OBO-Edit Working Group, Tuesday September 15th, 2009 9.30 a.m. PDT
Conference call details:
Outside US: 1-719-867-3417
Attendees: Karen C, Amina, Harold, Chris, Midori, Melissa
Action items carried over
- None :)
- Updates from the development front
- Working on reasoner stuff
- OBO-Edit2.1 release next week
Discussion: Amina has been working on incremental reasoning and plans to have a new release 2.1 by next week before the meeting. She will do a quick update of the documentation, but after the meeting the OEWG can flesh out any remaining details that need to be updated or included to fully document the new behavior of the reasoner.
- Meeting next Tuesday 9/22 instead of Thursday 9/24 due to the GO consortium meeting.
all present agreed
Discussion: Chris stated that the desired behavior is to NOT show disjoint relationships in the GraphViz viewer. Amina will talk to Jen in order to find the correct terms to view the issue that Jen brought up, and then update the SF tracker item appropriately.
Chris also asked if people are happy with the current situation with respect to which components do or do not show disjoint relationships. Midori stated that she did not currently have a strong opinion on the subject, though might perhaps form one if there were more of these relationships in GO.
- indestructable XPs See Comment
Discussion: Amina said that the issue seems to be that you must make sure you Commit. Once you've done that, it is possible to delete things normally. She has updated the tracker item with a comment.
Discussion: Amina cannot duplicate this bug. She will email the submitter after the 2.1 release to ask them to check on it.
- 2.0 graph viewer now shows only one parent Discussed a couple of weeks back - no consensus on behavior
Discussion: We discussed this first in order to have Harold present. We agreed that the desired behavior would be for the Graph Viewer to show asserted links without needing the reasoner to be on. However, in light of Amina's comment that this component will not be trivial to fix, we also agreed that it is not high priority at the moment because there are other ways to view full asserted parentage without the reasoner on. For the moment, documentation of existing behavior may have to suffice.
- scroll lock (aka lock view) for global OTE DONE
- TO DO: allow only one OTE to be locked at a time
- TO DO: keyboard shortcut for locking
Discussion: no further information beyond what is here.
- Midori to communicate audience response to Amina during the OBO-Edit demo.
Discussion: Correction: Midori will perform this function during Amina's OBO-Edit presentation. Chris will present a demo later in the day.
- Setup for webex and teleconfernce?
- Voice through webex was good during the OE demo last week.
Discussion: Amina asked about the possibility of testing Webex since she will be presenting remotely. Midori will check into availability of the room.
- Discussion of has_part relationship and follow-on consequences
- Mike Cherry is also interested in making sure that this is discussed so if anyone from this group is planning to put an item on the agenda about this, please coordinate with him. Possible discussion issues include:
- display of has_part in AmiGO and in OBO-Edit
- annotation mapping issues relating to using has_part instead of part_of relationships
- Examples where the has_part relationship is used:
- in component, relationships between spliceosomal snRNPs and spliceosomal complexes
- in process, relationships relating to mRNA surveillance
Discussion: Midori said that Jane's item has a general subject title, so may be hard to find if you are looking specifically for has_part. Her item is about "General discussion about graph visualization for AmiGO and OBO-Edit" and is under "Display issues" in this section of the agenda:
# 4.3.5 2:00 PM Ontology Structure/Logic/Engineering/etc. * 184.108.40.206 GO & internal cross-products * 220.127.116.11 Function-process links * 18.104.22.168 Display issues