OEWG 20090429: Difference between revisions

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==Discussion items==
==Discussion items==
* Amina presents: Assert Implied Links Component Demo  
=== Amina presents: Assert Implied Links Component Demo ===
** feedback1: Undo for links asserted action
* feedback1: Undo for links asserted action
** DavidH: To undo - delete link and run reasoner again
* 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  
* 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
* Midori: existing remove redundant links behaviour: list - click to check what its found
** feedback2: Reverse select term- link from OTE to AssertTable
* feedback2: Reverse select term- link from OTE to AssertTable


DS: multiple problems with this<br>
DS: multiple problems with this<br>
Line 63: Line 63:


<p>
<p>
* Verification Check issues?
=== Verification Check issues? ===
KC: non-critical warnings<br>
 
fix hundreds of warnings.. <br>
background is explained in an email from Karen:
start ignoring the warnings..<br>
 
mistakes that should've never been committed.. things that are being carried over from time to time<br>
<pre>
KC's email to the WG<br>
Date: Tue, 28 Apr 2009 14:46:30 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: GO Ontology Editors <ontology-editors@genome.stanford.edu>
Cc: OBO-Edit Working Group
    <geneontology-oboedit-working-group@lists.sourceforge.net>
Subject: [OBO-Edit Working Group] non-critical warnings on GO file
 
Hi GO ontology editors,
 
I did an edit today and noticed that there were 26 non-critical warnings.  
I went through all of them to see what they were. There are a couple types
of warnings where we should probably change what the verification check
looks for (which is why I cc'd the OEWG on this), but there were a bunch
of user errors which people should have fixed before they committed.
 
In the process of releasing OE2, Jen did a lot of work to clean up the
hundreds of these that we used to have, so that people could actually use
the verification checks to catch problems they introduced. But if we start
collecting a whole bunch of these again, then everyone will ignore the
verification checks again and we'll be back to where we were, and
eventually someone will have to go through and clean them up again.
 
I think it would be best if we can keep GO "clean" of these types of
problems so that the verification checks are useful to each person as they
save, so they can use it to fix their own problems BEFORE they commit
them.
 
Below is what I found in going through the warnings. Maybe we can talk
about appropriate procedure to avoid accumulating these warnings, and
perhaps the OEWG can talk about whether two of the checks are picking up
things they shouldn't be.
 
thanks,
 
-Karen
</pre>
 
Relaxing the rule for verification marks will be easier than maintaining the file<br>
Relaxing the rule for verification marks will be easier than maintaining the file<br>
Short term fix: AI - Jen - fix period words file and commit to svn<br>
Short term fix: AI - Jen - fix period words file and commit to svn<br>
Line 76: Line 112:
MH: on text commit bug... wasn't actually doing the check<br>
MH: on text commit bug... wasn't actually doing the check<br>


**ID's in xps tab in Text Editor
=== other topics ===
 
*ID's in xps tab in Text Editor
*ID where there isn't a name available AI- Amina
*ID where there isn't a name available AI- Amina


**Tough ontology to test: chebi reasons well
*Tough ontology to test: chebi reasons well






* Upcoming Demos<br>
=== Upcoming Demos===
** Incremental reasoning<br>
* Incremental reasoning
** Parent Editor
* Parent Editor


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


* Discussion b/w Harold and Alex<br>
* Discussion b/w Harold and Alex<br>
(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?)
(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==
==Action Items==

Revision as of 17:53, 29 April 2009

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?

background is explained in an email from Karen:

Date: Tue, 28 Apr 2009 14:46:30 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: GO Ontology Editors <ontology-editors@genome.stanford.edu>
Cc: OBO-Edit Working Group
    <geneontology-oboedit-working-group@lists.sourceforge.net>
Subject: [OBO-Edit Working Group] non-critical warnings on GO file

Hi GO ontology editors,

I did an edit today and noticed that there were 26 non-critical warnings. 
I went through all of them to see what they were. There are a couple types 
of warnings where we should probably change what the verification check 
looks for (which is why I cc'd the OEWG on this), but there were a bunch 
of user errors which people should have fixed before they committed.

In the process of releasing OE2, Jen did a lot of work to clean up the 
hundreds of these that we used to have, so that people could actually use 
the verification checks to catch problems they introduced. But if we start 
collecting a whole bunch of these again, then everyone will ignore the 
verification checks again and we'll be back to where we were, and 
eventually someone will have to go through and clean them up again.

I think it would be best if we can keep GO "clean" of these types of 
problems so that the verification checks are useful to each person as they 
save, so they can use it to fix their own problems BEFORE they commit 
them.

Below is what I found in going through the warnings. Maybe we can talk 
about appropriate procedure to avoid accumulating these warnings, and 
perhaps the OEWG can talk about whether two of the checks are picking up 
things they shouldn't be.

thanks,

-Karen

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

other topics

  • 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

Back to OEWG Meeting agenda and minutes List