OBO-Edit Working Group, Thursday June 18th, 2009 9.30 a.m. PST
Conference call details:
Outside US: 1-719-867-3417
Attendees:DavidOS, Midori, Jen, Meslissa, Harold, KarenC, Chris and Amina.
- 1 Action items carried over
- 2 Discussion items
- 3 Action Items
- 4 Links
Action items carried over
We attempted to use a new, cheaper conference call line, but while it allowed everyone to call in and listen to cheesy jazz saxophone, it did not actually allow anyone on the line to communicate with everyone else. Apparently, this number is still in demo mode and the person Harold had emailed did not respond in time to set up the meeting for us. We may try this again with appropriate advance preparation.
possible change to meeting time
Amina indicated that a number of people who would like to attend cannot make the current time of Tuesday from 9:30 to 10:30 Pacific. She set up a Doodle poll to see what time might work better.
Amina - Dev updates
- Ontology change tracker
- she wanted to know if anyone has been using this tool
- Jen uses it, finds it useful
- it worked only with IDs, which was a problem for Melissa who works with an ontology that doesn't have IDs
- Assert Implied Links
- this is available from the Edit menu
- DavidOS hasn't used this; he uses the assert implied links option available upon saving
- Filtered save
Basically, the improvements David requested in preparation for the upcoming workshop should be ready on time. Amina will have demos soon.
Using OE2 for cross products and filtering
Chris met with the GO editorial office people and demonstrated using OE2 for making cross products and filtering. This was really useful; people learned some useful tidbits. Basically, everyone felt that it's really great that OE2 is available for use now so that they can proceed with a number of projects that were on hold waiting for OE2.
Jen has put in a couple feature requests arising from this meeting.
Jen has posted some screen shots and info about doing cross products for GO on the wiki. Midori commented that this is fine for now, but that this procedure will likely change. Sample of doing cross products for GO with OE2
Prioritizing bugs and feature requests
Midori brought up the need for the OEWG to decide on priorities for the various bugs and feature requests. It was noted that it would be better to make such decisions now rather than wait till just a month before the next GO meeting, so that there is time to actually act on the agreed upon priorities for fixes and new features.
Tips of the Week
Using multiple results from a search
If you do a search, you can select multiple results and then use them in the Ontology Tree Editor, to make them all a parent or child of a designated term, by dragging the group of selected terms in the OTE to the designated target term and then choosing the desired option from the menu that pops up upon dragging.
Copying from search results
If you do a search, you can select multiple results and then copy/paste them into a text window. This works best with local selection mode so that the display doesn't try to show everything that is selected.
OE2 issues: loading a different ontology
Harold has been training some people new to using OE2 and has seen some odd behaviour with loading another ontology using the Load Ontologies option from the File menu. Most of the time, it will load the new ontology, replacing the one that was loaded. However, occasionally, it will just crash. To avoid the crash, he sometimes selects New Ontology from the File menu, to purge the existing one, before loading a new one, but the crash is so rare, it is not clear if this makes a difference or not.
(Karen had to leave before conclusion of this discussion)
- Richard Smith at jax is at a dead end with editing his ontology as he needs support for pictures associated with terms.
Chris suggested the metadata should be in the ontology file as xref or dbxref and link to standard id space for images stored on the web.
- Midori - Working group members should prioritize tracker items.
- Jen - This is a critical bug that needs to be fixed
- Harold - Loading a new ontology when an exiting one is loaded causes OE to crash or become unresponsive.
- Amina - Will look into these items
- Melissa - I might have to get a new machine. With the OTE you have to be very careful where you click - if you don't click middle of the row it won't select - very fussy.
- Working group discusses Melissa's system configuration.
- David: Protege menu items broken by mac java update