GO 18th Consortium Meeting Minutes Day 2: Difference between revisions

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# Evidence code Revise evidence code documentation so that a mutation in only one gene can only be IMP (protein localization IGI example)
# Evidence code Revise evidence code documentation so that a mutation in only one gene can only be IMP (protein localization IGI example)
# (Curators) Check whether you have used IGI in this way and update annotations
# (Curators) Check whether you have used IGI in this way and update annotations
# (Curators) with column optional for NAS - document

Revision as of 15:39, 24 September 2007

(Day 1 Minutes)

Monday 24th September 2007, Princeton University, NJ

Broad Agenda

  1. Plans for immediate future (SL)
    1. regulation
    2. cross products
  2. Database report
    1. schema changes
    2. production
  3. GA files (MC)
  4. OBO-Edit (JDR)
  5. Evidence codes (MA)

Overview of cross products by CJM

CP results in scratch directory.

Discussion gene_ontology_edit.obo file vs original file confused.

JDR – add obo version number to the filename. Then use original name as release version of file.

MA/Mike – change ‘edit’ in curators version to ‘pre_release’ to better describe it’s use. Orig file updated nightly by Stanford.

CJM: need to take versioning a little more seriously – impossible to replicate analyses. How do we cite what version of the GO we use?

Michelle – do we hide pre release file?

Cjm: no, culture of using the latest file.

Michelle: However, orig file updated daily anyway.

DB: not straightforward to find when people took data


SO and Chromosonal Location – CJM and KE discuss offline.

John Day-Richter - Term Lifecycle

GET SLIDES FROM JDR

Term requests to instatiation int he ontology has been reported to be a bottleneck. Users request terms, then need to wait for implementation to use them.

Proposed solution. Give users a temporary ID to work with when they need a new term. Create mini ontology file they can update all their annotations with the new term id.

However many terms are rejected as requests are inappropriate, so need to feedback to them outcome of term request? How? Everyone has some way of dealing with term obsoletion – therefore we can use obsoletion mechanisms to feedback to user. When request closed, use ‘consider’ or ‘replace_by’ tags to get correct term. the term is obsoleted in the users private ontology.

Discussion:

PG: new groups might not be able to handle this.

MC: automation not a human friendly approach, this is not user support per se.

MH: how much more burden to track down terms to suggest and consider a replace_by?

JD: most term requests a lot of work, might be easier to phone the person and do the request on the spot.

SL: but this is an extra to personal communication.

JDR: Seth has already done this – but sounds like we shouldn’t release this publicly.

JB/JDR: not much support for this – put on backburner until we find a good project for this to be used on. Possibly to use for Reactome requests, but Midori pointed out that ALL Reactome requests (ONLY 15), had been dealt with very promtly (12 within 2 days and all within 3 weeks).

Seth ORB (Ontology Request Broker)

Will be linked to AmiGO. If a user searhces for a term in AmiGO but gets no results follow link to ‘add new term’. Form is provided to add term name, definition, additional details and they get an SF ID. The user can then retrieve their terms with orb_default ids in OBO format.

SourceForge username becomes part of the ID to help tracking.

Discussion follows:

DH: nice that users need to get SF login. Don’t like temporary IDs though.

MA: produces stanza

ED: how do you handle spam? Need to enter email address?

MA: yes contact should be requirement

Michelle: provide link to new term best practise documentation

JDR: Use one batch tracker id?

SC: generate SF ids using another system?


ACTION ITEM (David Midori Seth) Deploy the part that created SF items based on a friendly webform, and would like to see a obo format in the SF item.

ACTION ITEM Link to how to make a perfect GO term

Schema changes - Chris Mungall

SWUG:Database changes 2007

  • Support for multi species annotation files
  • Support for new properties column. Test data from MGI received (they use structured notes field)
  • Support in schema for taxon based queries, species, kingdom etc.
  • GOOSE new interface to MySQL DB. Aimed at intermediate to advanced users. EBI mirror>5000 hits so far.

GOOSE

SQL query interface for intermediate to advanced user.

http://www.berkeleybop.org/goose

Provides example SQL queries example: Stale ISS assignments


Q ST: web services? A CJM – yes, sparkle already ready

New architecture road map on Amigo. More interactive components on front end.

Seth and Amelia have been refactoring the server based code. Transitioning from Perl to Java. Re-use existing OBO-Edit code, mature and robust. Therefore saving development time in future.

Renovated GO database info page.

ACTION ITEM Amelia link GOOSE from front page - DONE

Mike Cherry – Gene Association Files

SGD wants to have 2 files – one manual, one IEA.

Discussion follows….

CM: need consistency if SGD do it - then we all should do it.

DB: want it clear to researchers that they are using correct experimental data.

MA: propose we do this at download time for the user.

JD: help education of IEA.

ACTION ITEM Write GA file filter script ???

ACTION ITEM More advanced interface to download custom files by versioning

OBO Edit Working Group - JDR

About to rel 2.000 beta-14

89 bugs fixed.

OBO Edit toolkit now used in Phenote.

Reasoner much faster. Edit in real-time with reasoner on.

JOHN DEMO OBO EDIT NEW FEATURES

  • Auto-complete
  • advanced searching for power users, Boolean querying
  • advanced sub query feature
  • docking panels to personalise interface.
  • Graph based editing updated automatically
  • Wrench icon for every panel to set up personal preferences, filtering, view options etc.
  • Create new terms and relationships in graph editor by drawing
  • Graph overview preview
  • Graph DAG Viewer
  • Spell checking
  • external contributions from..... CJM

File:OBOEditWorkingGroup GOC PU 2007.ppt

File:Term Requests GOC PU 2007.ppt

David Botstein Discussion about availability of predictions

There is lots of masturbatory literature of researchers stimulating themselves with the same information GO open to abuse There should be a more rapid iterative process to make predicted annotations available, especially to curators who would be prompted to look for the possibility that a biological process could occur.

When people have looked for statistical links between genes to looks for possible associations, most predictions turned out to be good. They found evidence for this that wasn’t currently included in GO (i.e unannotated but information present in literature)

Judy, this is a priority issue

??? Need more curators

David did this exercise with Fritz Roths dataset fell into 3 categories:

correct annotation should clearly be made

enough circumstantial stuff to make this annotation, but not tested

from outer space

Sue Rhee: Users group to focus on predictions? Mike: Build into future David Botstein Some are one offs, others are systems which should be a semi automation. Does anything arise from the algorithm which isn’t obvious from reading the paper. Use the best of the methods routinely

Rex: Grant using expert GO annotation to validate predictions

??? Reports from people who have done these types of collaborations

Suzi: something we build in to the long term. If GO becomes responsible for running SW/ limiting.

DAVID suggestion, run on reference genome gene of the month

Need to leverage the groups who are doing these things Jim: Suggested Making a repository for predictions (POSSIBLE ACTION ITEM ???) Set up a thing where people can dump their results, and we will look at them.


TOUR OF LEWIS SIGLER INSTITUTE

Group Photo

LUNCH

Annotation Evidence Codes - Mike Cherry

...


Summary of Action points from Day 2

  1. (David Midori Seth) Deploy the part that created SF items based on a friendly webform, and would like to see an OBO format in the SF item.
  2. Seth, ORB: Make link to how to make a perfect GO term from the term request tool NO LONGER NEEDED?
  3. Amelia link GOOSE from front page -DONE
  4. DH: Cross products: need to have webex meeting to everyone understands what to do.
  5. OBO file renaming. JB: add a link to Wiki: http://gocwiki.geneontology.org/index.php/Versionning_Proposal On the best practises page: http://gocwiki.geneontology.org/index.php/Best_Practises
  6. Midori etc to work on specification needed for new Amigo features.
  7. Gene Association files: to work on a more advanced interface to download custom files (Chris)
  8. Gene Association files: to filter files as they come in. (Chris)
  9. Judy: Predictive Activities. Collaborations with external groups. Reports into next GOC meeting as to these kinds of activities.
  10. Jim: Suggested Making a repository for predictions POSSIBLE ACTION ITEM?
  11. Finalizing proposed evidence code documentation – abbreviated version on web pages and more detailed on GOC Wiki (Rama)
  12. Eurie: querying communities on awareness of evidence codes – do you know what it is, what do you use it for? Also proposal of expanding, then get a feel for what would benefit them? So that we have a large audience.
  13. Sue, Michelle, Rama put evidence code proposal in the context of what we discussed today
  14. Evidence code committee. Documentation for users and curators.
  15. Evidence code Revise evidence code documentation so that a mutation in only one gene can only be IMP (protein localization IGI example)
  16. (Curators) Check whether you have used IGI in this way and update annotations
  17. (Curators) with column optional for NAS - document