore the options.

-> Adding dates to file done but nothing further happened.


35. Action Item (John & Jane): Come up with a proposal for a history tracking tool, including timeframe and priority, and send out email.

-> ???

36. Action item (David, Jane): Organize first training meeting.(postponed due to the amount happening at this meeting)


-> ???

37. Action Item (Nicole, Jane, John, Mark): Create proposal to group for term submission software, including the “minimum standards for each term”.

-> JOHN not done – proposal considered.

38. NOT DONE! Action Item (AmiGO Working Group): Change AmiGO to hide (by default) structured comments of certain types. Obsolete comments will not be shown. Structured comments that don’t belong will not be shown. Have option to hide comments. [different types of comment not specified so no action]

-> Need more specification/requirements. Amelia.

39. Action Item (Karen E.): Send the information [microarray tool evaluation] to the group

-> Probably obsolete. Therefore Done?

Items 50-52 were all about the WITH field for the IPI code.

51. Action Item (Chris, Ben): Work through any database implications.

-> ???

52. Action Item (User Advocacy): Announce in newsletter, “what's new” section of GO site.

-> ???


60. Action Item (Evidence Code Working Group): Develop a decision tree for choosing an evidence code. Present results at next consortium meeting. (large scale/small scale, reviewed/un-reviewed. Similarity/not-similarity etc).

-> TO BE DISCUSSED AT THIS MEETING

61. Action Item (Rex): Assign programmer to check integrity of WITH field for annotations.

-> NEED NEW PROGRAMMER

63. Action Item (Evidence Code Working Group): Send RCA code back to committee.

-> TO BE DISCUSSED AT THIS MEETING



78. Action Item (User Advocacy): Draft an official GO brochure.

-> TODO



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.

GET SLIDES FROM PETER

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.)


Action: Get Reactome data into GOC before next meeting.


Jen – taxon and GO

JEN IS DOING THE MINUTES FOR THIS ONE

Comments:

DH: useful for ipro2go annotations

VW: ditto

EH: helps annotators, not necessarily good for users, but helpful for new groups?

RL: does it really need to be that complicated?

JB: could be accomplished by triggers, a rulebase. Therefore by definition this would only be seen in a taxa. Efforts should be on annotation of literature. One off triggers.

Sue Rhee: Should explore using goslims? Possibly create a file of cross products to taxa on terms, therefore multiple taxa per terms.

SL: Nice to have an evaluation. Take existing annotations and say that this term has been used in this species.

JDR: large scale derivation of annotation data BAD idea – propagating the garbage. Do something on a higher level – say 10 and see what filth it uncovers.

MC: Too much work. Another piece of SW to be built.

VW: relevant_to and not_releavant_to would be a minimum

RC: no objection to relevant_to but opposed to universals – i.e. is_only_relevant_to.

Missed judy and Michael here…. BH: what fraction of problems would be solved if there were CPs to anatomy ontology missing?

Consensus: using this for error checking would be very useful

RL: taxa isn’t a be all an end all for help in term definition

Consensus: Some of us have doubts and it will cost so some sleep time needed.

Action: as creating new terms – see if ths is the way to go?

PG: Would not use restricted GO set to curate – what would you be missing?

JDR Proposal,

Objections – unmaintainable useless and a waste of time. jen to do pilot pass to see what happens, then she presents it at next meeting

JB proposal – get another group to do it.

JH: issues with true path – when going up levels, start to see untruths

ACTION Jen do experiment