OEWG 20090505

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OBO-Edit Working Group, Tuesday May 5th, 2009 9.30 a.m. PST

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

Agenda/Chair: Amina
Minutes: Harold/Amina
Attendees: AA, hjd, KarenC, Midori, DavidOS, cjm, Thomas Wachter

Action items carried over


  • Assert Implied Links Component
    • - Reverse select term- link from OTE to AssertTable - useful when looking at a long list of asserted links
    • - Bubble pop-up display for Explanation not sufficient to all levels of the explanation - clicking on the info icon opens the explanation in the Explanation Component. - DONE
  • Graph Editor Crashes


    • Explanation of Error message on OSX: [0x0-0xb7fb7f].com.install4j.7283-8148-3557-2000.8[46157] Invalid access of

stack red zone b0c95ffc eip=642afeb9

Each block of memory allocated to an application comes with a leading and trailing "redzone" which is a special signature in memory just before and just after the memory allocated to the application. If the application were to overwrite outside this region, the redzone signature would be overwritten. Then later on the application crashes and you get this abend when the memory is returned, and the OS can inspect the redzones.

Amina: David how much memory did you allocate to the application?
David: over 1024Mb
Chris: something to do with # of links showing up in the graph editor.
Amina: too many links yes memory hog.
David: tries to put every link in even if they are redundant. Feature request to trim the graph on demand.
Amina: we could have some kind of warning when the graph is getting out of control suggesting it might result in a crash or just allow the graph editor by itself to crash - will look into it.

  • Config Manager memory settings not in sync - DONE
  • Configuration Manager -> Text Editing -> Allow extended characters options
    • Code reveals this currently does not do anything - I think its placeholder for future implementation.
    • AI Amina: UTF8 support

Midori: Yes UTF8 support is not that crucial for GO but other users want it.

  • Potential Parent Editor Improvements: show which links are asserted and which ones are implied
    • Chris's idea: check boxes to promote or demote intersection links
  • Jen: update period words and repeated words files
  • Karen: file verification feature request
item opened - SF 2784022
  • Midori: check if the "on text commit" verification manager check is fixed
still broken - SF 2785044
  • Jen: visiting Colin's group

- Jen hasn't visited Colin yet
Colin: Chebi has never worked well for him
David: last time he tried, it worked; but may be too large for the reasoner.
Chris: run reasoner with Chebi ? Yes.

Discussion items

  • Incremental Reasoning on/off demo postponed to next meeting - May 12th
  • Teaching Resources/ Demos/ Cool Stuff section on the OBO-Edit website
    • Need contributions from the Working Group
    • Record Demos

David has some more OBO-Edit specific material he can share for the resources/demo's sections.

  • verification plugin - not seeing dictionary? - ID: 2784937


  • OBO-Edit2-rc still present - ID: 2785074


  • reasoner active even in OFF mode


David: the Graph Viewer does not refresh after switching the reasoner off and its confusing switching b/w reasoners.
Will try to break the Reasoner Manager and report next week.

  • Multiple hi-res image display support
    • flickrj api - upload images to a service like flickr through the OBO-Edit user interface or have wiki pages?

Chris: all the image data needs to be posted online.

  • David Hill reported an issue last week with adding child terms to a parent. The children were added to root and not the parent term in the OTE while the graphviz viewer displayed the correct hierarchy. I could not replicate the problem. David will try to replicate the problem and get back to me.
  • Melissa: OE clunky on windozzze

Amina: Melissa will be visiting Berkeley soon - will work with her then

  • Thomas Wachter presented the Ontogen plugin.
    • David has hundreds of pdf's he would like to mine.

Action Items


Back to OEWG Meeting agenda and minutes List