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(Created page with "=Charles Hoyt= Dr. Charles Tapley Hoyt is a Postdoctoral Research Fellow in the Laboratory of Systems Pharmacology at Harvard Medical School based out of Germany. He received his Ph.D. in Computational Life Sciences from the University of Bonn. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. He is an advocate of open source software, reproducibility, and open sci...")
 
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=Charles Hoyt=
= Joint [[Ontolog]]-[[OOR]] Panel Discussion Session - Thu 15-Oct-2009  =
Dr. Charles Tapley Hoyt is a Postdoctoral Research Fellow in the Laboratory of Systems Pharmacology at Harvard Medical School based out of Germany. He received his Ph.D. in Computational Life Sciences from the University of Bonn. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. He is an advocate of open source software, reproducibility, and open science.


His work in ontologies is focused on the standardization of prefixes, CURIEs, and URIs. He developed and maintains the Bioregistry (https://bioregistry.io) as a nexus of these efforts and a community resource. Further, he works with the Open Biological and Biomedical Ontology (OBO) Foundry in order to improve the FAIRness of high quality ontologies in the biomedical and health space.
Title: '''OOR Sandbox and OOR Requirements - Comparative Analysis'''


See also:
Panelists:  


* https://cthoyt.com
* Chair: '''Dr. ToddSchneider''' (Raytheon) - "[[OOR]]-BioPortal Comparative Analysis" - [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/Ontolog_OOR-BioPortal_ComparativeAnalysis--ToddSchneider_20091015.ppt slides] ]
* https://github.com/cthoyt
* '''Dr. Natasha Noy & Mr. MichaelDorf''' (NCBO-Stanford) - "BioPortal as (the only functional) OOR [[SandBox]] (so far)" - [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_Panel_BioPortal--NatashaNoy-MichaelDorf_20091015.ppt slides] ]
* '''Professor KenBaclawski''' (Northeastern) - "OOR in the Classroom: An Experience Report" - [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-in-the-Classroom--KenBaclawski_20091015.ppt slides] ]
* '''Ms. ElisaKendall''' (Sandpiper Software) - "Requirements and Initial Steps Towards An OOR for Standards Management" - [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-for-Standards--ElisaKendall_20091015.ppt slides] ]
* '''Mr. MikeDean''' (BBN) - "OOR: Vision vs. Current State" - [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_vision-vs-current-state--MikeDean_20091015.ppt slides] ]
 
=== Archives  ===
 
* '''[[ConferenceCall_2009_10_15|Abstract]]'''
* '''Our panel's prepared slides''' can be accessed by clicking on each of the [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/ title links] below:
** '''Slides: . [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/Ontolog_OOR-BioPortal_ComparativeAnalysis--ToddSchneider_20091015.ppt 1-Schneider] ] . [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_Panel_BioPortal--NatashaNoy-MichaelDorf_20091015.ppt 2-Noy / Dorf] ]  . [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-in-the-Classroom--KenBaclawski_20091015.ppt 3-Baclawski] ] . [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-for-Standards--ElisaKendall_20091015.ppt 4-Kendall] ] . [ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_vision-vs-current-state--MikeDean_20091015.ppt 5-Dean] ]'''
* '''[ [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-comparative-analysis_20091015.mp3 Audio Recording of the session] ]''' (mp3)
* '''[ [[ConferenceCall_2009_10_15|Transcript of the online chat session]] ]''' during the panel discussion
* '''[[ConferenceCall_2009_10_15|Resources]]'''
 
=== [[MeetingsCalls|Conference Call]] Details  ===
 
* Date: '''Thursday, October 15, 2009 '''
* Start Time: 10:30am PDT / 1:30pm EDT / 7:30pm CEST / 6:30pm BST / 17:30 UTC
** see [http://www.timeanddate.com/worldclock/fixedtime.html?month=10&day=15&year=2008&hour=10&min=30&sec=0&p1=224 world clock] for other time zones
* Expected Call Duration: 2.0~2.5 hours
* Dial-in Number:
** from a '''US telephone (US): +1-218-844-8060''' (domestic long distance cost will apply)
** When calling in from a phone, use '''Conference ID: "4389979#"'''
** '''from Europe, call:'''
*** Austria 0820-4000-1577
*** Belgium 070-35-9992
*** France 0826-100-280
*** Germany 01805-00-7642
*** Ireland 0818-270-037
*** Italy 848-390-179
*** Spain 0902-886-056
*** Switzerland 0848-560-327
*** UK 0844-581-9148
** callers '''from other countries''' please dial into either one of the US or European numbers
 
* '''Discussions and Q & A:'''
** (Unless the conference host has already muted everyone) '''Please mute your phone, by pressing "*2"''' on your phone keypad, when a presentation is in progress. '''To un-mute, press "*3"'''
** You can '''type in your questions or comments through the browser''' based  [[ConferenceCall_2005_09_01|chat session]] by:
*** pointing a separate browser tab (or window) to http://webconf.soaphub.org/conf/room and enter: Room="'''ontolog_20091015'''" and My Name="Your Own Name" (e.g. "JaneDoe")
** or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20091015
*** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
** (when everyone is muted) '''If you want to speak''' or have questions or remarks to make, '''please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). ''Test your voice and introduce yourself first before proceeding with your remarks, please.'' (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)
** thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ontolog_20091015@soaphub.org ... Handy for mobile devices!
 
* Please review our Virtual Session Tips and Ground Rules - see: [[VirtualSpeakerSessionTips]]
 
* This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: [[ConferenceCall_2009_10_15]]
 
* Please note that this session will be recorded, and the entire proceedings including the audio archives are expected to be made available as open content to our community membership and the public at-large under [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].
 
=== Attendees  ===
 
* Attended:
** [[ToddSchneider|Todd Schneider]]
** [[ElisaKendall|Elisa Kendall]]
** [[User:KennethBaclawski|Ken Baclawski]]
** [[PeterYim|Peter P. Yim]]
** [[TerryLongstreth|Terry Longstreth]]
** [[JoelBender|Joel Bender]]
** [[ThomasBrunner|Thomas Brunner]]
** Willa Pickering (Lockheed Martin)
** [[JeffreySchiffel|Jeffrey Schiffel]]
** Natasha Noy
** MichaelDorf
** [[HaroldSolbrig|Harold Solbrig]]
** [[MichaelGruninger|Michael Grüninger]]
** [[KurtConrad|Kurt Conrad]]
** [[SteveRay|Steve Ray]]
** [[CarlosRueda|Carlos Rueda]]
** Terry Patten (Charles River Analytics)
** [[YavuzEren|Yavuz Eren]]
** [[BartGajderowicz|Bart Gajderowicz]] (may be late)
** [[LinePouchard|Line Pouchard]]
** [[MikeDean|Mike Dean]]
** [[LeoObrst|Leo Obrst]]
** [[NancyWiegand|Nancy Wiegand]]
 
* Expecting:
** [[JerrySmith|Jerry Smith]]
 
* Regrets:
** [[EdDodds|Ed Dodds]]
 
=== Abstract  ===
 
:Title: '''OOR Sandbox and OOR Requirements - Comparative Analysis''' - by [[ToddSchneider|Todd Schneider]] - [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/Ontolog_OOR-BioPortal_ComparativeAnalysis--ToddSchneider_20091015.ppt slides]
 
: '''With the benefit of the NCBO [[BioPortal]] as a sandbox for OOR testing and experimentation, an analysis comparing the sandbox against the OOR requirements is needed. This comparison should provide a) future directions for [[BioPortal]], and b) facilitate the understanding of the OOR architecture and its development priorities.'''
 
: Here are the abstracts of the briefings from our other panelists who will be seeding our discussion:
 
* '''"BioPortal as (the only functional) OOR [[SandBox]] (so far)"''' - by Natasha Noy / MichaelDorf - [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_Panel_BioPortal--NatashaNoy-MichaelDorf_20091015.ppt slides]
** ''Abstract:'' [[BioPortal]] is a community-based repository of biomedical ontologies (http://bioportal.bioontology.org). [[BioPortal]] code currently forms the basis of the OOR sandbox. However, [[BioPortal]] has its own requirements and user community and therefore some of the [[BioPortal]] current status and outlook differs from the OOR Requirements. In this talk, we will focus on OOR requirements that are not yet addressed by [[BioPortal]] and will discuss our team's plans with respect to these requirements.
 
* '''"OOR in the Classroom: An Experience Report"''' - by [[User:KennethBaclawski|Ken Baclawski]] - [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-in-the-Classroom--KenBaclawski_20091015.ppt slides]
** ''Abstract:'' It is sometimes said that the best way to understand a subject is to try to teach it. Accordingly, I will report on what I learned about OOR from my current attempt to use it in a course. In particular, I learned that even after introducing students to the concepts underlying ontologies and the Semantic Web it was still unclear what OOR was storing and how it differed from a generic repository such as subversion. I will discuss some of the issues that were already raised in the course as well as issues that I anticipate will be encountered as the course proceeds.
 
* '''"Requirements and Initial Steps Towards An OOR for Standards Management"''' - by [[ElisaKendall|Elisa Kendall]] - [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR-for-Standards--ElisaKendall_20091015.ppt slides]
** ''Abstract:'' this talk will cover some of the background and plan at OMG towards setting up an OOR for their standards
 
* '''"OOR: Vision vs. Current State"''' - by [[MikeDean|Mike Dean]] - [https://ontologforum.s3.amazonaws.com/OOR-Ontolog-Panel/2009-10-15_OOR-BioPortal-Comparative-Analysis/OOR_vision-vs-current-state--MikeDean_20091015.ppt slides]
** ''Abstract:'' Ontology Summit 2008 yielded a vision and roadmap for OOR.  We'll revisit these and compare them to the current instantiation.
 
== Resources  ==
 
* '''[http://www.bioontology.org/ NCBO] [http://bioportal.bioontology.org/ BioPortal]''' project sites
* '''[[OpenOntologyRepository]]''' - homepage for the OOR initiative - http://OpenOntologyRepository.org
* [[NCBO]]-[[OOR]] development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development
* from the three recent Ontolog-OOR panel sessions:
** '''[[ConferenceCall_2009_07_16]]'''
** '''[[ConferenceCall_2009_07_30]]'''
** '''[[ConferenceCall_2009_08_06]]'''
 
=== Agenda  ===
 
1. Opening by session Chair (ToddSchneider)
 
2. Briefings from the Panel -- [[ToddSchneider|Todd Schneider]], Natasha Noy / MichaelDorf, [[User:KennethBaclawski|Ken Baclawski]], [[ElisaKendall|Elisa Kendall]] & [[MikeDean|Mike Dean]]
 
3. Q & A and Open Discussion (All) -- please refer to [[ConferenceCall_2009_10_15|process above]]
 
4. Summary and wrap-up (ToddSchneider)
 
== Proceedings  ==
 
Please refer to the [[ConferenceCall_2009_10_15|archives above]]
 
===IM Chat Transcript captured during the session===
 
''(The chat transcript below has been lightly edited to help improve on clarity of the conversation.)''
 
[[PeterYim|Peter P. Yim]]: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 15-Oct-2009
 
Title: OOR Sandbox and OOR Requirements - Comparative Analysis
 
Panelists:
 
* Chair: Dr. [[ToddSchneider|Todd Schneider]] (Raytheon) - "OOR-BioPortal Comparative Analysis"       
 
* Dr. Natasha Noy & Mr. MichaelDorf (NCBO-Stanford) - "BioPortal as (the only functional) OOR [[SandBox]] (so far)"       
 
* Professor [[User:KennethBaclawski|Ken Baclawski]] (Northeastern) - "OOR in the Classroom: An Experience Report"       
 
* Ms. [[ElisaKendall|Elisa Kendall]] (Sandpiper Software) - "Requirements and Initial Steps Towards An OOR for Standards Management"       
 
* Mr. [[MikeDean|Mike Dean]] (BBN) - "OOR: Vision vs. Current State"
 
Please refer to details on the session page at:       
 
[[ConferenceCall_2009_10_15]]
 
[[JoelBender|Joel Bender]]: w00t!
 
anonymous morphed into [[ElisaKendall|Elisa Kendall]]
 
anonymous morphed into MichaelDorf
 
Terry Patten morphed into [[TerryPatten|Terry Patten]]
 
anonymous morphed into [[MichaelGruninger|Michael Grüninger]]
 
Tom B morphed into [[TomBrunner|Tom Brunner]]
 
Terry Longstreth morphed into [[TerryLongstreth|Terry Longstreth]]
 
Natasha Noy: To Todd: you mentioned the work of [[TopQuadrant]] as the best       
 
example of being ontologically driven. Which work are you referring to?
 
[[PeterYim|Peter P. Yim]]: @Todd: slide#14 ... I suggest we should weight the pros and       
 
cons of providing "editing/creation" support from OOR (as other       
 
dedicated editing platforms would probably do a better job)
 
[[PeterYim|Peter P. Yim]]: @Todd: slide#17 - why "thick client"?
 
[[MichaelGruninger|Michael Grüninger]]: Todd: Can you elaborate what you meant by       
 
modularization?
 
[[PeterYim|Peter P. Yim]]: @Todd - slide#21 - good stuff!
 
[[HaroldSolbrig|Harold Solbrig]]: WSDL and REST don't work that well together. What is the       
 
current state of the WADL spec?
 
[[CarlosRueda|Carlos Rueda]] (MBARI): @Ken = slide 5: good point. An strategy we have       
 
integrated into our deployment of [[BioPortal]] is to use the URIs of the       
 
ontologies and their concepts as the main identifiers. In other words,       
 
at least in our case, this has been motivated by our requirement to make       
 
URIs first-class citizens in our ontology registry.
 
[[MichaelGruninger|Michael Grüninger]]: @Ken: By transformations do you mean mappings between       
 
an ontology that is represented in multiple languages (e.g. OWL-Time vs       
 
CL-Time) or is it between two ontologies that are logically equivalent?
 
[[User:KennethBaclawski|Ken Baclawski]]: @Carlos - Great! Please send me the details.
 
[[User:KennethBaclawski|Ken Baclawski]]: @Michael - I was mainly thinking of transformations       
 
between representations in different languages. Not just ontologies BTW       
 
since the OOR has more in it than just ontologies. Transformations       
 
between ontologies that are logically equivalent is also interesting,       
 
but I was not dealing with that since it is not as relevant for the OOR       
 
at least in the near to mid-term.
 
[[CarlosRueda|Carlos Rueda]] (MBARI): @Ken: unfortunately, this is in need of good       
 
documentation :/ .. in the meantime, I'll be happy to talk about it if       
 
you wish. A quick note, however: we haven't done any modifications to       
 
the [[BioPortal]] back-end; rather this is handled by a new interface layer       
 
we have developed.
 
[[User:KennethBaclawski|Ken Baclawski]]: @Harold - The latest version of WSDL, version 2.0, can       
 
specify RESTful services, so it isn't so clear that WADL is very useful       
 
anymore.
 
[[HaroldSolbrig|Harold Solbrig]]: @Ken - tried to use it briefly, but ran into problems.       
 
Will give it another look if you think that it really subsumes WADL       
 
functionality...
 
[[MichaelGruninger|Michael Grüninger]]: @Ken: What else does OOR contain besides ontologies       
 
that you would want to transform?
 
[[ToddSchneider|Todd Schneider]]: To All: I'll have to get back on any questions asked of me.
 
[[MichaelGruninger|Michael Grüninger]]: @Todd: Can you give more detailed examples of rules       
 
and policies in OOR?
 
[[TerryLongstreth|Terry Longstreth]]: @Todd: ..can you expand on the issue of real time?
 
[[User:KennethBaclawski|Ken Baclawski]]: @Michael - There are many examples, such as rules,       
 
policies, and configurations.
 
[[PeterYim|Peter P. Yim]]: @Todd: I don't believe I can get my vice through ... but I       
 
had two questions (see above) ... one on doing editing in the context of       
 
OOR (rather than doing that elsewhere) and the other on your choice of       
 
thick client ... can you discuss that, please?
 
[[PeterYim|Peter P. Yim]]: yes ... thanks (although I would still hope we focus first on       
 
the thin client)
 
[[PeterYim|Peter P. Yim]]: thank you, Todd, thanks everyone ... great session!
 
[[PeterYim|Peter P. Yim]]: session adjourned 12:48 pm PDT
 
[[Category:Event_Meeting]]

Latest revision as of 21:46, 25 February 2023

Joint Ontolog-OOR Panel Discussion Session - Thu 15-Oct-2009

Title: OOR Sandbox and OOR Requirements - Comparative Analysis

Panelists:

  • Chair: Dr. ToddSchneider (Raytheon) - "OOR-BioPortal Comparative Analysis" - [ slides ]
  • Dr. Natasha Noy & Mr. MichaelDorf (NCBO-Stanford) - "BioPortal as (the only functional) OOR SandBox (so far)" - [ slides ]
  • Professor KenBaclawski (Northeastern) - "OOR in the Classroom: An Experience Report" - [ slides ]
  • Ms. ElisaKendall (Sandpiper Software) - "Requirements and Initial Steps Towards An OOR for Standards Management" - [ slides ]
  • Mr. MikeDean (BBN) - "OOR: Vision vs. Current State" - [ slides ]

Archives

Conference Call Details

  • Date: Thursday, October 15, 2009
  • Start Time: 10:30am PDT / 1:30pm EDT / 7:30pm CEST / 6:30pm BST / 17:30 UTC
  • Expected Call Duration: 2.0~2.5 hours
  • Dial-in Number:
    • from a US telephone (US): +1-218-844-8060 (domestic long distance cost will apply)
    • When calling in from a phone, use Conference ID: "4389979#"
    • from Europe, call:
      • Austria 0820-4000-1577
      • Belgium 070-35-9992
      • France 0826-100-280
      • Germany 01805-00-7642
      • Ireland 0818-270-037
      • Italy 848-390-179
      • Spain 0902-886-056
      • Switzerland 0848-560-327
      • UK 0844-581-9148
    • callers from other countries please dial into either one of the US or European numbers
  • Discussions and Q & A:
    • (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when a presentation is in progress. To un-mute, press "*3"
    • You can type in your questions or comments through the browser based chat session by:
    • or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20091015
      • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
    • (when everyone is muted) If you want to speak or have questions or remarks to make, please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)
    • thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ontolog_20091015@soaphub.org ... Handy for mobile devices!
  • This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: ConferenceCall_2009_10_15
  • Please note that this session will be recorded, and the entire proceedings including the audio archives are expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

Abstract

Title: OOR Sandbox and OOR Requirements - Comparative Analysis - by Todd Schneider - slides
With the benefit of the NCBO BioPortal as a sandbox for OOR testing and experimentation, an analysis comparing the sandbox against the OOR requirements is needed. This comparison should provide a) future directions for BioPortal, and b) facilitate the understanding of the OOR architecture and its development priorities.
Here are the abstracts of the briefings from our other panelists who will be seeding our discussion:
  • "BioPortal as (the only functional) OOR SandBox (so far)" - by Natasha Noy / MichaelDorf - slides
    • Abstract: BioPortal is a community-based repository of biomedical ontologies (http://bioportal.bioontology.org). BioPortal code currently forms the basis of the OOR sandbox. However, BioPortal has its own requirements and user community and therefore some of the BioPortal current status and outlook differs from the OOR Requirements. In this talk, we will focus on OOR requirements that are not yet addressed by BioPortal and will discuss our team's plans with respect to these requirements.
  • "OOR in the Classroom: An Experience Report" - by Ken Baclawski - slides
    • Abstract: It is sometimes said that the best way to understand a subject is to try to teach it. Accordingly, I will report on what I learned about OOR from my current attempt to use it in a course. In particular, I learned that even after introducing students to the concepts underlying ontologies and the Semantic Web it was still unclear what OOR was storing and how it differed from a generic repository such as subversion. I will discuss some of the issues that were already raised in the course as well as issues that I anticipate will be encountered as the course proceeds.
  • "Requirements and Initial Steps Towards An OOR for Standards Management" - by Elisa Kendall - slides
    • Abstract: this talk will cover some of the background and plan at OMG towards setting up an OOR for their standards
  • "OOR: Vision vs. Current State" - by Mike Dean - slides
    • Abstract: Ontology Summit 2008 yielded a vision and roadmap for OOR. We'll revisit these and compare them to the current instantiation.

Resources

Agenda

1. Opening by session Chair (ToddSchneider)

2. Briefings from the Panel -- Todd Schneider, Natasha Noy / MichaelDorf, Ken Baclawski, Elisa Kendall & Mike Dean

3. Q & A and Open Discussion (All) -- please refer to process above

4. Summary and wrap-up (ToddSchneider)

Proceedings

Please refer to the archives above

IM Chat Transcript captured during the session

(The chat transcript below has been lightly edited to help improve on clarity of the conversation.)

Peter P. Yim: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 15-Oct-2009

Title: OOR Sandbox and OOR Requirements - Comparative Analysis

Panelists:

  • Chair: Dr. Todd Schneider (Raytheon) - "OOR-BioPortal Comparative Analysis"
  • Dr. Natasha Noy & Mr. MichaelDorf (NCBO-Stanford) - "BioPortal as (the only functional) OOR SandBox (so far)"
  • Professor Ken Baclawski (Northeastern) - "OOR in the Classroom: An Experience Report"
  • Ms. Elisa Kendall (Sandpiper Software) - "Requirements and Initial Steps Towards An OOR for Standards Management"
  • Mr. Mike Dean (BBN) - "OOR: Vision vs. Current State"

Please refer to details on the session page at:

ConferenceCall_2009_10_15

Joel Bender: w00t!

anonymous morphed into Elisa Kendall

anonymous morphed into MichaelDorf

Terry Patten morphed into Terry Patten

anonymous morphed into Michael Grüninger

Tom B morphed into Tom Brunner

Terry Longstreth morphed into Terry Longstreth

Natasha Noy: To Todd: you mentioned the work of TopQuadrant as the best

example of being ontologically driven. Which work are you referring to?

Peter P. Yim: @Todd: slide#14 ... I suggest we should weight the pros and

cons of providing "editing/creation" support from OOR (as other

dedicated editing platforms would probably do a better job)

Peter P. Yim: @Todd: slide#17 - why "thick client"?

Michael Grüninger: Todd: Can you elaborate what you meant by

modularization?

Peter P. Yim: @Todd - slide#21 - good stuff!

Harold Solbrig: WSDL and REST don't work that well together. What is the

current state of the WADL spec?

Carlos Rueda (MBARI): @Ken = slide 5: good point. An strategy we have

integrated into our deployment of BioPortal is to use the URIs of the

ontologies and their concepts as the main identifiers. In other words,

at least in our case, this has been motivated by our requirement to make

URIs first-class citizens in our ontology registry.

Michael Grüninger: @Ken: By transformations do you mean mappings between

an ontology that is represented in multiple languages (e.g. OWL-Time vs

CL-Time) or is it between two ontologies that are logically equivalent?

Ken Baclawski: @Carlos - Great! Please send me the details.

Ken Baclawski: @Michael - I was mainly thinking of transformations

between representations in different languages. Not just ontologies BTW

since the OOR has more in it than just ontologies. Transformations

between ontologies that are logically equivalent is also interesting,

but I was not dealing with that since it is not as relevant for the OOR

at least in the near to mid-term.

Carlos Rueda (MBARI): @Ken: unfortunately, this is in need of good

documentation :/ .. in the meantime, I'll be happy to talk about it if

you wish. A quick note, however: we haven't done any modifications to

the BioPortal back-end; rather this is handled by a new interface layer

we have developed.

Ken Baclawski: @Harold - The latest version of WSDL, version 2.0, can

specify RESTful services, so it isn't so clear that WADL is very useful

anymore.

Harold Solbrig: @Ken - tried to use it briefly, but ran into problems.

Will give it another look if you think that it really subsumes WADL

functionality...

Michael Grüninger: @Ken: What else does OOR contain besides ontologies

that you would want to transform?

Todd Schneider: To All: I'll have to get back on any questions asked of me.

Michael Grüninger: @Todd: Can you give more detailed examples of rules

and policies in OOR?

Terry Longstreth: @Todd: ..can you expand on the issue of real time?

Ken Baclawski: @Michael - There are many examples, such as rules,

policies, and configurations.

Peter P. Yim: @Todd: I don't believe I can get my vice through ... but I

had two questions (see above) ... one on doing editing in the context of

OOR (rather than doing that elsewhere) and the other on your choice of

thick client ... can you discuss that, please?

Peter P. Yim: yes ... thanks (although I would still hope we focus first on

the thin client)

Peter P. Yim: thank you, Todd, thanks everyone ... great session!

Peter P. Yim: session adjourned 12:48 pm PDT

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