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.
        • Default will be NOT to exclude obsolete terms from autocomplete lists (i.e., the current behavior)--user will have to change this option in Configuration Manager to make it exclude obsolete terms.
      • I'm also looking into ways to speed up autocomplete.
      • There was a request to show obsolete terms as red in the autocomplete list. Nomi isn't sure how complicated it would be but suggests Terry adds it as a feature request.
  • built in icons missing (Ramona)
    • Terry has sent a set of ready-made icons to Nomi (thank you).
    • Nomi: Should we add those to the set of icons that come with OE, because "Browse built-in icons" is already slow, and might be slower if we add a lot more icons.
      • UPDATE: it's not much slower, so I'll go ahead and include them.
    • On a related note, Nomi looked into the issue where when you add a new relationship that doesn't have a relationship icon, it is rendered in the Graph Editor in an unreadable font. She tried to add tooltips to show the relationship name when you hover over the relationship icon, but it turns out that the classes used in the Graph Editor don't provide that functionality. Oh well.

Next bugs to work on:



Action Items

  • Rescheduling OEWG meeting [DONE]
    • Karen will check whether AmiGO Hub meeting is still happening on 1st and 3rd Tuesdays [DONE]
    • Rebecca will add OEWG meeting dates to GO calendar [DONE]
  • Nomi to add Terry's instructions on how to use renderers to color terms by namespaces to the user guide. [DONE]
  • Nomi will add note about reasoner & memory to user guide. [DONE]
  • Nomi will make exclusion of obsolete terms from autocomplete lists user-configurable. [DONE]
  • Harold asked for more prominent announcements for new OE releases. Midori said you could ask SourceForge to let you know of new releases (but SF is a bit buggy) but Nomi will make the announcements clearer. [DONE, I think]
  • Nomi will add generic relationship icons (letters of the alphabet, etc.) to OE's set of built-in icons [DONE]


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