Difference between revisions of "OEWG 20090609"

From GO Wiki
Jump to: navigation, search
(Discussion items)
Line 18: Line 18:
  
 
==Discussion items==
 
==Discussion items==
 
*Feature request (carried over from last week): A system for saving appropriate subsets of terms from one ontology for reasoning in another:
 
**See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260.  Details of how this could work require some discussion.
 
  
 
* Reminder: help prioritize tracker items
 
* Reminder: help prioritize tracker items
Line 31: Line 28:
 
* A bug reported by Melissa was dicussed: gets wrong menu in tree editor popping up on a Windows machine. Amina: Java & Windows interaction. Does menu popup on it's own just by mousing over? Or something acts like a direct click when you are right-clicking. Does this effect all Java Apps?  Amina will explore this further.
 
* A bug reported by Melissa was dicussed: gets wrong menu in tree editor popping up on a Windows machine. Amina: Java & Windows interaction. Does menu popup on it's own just by mousing over? Or something acts like a direct click when you are right-clicking. Does this effect all Java Apps?  Amina will explore this further.
  
* Feature request: carry over from last week. David: the feature request to  
+
* Feature request (carried over from last week): A system for saving appropriate subsets of terms from one ontology for reasoning in another:
make tool that allows you to update to grab terms from other ontologies while working on another. For example, for each term you are using, want all paths to the root for that term in the other ontology? Or if using working on one ontology that has external XPs to other ontologies, be able to choose ID prefix of those ontologies (eg, GO or Chebi,etc. ) and find and bring back every term in those external ontologies that ares used in a relationship in an XP in your current ontology. (please edit this to make more sense hd)
+
** See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260. 
 +
** David: The general problem is, when an ontology developer uses foreign terms to define the terms in their ontology, they need some way to import sufficient terms and relationships from that foreign ontology for reasoning to work. Effectively this means: all the foreign terms used and all of their is_a ancestor terms.  The same mechanism used for initial import of these terms needs to be useful for updating terms and relationships when their ontologies change.
 +
 
 +
 
 +
*** One solution that should be relatively easy to achieve, is outlined in the ticket above. Briefly: A user would specify two ID prefixes - one for the master (host?) ontology (the one being worked on) and one for the foreign ontology from which terms are needed. This can be used to generate an is_a path to root filter using the IDs of every foreign term with the specified ID prefix used in a relationship or intersection with a term from the master ontology.  Users can then generate the cut of the foreign ontology they need by loading that ontology and using the filter they have generated in a filtered save.
 +
**** Potential issue - How stable is XML spec to specify filters. Should we worry?
  
* A more global question since XML is used for filters: How stable is XML spec to specify filters. Should we worry?
 
  
* New request: Use web services to fetch bits of ontologies that you need from respective sites. Research using web services in OE.
+
*** Alternative approach: Use web services to fetch bits of ontologies that you need from respective sites. OLS? BioPortal? - do either support SPARQL?
 +
**** This has the advantage of not relying on the ability to run a reasoner on the ontology (e.g.- CHEBI won't reason with OE2 reasoners).  It could also be the basis of a seamless method for updating, not requiring users to do multiple loading, saving, filtering and merging of OBO-files.
 +
**** Jen says she will investigate - in particular can talk to OLS developers about whether their web services are suitable.
  
 
==Action Items==
 
==Action Items==

Revision as of 14:48, 9 June 2009

OBO-Edit Working Group, Tuesday June 9th, 2009 9.30 a.m. PST

Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425


Agenda/Chair: Midori
Minutes: Harold
Attendees: Amina, Midori, Jen, Harold, David O, Karen, Melissa H

Action items carried over

  • OBO-Edit 2.1 release - Pending fixes
  • UTF8 support - post 2.1 release


Discussion items

  • Reminder: help prioritize tracker items
  • Discussion of Michael's gaz ontology (kind of an OBO version of a world atlas): appeared that tree editor only showing transitive relationships. This is a default setting but can be changing using appropriate filters. Graphviz always shows links from term all the way up to root; may need to examine DOT file preferences.
  • Amina: if see an message on OSX system "JavaAppLaunchError" in using OE2; could mean java updates required
  • Melissa - OE buggy on windows - unintended OTE right click menu starting to be a problem
  • A bug reported by Melissa was dicussed: gets wrong menu in tree editor popping up on a Windows machine. Amina: Java & Windows interaction. Does menu popup on it's own just by mousing over? Or something acts like a direct click when you are right-clicking. Does this effect all Java Apps? Amina will explore this further.
  • Feature request (carried over from last week): A system for saving appropriate subsets of terms from one ontology for reasoning in another:
    • See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260.
    • David: The general problem is, when an ontology developer uses foreign terms to define the terms in their ontology, they need some way to import sufficient terms and relationships from that foreign ontology for reasoning to work. Effectively this means: all the foreign terms used and all of their is_a ancestor terms. The same mechanism used for initial import of these terms needs to be useful for updating terms and relationships when their ontologies change.


      • One solution that should be relatively easy to achieve, is outlined in the ticket above. Briefly: A user would specify two ID prefixes - one for the master (host?) ontology (the one being worked on) and one for the foreign ontology from which terms are needed. This can be used to generate an is_a path to root filter using the IDs of every foreign term with the specified ID prefix used in a relationship or intersection with a term from the master ontology. Users can then generate the cut of the foreign ontology they need by loading that ontology and using the filter they have generated in a filtered save.
        • Potential issue - How stable is XML spec to specify filters. Should we worry?


      • Alternative approach: Use web services to fetch bits of ontologies that you need from respective sites. OLS? BioPortal? - do either support SPARQL?
        • This has the advantage of not relying on the ability to run a reasoner on the ontology (e.g.- CHEBI won't reason with OE2 reasoners). It could also be the basis of a seamless method for updating, not requiring users to do multiple loading, saving, filtering and merging of OBO-files.
        • Jen says she will investigate - in particular can talk to OLS developers about whether their web services are suitable.

Action Items

  • Request to research using web services in OE

Links

Back to OEWG Meeting agenda and minutes List