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

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

Revision as of 10:59, 24 September 2007

Day 1 Minutes

Monday 24th September 2007, Princeton University, NJ

Board Agenda

1. Plans for immediate future (SL) a. regulation b. cross products

2. Database report a. schema changes b. production

3. GA files (mike)

4. OBO-Edit (john)

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

Give users a temporary ID to work with when they need a new term.

However many terms rejected

Need to feedback to them outcome of term request.

How do this?

Everyone has some way of dealing with term obsoletion – therefore we can use these mechanisms to feedback to user.

When request closed, use ‘consider’ or ‘replace_by’ tags to get correct term.

Create mini ontology file they can update all their annotations with the new term id.

Discussion follows….

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.


Seth’s Demo ORB

Search in amigo – get no results follow link to ‘add new term’.

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.

SF 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 barch tracker id? SC: generate SF ids using another system?


ACTION: david midori and seth to meet in rose garden to finalise details. ORB

CJM – Schema changes

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.

http://www.berkeleybop.org/goose

example: Suspect ISS assignments


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

New architecture roadmap on amigo. More interactive components on front end.

Transitioning from perl to java. Re-use existing OBO-Edit code, mature and robust. Therefore saving development time in future.

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.