OEWG 20110503

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OBO-Edit Working Group Meeting: Tuesday, May 5, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes:
Attendees:

Bug and Feature Trackers

Discussion items

  • OBO-Edit 2.1-beta12 released on April 25--release notes are here
  • SourceForge trackers closed to anonymous posting due to spam.
  • A user was puzzled that her Typedefs were disappearing from her filtered save results. David O-S said that she needed to check off the 'always save properties' option in the filtered save interface. This fixed the user's problems. Nomi added more info about this to the userguide.

Fixed since last meeting

  • Cycle over mixed relationship types -> infinite loop
    • Can't save fly_anatomy_XP.obo because OE goes into an infinite loop while running verification checks.
    • Chris thought this was because fly_anatomy_XP has cycles over mixed relationship types, which is valid but was not considered valid when OBO-Edit was originally developed. This may be true, but in fact it turned out that the infinite loop was caused by a term that listed itself as an alternate ID. The validation process involves recursively checking the term's alternate ID, and since it's the same term, it just recurses over and over.
    • Two ways to fix the infinite loop (it now does both):
      • Before recursing on alt_id in the validation check, check whether it's the same as the primary ID.
      • When reading in ontology, check for alt_id == primary_id and refuse to add it.
  • adding words to dictionary removes uncommitted text edits
  • ID Profile Mismatch dialogue box and multiple ontologies
    • Loading multiple ontologies--PATO, GO, cell etc, Marcus gets message "ID profile mismatch--use profile loaded from the file"? Which ontology file is it referring to? It should say which.
    • Thanks to Midori for providing two tiny ontologies with ID profiles so I could test this.
    • This message now lists the two ID profiles, so at least it's somewhat clearer. However, it still seems a bit random which one it chooses as the new one if you have multiple ontologies loaded, and I have not yet added the new feature to let you select which of multiple ID profiles you want to use. (If there are only two, it does let you choose between the two.)
  • Bogus warning messages during validation: if you have a URL in a comment or definition, you get complaints about there not being spaces between "sentences" and lack of capital letters.
    • I have decreased the number of these (though not totally solved the problem)
  • Search aspect is missing the "can be reached via" selector
    • Fixed in 2.1-b13

Currently working on

  • Weird nondeterministic behavior in Ontology Tree Editor: for some ontologies (such as teleost_anatomy_VAO_edit.obo), Tree Editor sometimes displays some non-root terms as roots. Which terms are shown as roots varies each time you restart!

    • David O-S figured out how to prevent this weird nondeterministic behavior: "Strip our the OBO_REL: prefix from the relations that have it* and, as far as I can tell, the odd behavior goes away...My guess is that OBO-Edit has trouble parsing relationships and/or intersections with these relations."
    • That fixes the weird behavior, but I still don't know what causes it!
  • Is_a closure broken
    • Filtered save with "is_a closure" checked doesn't save all the terms it should.
  • A user was puzzled that older versions of OBO-Edit included Ancestor and Dependent in the Aspect menu but the latest OE didn't. We explained that OE can't get the right answers to Ancestor and Dependent searches unless the reasoner is on, so these searches are not included in the Aspect menu when the reasoner is off.
    • I agree that it's a bit unintuitive to have those search aspects simply disappear from the aspect menu without a trace. What I wanted to do was to leave them in the menu, but disable them (so they'd be grayed out). This turned out not to be possible with the current setup; I would have had to rewrite the whole pulldown menu class that the search aspect uses. I also would have liked to add a tooltip so that if you hovered your mouse over the aspect menu, it would explain that the missing aspects could be enabled by turning on the reasoner. Again, it turned out that the class that handles that menu can't add tooltips. It didn't seem worth spending a huge amount of time on this, so I did the best I could and added a tooltip to the word "in" next to the Aspect menu:

    • The need to turn on the reasoner to see Ancestor and Dependent search aspects is explained in the user guide page about "Advanced Searching" (see below)--if anyone has ideas about where else in the documentation I can explain it let me know.
User guide page about search aspects
  • David O-S said: "Oddly, filtered saves on earlier versions of OE 2 that use restrictions on ancestor/descendant work fine without a reasoner being turned on first. I believe that this is because a reasoner (most likely the rule-based-reasoner) is being run as part of the save process. From the few tests I've done, I believe the output of these filtered saves sans reasoner to be reliable. In fact, this is extremely useful to me - as, for the ontology I work with, trying to get a filtered save to work after running a reasoner is painfully slow and dangerously close to using up OE2s available memory."
    • The code that does filtered save invokes the reasoner (if the reasoner hasn't already been activated). If I allow the Ancestor aspect to be chosen in the filtered save interface, it does the right thing (for the test example).
    • I am investigating whether I can make search also invoke the reasoner for searches that need it (ancestor/dependent). Then we wouldn't have to remove those search aspects from the menu.
  • Search for children misses some (unless reasoner on)
    • If you turn on one of the reasoners, you find more children. But what do we really mean by "children"? (Do we include inferred children or just asserted?)
    • Maybe this can be fixed by the same fix that will (hopefully) allow ancestor/dependent searches to invoke the reasoner as needed--maybe child search also requires a reasoner?

Next bugs to work on

Discussion

Links

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