OEWG 20090429

OBO-Edit Working Group, Wednesday April 29th, 2009 9.30 a.m. PST

Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425

Agenda/Chair: Melissa
Minutes: Amina
Attendees: Midori, Jen, Melissa, Tanya, David Hill, David Sutherland, KarenC, Nomi, Harold, Thomas, Amina

Action items carried over

• Action items: Amina
  • Finish work on assert-implied-links component, and email OEwg list

• Action item: Midori
  • Inform a few others who might be interested in the demo

• Action item: Jen
  • Visit Colin's group, watch users, try to solicit bug reports, etc.

• Action item: Working Group
  • Prioritize a bug and feature tracker
  • Pick one bug you would like to see fixed by the next meeting

Discussion items

• Amina presents: Assert Implied Links Component Demo
  • feedback1: Undo for links asserted action
  • DavidH: To undo - delete link and run reasoner again
  • DavidS: what do you do with these hard links? I'm less trusting of the remove redundant links calculations
  • Midori: existing remove redundant links behaviour: list - click to check what its found
  • feedback2: Reverse select term- link from OTE to AssertTable

DS: multiple problems with this
previous releases of the reasoner - over-flagged redundancy
the only one I trust is RBR
did a lot of checks - and works alright
will be interesting to see how the two different links span out.
problems and how it works out with GO

Amina: how will incremental reasoning fit in to the assert links? DPH: yes; assert 1rst, turn reasoner off, then on again to look. But need to wait for Chris's script to run the make XP's. Incremental appears too slow. David O has to always have the reasoner running. GO doesn't; they edit first with off, then turn on to check.

DH: run reasoner again
unless we start creating cross-products ourself - we need to run chris's script
we'll create a xp and then run the reasoner again

DS: Im afraid I'll hit the limit so I turn off the reasoner
MH: for years we've had that as a goal for GO to edit with the resoner on
All: its just really slow
MH: you can have 20 cups of coffee waiting for it
DS: switching the incremental reasoning off should solve this issue

Does remove redundant links work with rule-based vs link-part reasoner. DavidS says it didn't before with link-based. Midori: it does give you a list first so you can check the ones you want removed. David O trusts the rule-based reasoner to not make errors.

Thomas: explaining the ontology generation plugin - presented at the biocurator conference (documentation available in OBO-Edit User Guide) Jen: can we have 3 separate tabs for the 3 steps

• Verification Check issues?

KC: non-critical warnings
fix hundreds of warnings..
start ignoring the warnings..
mistakes that should've never been committed.. things that are being carried over from time to time
KC's email to the WG
Relaxing the rule for verification marks will be easier than maintaining the file
Short term fix: AI - Jen - fix period words file and commit to svn
Long term fix: AI - Amina - edit verification chck rule

Harold: during text edit in the verification manager
MH: on text commit bug... wasn't actually doing the check

• • ID's in xps tab in Text Editor
• ID where there isn't a name available AI- Amina

• • Tough ontology to test: chebi reasons well

• Upcoming Demos
  
  • Incremental reasoning
    
  • Parent Editor

Amina

• • parent editor
• Potential Parent Editor Improvements: show which links are asserted and which ones are implied
  • doesn't need anything else

• Discussion b/w Harold and Alex
  

(Idea: ability to save the non-fatal errors list to a file. Also, discussing this with Alex: why do we care about extra white space since it's non-fatal. What will it harm?)

Action Items

• Amina
  • feedback2 for Assert Implied Links Component: Reverse select term- link from OTE to AssertTable - useful when looking at a long list of asserted links
  • 2.1 release
  • bug fixes
  • Graph Editor Crashes
  • Config Manager memory settings not in sync
  • Look at Graph Viewer again and try to figure out what's going on
  • Look into extended character support

Jen: update period words file
Karen: file feature request Midori: check if the "on text commit" verification manager check is fixed
Jen: visiting Colin's group

Links

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