ConferenceCall 2009 10 15

= 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. NatashaNoy & 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

 * Abstract
 * Our panel's prepared slides can be accessed by clicking on each of the title links below:
 * Slides: . [ 1-Schneider ] . [ 2-Noy / Dorf ] . [ 3-Baclawski ] . [ 4-Kendall ] . [ 5-Dean ]
 * [ Audio Recording of the session ] (mp3)
 * [ Transcript of the online chat session ] during the panel discussion
 * Resources

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 world clock for other time zones
 * Expected Call Duration: 2.0~2.5 hours
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Attendees

 * Attended:
 * ToddSchneider
 * ElisaKendall
 * KenBaclawski
 * PeterYim
 * TerryLongstreth
 * JoelBender
 * ThomasBrunner
 * Willa Pickering (Lockheed Martin)
 * JeffreySchiffel
 * NatashaNoy
 * MichaelDorf
 * HaroldSolbrig
 * MichaelGruninger
 * KurtConrad
 * SteveRay
 * CarlosRueda
 * Terry Patten (Charles River Analytics)
 * YavuzEren
 * BartGajderowicz (may be late)
 * LinePouchard
 * MikeDean
 * LeoObrst
 * NancyWiegand


 * Expecting:
 * JerrySmith
 * ... 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  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * EdDodds

Abstract

 * Title: OOR Sandbox and OOR Requirements - Comparative Analysis - by ToddSchneider - [ 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 NatashaNoy / 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 KenBaclawski - [ 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 - [ 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 - [ slides ]
 * Abstract: Ontology Summit 2008 yielded a vision and roadmap for OOR. We'll revisit these and compare them to the current instantiation.

Resources:

 * NCBO BioPortal project sites
 * OpenOntologyRepository - homepage for the OOR initiative - http://OpenOntologyRepository.org
 * our first sandbox instance of OOR - http://oor-01.cim3.net/ (currently still on the BioPortal v1.0 revision level)
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development
 * UML-EA diagrams on the recently released BioPortal (v1016 of Jul-2009) system
 * from the three recent Ontolog-OOR panel sessions:
 * ConferenceCall_2009_07_16
 * ConferenceCall_2009_07_30
 * ConferenceCall_2009_08_06
 * Join us at the [ oor-forum ] listserv. See message archive at - http://ontolog.cim3.net/forum/oor-forum/
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
 * developer issues should be discussed on the [ oor-dev ] listserv, whose archive is at - http://ontolog.cim3.net/forum/oor-dev/
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-dev ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

Agenda
1. Opening by session Chair (ToddSchneider)

2. Briefings from the Panel -- ToddSchneider, NatashaNoy / MichaelDorf, KenBaclawski, ElisaKendall & MikeDean

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.)

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

Please refer to details on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_10_15

JoelBender: w00t!

anonymous morphed into ElisaKendall

anonymous morphed into MichaelDorf

Terry Patten morphed into TerryPatten

anonymous morphed into MichaelGruninger

Tom B morphed into TomBrunner

Terry Longstreth morphed into TerryLongstreth

NatashaNoy: To Todd: you mentioned the work of TopQuadrant as the best example of being ontologically driven. Which work are you referring to?

PeterYim: @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: @Todd: slide#17 - why "thick client"?

MichaelGruninger: Todd: Can you elaborate what you meant by        modularization?

PeterYim: @Todd - slide#21 - good stuff!

HaroldSolbrig: WSDL and REST don't work that well together. What is the current state of the WADL spec?

CarlosRueda (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: @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?

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

KenBaclawski: @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 (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.

KenBaclawski: @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: @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: @Ken: What else does OOR contain besides ontologies that you would want to transform?

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

MichaelGruninger: @Todd: Can you give more detailed examples of rules and policies in OOR?

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

KenBaclawski: @Michael - There are many examples, such as rules, policies, and configurations.

PeterYim: @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: yes ... thanks (although I would still hope we focus first on        the thin client)

PeterYim: thank you, Todd, thanks everyone ... great session!

PeterYim: session adjourned 12:48 pm PDT


 * Further Question & Remarks - please post them to the [ oor-forum ] listserv
 * if you are already subscribed, post to 
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

Audio Recording of this Session

 * To download the recording of the session, click here
 * the playback of the audio files require the proper setup, and an MP3 compatible player on your computer.
 * Conference Date and Time:	15-Oct-2009 10:40am~12:39am PDT
 * Duration of Recording:	1 Hour 51 Minutes
 * Recording File Size:	       13 MB (in mp3 format)
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 * Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the archives of noteworthy past Ontolog events. (References on how to subscribe to our podcast can also be found there.)

For the record ...

How To Join (while the session is in progress)

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