OEWG 20100928

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OBO-Edit Working Group, Tuesday September 28th, 2010 8.30 a.m. PDT

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

Agenda/Chair: Amina
Minutes: Amina
Attendees: Midori, Amina, Chris, Ramona, Lol, Marcus, Judy, Harold, Alex, Terry

Action items carried over

Bug and Feature Tracker Updates

Discussion items

  • deleting relations in the parent editor in version 2.1.6
    • Harold demo'd the bug in v2.1beta4.
    • Amina tried the filter and saved successfully in beta7 and will investigate the problem in beta4.
    • Amina to get back on the impact of "indicate if selected term matches filter - lightbulb" on save.
    • Midori and Amina discuss the working of the "lightbulb" and state it should be unrelated to save.

(Request from Ramona and Lol at PO) We want to have a consider term from another ontology for and obsolete term. We opened both ontologies, put in the relation, then did a filtered save, saving only the terms in the namespace of the ontology we are interested it. If you look at the flat file, the consider terms are in there, but only with the ID number from the other ontology, no other information, and the file won't open in OE 2.1.6 (it would open in 2.1.4). Is there another way to do this? For the time being, we just put the consider relations in the comment of the obsolete terms. Amina: Allow dangling references option should be enabled while loading ontologies that link to terms from other ontologies.

-Solution is to be sure to check allow dangling references during open. No way to have entire obo stanza imported (only ID) from external ontology. Best solution for now is probably to keep in comment. Also be sure that it is really appropriate to have replaced by term (since terms should have somewhat different meanings).

Terry: Should we meriot in terms from PO Chris: are the interim releases going to be public? Best solution is to add the reference terms in the comments.
Chris to work with Terry on referencing strategy for cell ontology.

Chris: In the long term OBO-Edit should not report errors for dangling terms
Amina: Yeah the file could be loaded and dangling references could be possibly reported by the verification manager.

Alex: *Beta 6 saving glitch Chris: need for standard relations that can be merioted in. Short term solution is for obo-edit to save referenced relations by default merioting will become more persistent over sessions.

Terry: Demonstrated the use of filters and his use case while doing a "is a closure".

Action Items

  • Amina:
    • Follow-up on Harold's bug in 2.1b4:
    • Update OEWG meeting calendar
    • Send out email about 8:30 am meeting time and switching back to weekly meetings until the 2.1 official release.
    • Get inputs from Lol and Ramona on discrepancies in documentation.
    • Amina to get back on the impact of "indicate if selected term matches filter" while saving.


Back to OEWG Meeting agenda and minutes List