GO 18th Consortium Meeting Minutes Day 2: Difference between revisions
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ACTION ITEM Link to how to make a perfect GO term | ACTION ITEM Link to how to make a perfect GO term | ||
== | == Schema changes - Chris Mungall== | ||
SWUG | [[SWUG:Database changes 2007]] | ||
Support for multi species annotation files | Support for multi species annotation files | ||
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GOOSE | === GOOSE === | ||
SQL query interface for intermediate to advanced user. | SQL query interface for intermediate to advanced user. | ||
http://www.berkeleybop.org/goose | http://www.berkeleybop.org/goose | ||
Provides example SQL queries | |||
example: Stale ISS assignments | example: Stale ISS assignments | ||
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ST: web services? CJM – yes, sparkle already ready | ST: web services? CJM – yes, sparkle already ready | ||
New architecture | New architecture road map on Amigo. More interactive components on front end. | ||
Transitioning from | 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. | Renovated GO database info page. |
Revision as of 13:56, 24 September 2007
Monday 24th September 2007, Princeton University, NJ
Broad Agenda
- Plans for immediate future (SL)
- regulation
- cross products
- Database report
- schema changes
- production
- GA files (MC)
- OBO-Edit (JDR)
- 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.
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 ITEM (David Midori Seth) Deploy the part that created SF items based on a freindle 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
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
ST: web services? CJM – yes, sparkle already ready
New architecture road map 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.
Renovated GO database info page.
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.
JDR –OBO Edit WG
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
- Autocomplete,
- advanced searching for power users,
- 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
David Botstein
...
TOUR OF LEWIS SIGLER INSTITUTE
Group Photo
LUNCH