OEWG 20110208

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OBO-Edit Working Group Meeting: Tuesday, February 8th, 2011, 8:30am PST

Conference call details: New GOC conference call numbers
US: 1 866 953 9688
UK: 0808 238 6001
pin: 801561

Agenda/Chair: Nomi Harris
Minutes: Rebecca Foulger
Attendees: Nomi, Harold, Terry, Karen, Midori, Rebecca

Bug and Feature Tracker Updates

Discussion items

  • GO ref genome and annotation calls are moving to Tuesdays at 8am PST, conflicting with the OE calls. Should we pick a different day of the week, or just start at 9 instead of 8:30?
    • The annotation and reference genome calls are now on Tuesdays 4-5pm GMT (8am Californian time), which means they will often clash with the OBO-Edit working group calls.
    • The AmiGO hub meetings are on the 1st and 3rd Tuesday of the month (normally 8:30-9:30 Californian time, 16:30-17:30 UK), which will also clash.
    • There may be another free phoneline we can use- people will investigate. Clackpoint tried out by Jen Deegan in the past wasn't successful, and it's thought that skype calls will so many users will not be clear.
    • AI: Karen will check with Rama about whether the AmiGO hub meetings are still active, then we can make a decision about whether to move days or times for the OEWG calls.
    • When the times are set, Rebecca will add them to the GO calendar, so no-one else will book the GO line at the same time. The next meeting may or may not be on Tuesday March 1st at 8:00 California time.
  • UPDATE: AmiGO hub meetings are no longer happening. We will hold OEWG meetings on the 1st and 3rd Tuesday of the month at 8:30am California time (16:30 UK time). The next meeting will be Tuesday, March 1st, at 8:30 California time.

Fixed since last meeting:

Issues and action items carried over from last meeting:

  • Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
    • Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.
  • Terry wrote instructors for configuring a renderer to color terms by namespace (Thanks, Terry!). Nomi needs to add this to user guide.
  • Nomi will also add comments on reasoner + memory to user guide.
    • Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
    • Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quitting/etc.
  • ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago). How important is this?
    • Most wg members don't even know what it does! Nomi will bring it up with Chris.

Currently working on:

  • Obsolete terms appear in autocomplete dropdown lists.
    • Current status: implemented removal of obsolete terms from autocomplete lists for searches of "Any text field" (will implement for other types of searches.
      • This extra test slows down creation of autocomplete list.
      • Accordingly, Becky suggested making this a user-configurable option (whether or not to exclude obsolete terms from autocomplete lists). Will add to Configuration Manager.
      • I'm also looking into ways to speed up autocomplete.
  • built in icons missing (Ramona)
    • I looked around and couldn't find H_UC.svg anywhere in any version. In all the versions I looked at, the built-in type icons (which live in src/org/oboedit/gui/resources/icons/typeicons) were the same 21 icons. I don't know where Becky got H_UC.svg from.
    • Amelia mentioned that she wrote a script (svg_script.pl) that generates icons (e.g. for letters). Maybe Ramona or someone else used this script once upon a time to make the now-lost icons? It doesn't look like they were every committed to SVN.

Next bugs to work on:

Demo

none

Action Items

  • Nomi to add Terry's instructions on how to use renderers to color terms by namespaces to the user guide.
  • Nomi will add note about reasoner & memory to user guide.
  • Reschedule meeting or find other phone line to use:
    • Ref genome and annotation meetings are now 2nd and 4th Tuesdays at 8am PST.
    • We could move OEWG meetings to 1st and 3rd Tuesdays at 8:30am, but the GO calendar lists AmiGO Hub meetings then.
      • Karen: find out if AmiGO Hub meeting is ongoing
    • ?: look into other possible free conferencing numbers
    • Nomi once had an OBF meeting on some commercial free conferencing number--what was that?
    • Becky: add OEWG meeting to GO calendar once we decide on dates

Links

Back to OEWG Meeting agenda and minutes List