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Joint Ontolog-OOR Panel Discussion Session - Thu 15-Oct-2009     (1)

Title: OOR Sandbox and OOR Requirements - Comparative Analysis     (1A)

Panelists:     (1B)

  • Chair: Dr. ToddSchneider (Raytheon) - "OOR-BioPortal Comparative Analysis" - [ slides ]     (1C)
  • Dr. Natasha Noy & Mr. MichaelDorf (NCBO-Stanford) - "BioPortal as (the only functional) OOR SandBox (so far)" - [ slides ]     (1D)
  • Professor KenBaclawski (Northeastern) - "OOR in the Classroom: An Experience Report" - [ slides ]     (1E)
  • Ms. ElisaKendall (Sandpiper Software) - "Requirements and Initial Steps Towards An OOR for Standards Management" - [ slides ]     (1F)
  • Mr. MikeDean (BBN) - "OOR: Vision vs. Current State" - [ slides ]     (1G)

Archives     (1H)

  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (1I5)
    • view-only password: "ontolog"     (1I5A)
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.     (1I5B)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides above and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (1I5C)
  • Discussions and Q & A:     (1I6)
    • (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"     (1I6A)
    • You can type in your questions or comments through the browser based chat session by:     (1I6B)
      • 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.     (1I6C1)
    • (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.)     (1I6D)
    • 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!     (1I6E)
  • 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.     (1I10)

Attendees     (1J)

  • Expecting:     (1J2)
    • ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...     (1J2B)

Abstract     (1K)

Title: OOR Sandbox and OOR Requirements - Comparative Analysis - by Todd Schneider - [ slides ]     (1K1)
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.     (1K2)
Here are the abstracts of the briefings from our other panelists who will be seeding our discussion:     (1K3)
  • "BioPortal as (the only functional) OOR SandBox (so far)" - by Natasha Noy / MichaelDorf - [ slides ]     (1K4)
    • 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.     (1K4A)
  • "OOR in the Classroom: An Experience Report" - by Ken Baclawski - [ slides ]     (1K5)
    • 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.     (1K5A)
  • "Requirements and Initial Steps Towards An OOR for Standards Management" - by Elisa Kendall - [ slides ]     (1K6)
    • Abstract: this talk will cover some of the background and plan at OMG towards setting up an OOR for their standards     (1K6A)
  • "OOR: Vision vs. Current State" - by Mike Dean - [ slides ]     (1K7)
    • Abstract: Ontology Summit 2008 yielded a vision and roadmap for OOR. We'll revisit these and compare them to the current instantiation.     (1K7A)

Resources     (1M)

1. Opening by session Chair (ToddSchneider)     (1M9A)

2. Briefings from the Panel -- Todd Schneider, Natasha Noy / MichaelDorf, Ken Baclawski, Elisa Kendall & Mike Dean     (1M9B)

3. Q & A and Open Discussion (All) -- please refer to process above     (1M9C)

4. Summary and wrap-up (ToddSchneider)     (1M9D)

Proceedings     (1N)

Please refer to the archives above     (1N1)

IM Chat Transcript captured during the session    (1N2)

(The chat transcript below has been lightly edited to help improve on clarity of the conversation.)     (1N2A)

Peter P. Yim: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 15-Oct-2009     (1N2B)

Title: OOR Sandbox and OOR Requirements - Comparative Analysis     (1N2C)

Panelists:     (1N2D)

  • Dr. Natasha Noy & Mr. MichaelDorf (NCBO-Stanford) - "BioPortal as (the only functional) OOR SandBox (so far)"     (1N2F)

Please refer to details on the session page at:     (1N2J)

anonymous morphed into Elisa Kendall     (1N2M)

anonymous morphed into MichaelDorf     (1N2N)

Terry Patten morphed into Terry Patten     (1N2O)

anonymous morphed into Michael Grüninger     (1N2P)

Tom B morphed into Tom Brunner     (1N2Q)

Terry Longstreth morphed into Terry Longstreth     (1N2R)

Natasha Noy: To Todd: you mentioned the work of TopQuadrant as the best     (1N2S)

example of being ontologically driven. Which work are you referring to?     (1N2T)

Peter P. Yim: @Todd: slide#14 ... I suggest we should weight the pros and     (1N2U)

cons of providing "editing/creation" support from OOR (as other     (1N2V)

dedicated editing platforms would probably do a better job)     (1N2W)

Peter P. Yim: @Todd: slide#17 - why "thick client"?     (1N2X)

Michael Grüninger: Todd: Can you elaborate what you meant by     (1N2Y)

modularization?     (1N2Z)

Peter P. Yim: @Todd - slide#21 - good stuff!     (1N2AA)

Harold Solbrig: WSDL and REST don't work that well together. What is the     (1N2AB)

current state of the WADL spec?     (1N2AC)

Carlos Rueda (MBARI): @Ken = slide 5: good point. An strategy we have     (1N2AD)

integrated into our deployment of BioPortal is to use the URIs of the     (1N2AE)

ontologies and their concepts as the main identifiers. In other words,     (1N2AF)

at least in our case, this has been motivated by our requirement to make     (1N2AG)

URIs first-class citizens in our ontology registry.     (1N2AH)

Michael Grüninger: @Ken: By transformations do you mean mappings between     (1N2AI)

an ontology that is represented in multiple languages (e.g. OWL-Time vs     (1N2AJ)

CL-Time) or is it between two ontologies that are logically equivalent?     (1N2AK)

Ken Baclawski: @Carlos - Great! Please send me the details.     (1N2AL)

Ken Baclawski: @Michael - I was mainly thinking of transformations     (1N2AM)

between representations in different languages. Not just ontologies BTW     (1N2AN)

since the OOR has more in it than just ontologies. Transformations     (1N2AO)

between ontologies that are logically equivalent is also interesting,     (1N2AP)

but I was not dealing with that since it is not as relevant for the OOR     (1N2AQ)

at least in the near to mid-term.     (1N2AR)

Carlos Rueda (MBARI): @Ken: unfortunately, this is in need of good     (1N2AS)

documentation :/ .. in the meantime, I'll be happy to talk about it if     (1N2AT)

you wish. A quick note, however: we haven't done any modifications to     (1N2AU)

the BioPortal back-end; rather this is handled by a new interface layer     (1N2AV)

we have developed.     (1N2AW)

Ken Baclawski: @Harold - The latest version of WSDL, version 2.0, can     (1N2AX)

specify RESTful services, so it isn't so clear that WADL is very useful     (1N2AY)

Harold Solbrig: @Ken - tried to use it briefly, but ran into problems.     (1N2AAA)

Will give it another look if you think that it really subsumes WADL     (1N2AAB)

functionality...     (1N2AAC)

Michael Grüninger: @Ken: What else does OOR contain besides ontologies     (1N2AAD)

that you would want to transform?     (1N2AAE)

Todd Schneider: To All: I'll have to get back on any questions asked of me.     (1N2AAF)

Michael Grüninger: @Todd: Can you give more detailed examples of rules     (1N2AAG)

and policies in OOR?     (1N2AAH)

Terry Longstreth: @Todd: ..can you expand on the issue of real time?     (1N2AAI)

Ken Baclawski: @Michael - There are many examples, such as rules,     (1N2AAJ)

policies, and configurations.     (1N2AAK)

Peter P. Yim: @Todd: I don't believe I can get my vice through ... but I     (1N2AAL)

had two questions (see above) ... one on doing editing in the context of     (1N2AAM)

OOR (rather than doing that elsewhere) and the other on your choice of     (1N2AAN)

thick client ... can you discuss that, please?     (1N2AAO)

Peter P. Yim: yes ... thanks (although I would still hope we focus first on     (1N2AAP)

the thin client)     (1N2AAQ)

Peter P. Yim: thank you, Todd, thanks everyone ... great session!     (1N2AAR)

Peter P. Yim: session adjourned 12:48 pm PDT     (1N2AAS)

  • Further Question & Remarks - please post them to the [ oor-forum ] listserv     (1N2AAT)
    • if you are already subscribed, post to <oor-forum [at] ontolog.cim3.net>     (1N2AAT1)
    • (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.     (1N2AAT2)

Audio Recording of this Session     (1O)


For the record ...     (1O6)

How To Join (while the session is in progress)     (1P)


This page has been migrated from the OntologWiki - Click here for original page     (1P4)