OEWG 20110517

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OBO-Edit Working Group Meeting: Tuesday, May 17, 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

Fixed since last meeting

Can't restrict ancestor search by relation type in 2.1b12 (same bug)

    • If you have the reasoner on and select "ancestor" or "descendant" as the search aspect, it's supposed to add a list of relations and the label "can be reached via", but that stopped happening in 2.1-b11 or 12
    • Fixed in 2.1-b13
  • Search for children is missing some (unless reasoner on)
    • This was an old bug. Turned out that when links to children were being collected, the code erroneously took the PARENT of each link instead of the child. (But when the reasoner was on, there was a different loop, which is why the child search worked ok with the reasoner on.)
    • Fixed in 2.1-b13
  • Filtered save with "child" aspect throws exception
    • Fixed in 2.1-b13
  • As suggested by OEWG, all search aspects are once again available in search aspect menu. If user selects an aspect (Ancestor or Descendant) that requires reasoning and the reasoner isn't on, they get a pop-up error message: "If you want to search Ancestors or Descendants, you must first turn on the Reasoner (use the Reasoner Manager component to do that).File:Aspect-message.jpg
    • (The previous solution--leaving Ancestor and Descendant out of the aspect menu

when reasoner was off--confused users.)

  • Also, you can (once again) do filtered saves with Ancestor and Descendant even when the reasoner is off, because the filtered save method can start a reasoner.
    • Some users complained that these filtered saves that silently invoked the reasoner took so long they thought OE had crashed. Now the Progress window says "This filtered save requires the reasoner--please be patient." (Note that the progress string is limited in length--if you make it longer than that it gets cut off.)

Next bugs to work on

Discussion

  • A user was puzzled that older versions of OBO-Edit included Ancestor and Descendent in the Aspect menu but the latest OE didn't. We explained that OE can't get the right answers to Ancestor and Descendent searches unless the reasoner is on, so these searches are not included in the Aspect menu when the reasoner is off.
    • Nomi described the attempts she had made to make this more obvious (none of which succeeded in making it particularly obvious), and then suggested a new possible approach: leave Ancestor and Descendent in Aspect menu, but if user chooses one when Reasoner is off and tries to do a search, they get a popup error message explaining that they need to turn the reasoner on to do that search.
      • Attendees liked that solution.
    • Chris said that it should be possible to make OBO-Edit run a simple reasoner (such as the OnTheFly reasoner) to do ancestor searches (as long as they are over all ancestors, not limited by a specific relationship type) without turning on the full reasoner.
      • Nomi said that could be added as a feature request but it probably would not be quick to implement.
  • Filtered save silently invokes a reasoner if the user asks to save inferred links
    • This can be slow--it was suggested that OE should pop up some sort of warning so that the user doesn't think OE has frozen up.
    • Nomi thought maybe running the reasoner for is_a closure filtered save would help fix it.
      • Chris didn't think that would help. (?? Did I remember that correctly??)
        • I don't remember whether Chris said anything. I found when I was testing that it didn't make any difference if I ran the reasoner before saving or not; the is_a closure didn't work as expected (except sort of in beta4). I don't know whether the reasoner was running during the save, nor do I have any idea whether it would help if it did. -Midori
  • Search for children misses some (unless reasoner on)
    • Nomi needs a small test case this. Someone (Marcus??) said they'd make one.
Marcus is making cross products with PATO as intersection genus, GO as differentia (?), saving with complete is_a closure  [I didn't get this all down, can someone help fill it in?]
    • In cross-product intersection box, it shows ugly java.lang.Object@303e7b (the gibberish after '@' seems to be unique per OE launch) (minor edit -Midori)
    • Midori sees that too IF she doesn't load the other ontologies (with allow dangling refs). If she loads the other ontologies, they look ok. (minor edit -Midori)
      • Yes - Marcus and I are both making cross-products using terms from PATO, GO, ChEBI, etc. The terms with the cross-product definitions live in our phenotype ontologies (FYPO for me), and we can load just the phenotype ontology, all of the ontologies used in xp defs, or a subset of the total. Terms from ontologies I load look fine in the cross-product panel; anything from an ontology I don't load gets a java.lang.Object@wackiness. If I load GO and FYPO, for example, FYPO terms and GO terms look good, but PATO and ChEBI terms show up as java.lang.Objects. (added -Midori)
    • If you're making a cross-product ontology, you can't reasonably ask users to load all the other ontologies
    • Chris said the java.lang thing should be posted as a bug report
    • Feature request: way to save just the terms from the ontologies that are needed in the cross-product ontologies (save is_a closure is intended to do this but doesn't really work right)

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