ConferenceCall 2009 02 19

= Joint Ontolog-OOR Panel Discussion - Thu 19-February-2009 =


 * Subject: Getting OOR Development Off the Ground (Take-2): the work begins ...


 * Session Chair: Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review" - [ slides ]


 * Panelists / Briefings:
 * Professor MarkMusen (NCBO, Stanford-BMIR) - "BioPortal-OOR" - [ slides ]
 * Dr. NatashaNoy (Stanford-BMIR, NCBO) - "Representing Metadata in NCBO BioPortal" - [ slides ]
 * Mr. MikeDean (BBN) - "Aligning the OOR Software Architecture for Collaboration" - [ slides ]
 * Dr. PaulBuitelaar / Mr. AndreasHarth (DERI, Galway) - "From OntoSelect towards OntoSelect-SWSE " - [ slides ]
 * Dr. Mathieu d'Aquin (Open University, UK) - "NeOn support for sharing and reusing ontologies (and related things)" - [ slides ]
 * Professor KenBaclawski (Northeastern University) - "Multilingual (and Other) Considerations in our OOR Implementation" - [ slides ]
 * Professor MichaelGruninger (University of Toronto) - "COLORE: Common Logic Ontology Repository" - [ slides ]


 * Archive:
 * slides: . [ 0-Schneider ] . [ 1-Musen ] . [ 2-Noy ] . [ 3-Dean ] . [ 4-Buitelaar / Harth ] . [ 5-d'Aquin ] . [ 6-Baclawski ] . [ 7-Gruninger ]
 * audio recording of the session (mp3)
 * the online chat session transcript captured during the panel discussion

Conference Call Details

 * Date: Thursday, Feb. 19, 2009
 * Start Time: 10:30am PST / 1:30pm EST / 7:30pm CET / 18:30 UTC
 * see world clock for other time zones
 * Expected Call Duration: 2.0 ~ 2.5 hours
 * Dial-in Number:
 * from a US telephone (US): +1-218-486-3600 (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 0848-390-179
 * Spain 0902-886-056
 * Switzerland 0848-560-327 or 0848-414-110
 * UK 0870-738-0765
 * callers from other countries please dial into either one of the US or European numbers


 * Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
 * view-only password: "ontolog"
 * 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.
 * 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.


 * Q&A and Discussion:
 * we will hold off Q&A and discussion until all presenters have finished their briefings.
 * (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:
 * pointing a separate browser tab (or window) to http://webconf.soaphub.org/conf/room and enter: Room="ontolog_20090219" and My Name="Your Own Name" (e.g. "JaneDoe")
 * or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20090219
 * 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_20090219@soaphub.org ... Handy for mobile devices!


 * For those who cannot join us, or who have further questions or remarks on the topic, please post them to the [oor-forum] listserv so that everyone in the community can benefit from the discourse.


 * Please review our Virtual Session Tips and Ground Rules - see: VirtualSpeakerSessionTips


 * RSVP to [mailto:peter.yim@cim3.com peter.yim@cim3.com] appreciated.


 * This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19


 * Please note that this session will be recorded, and the audio archive is expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

 * Attended:
 * MathieuDaquin
 * PaulBuitelaar
 * AndreasHarth
 * ToddSchneider (chair)
 * NatashaNoy
 * BenjaminDai
 * TrishWhetzel
 * MichaelGruninger
 * KenBaclawski
 * MarkMusen
 * MikeDean
 * PeterYim
 * RobertHoehndorf
 * MathieuDaquin
 * PaulBuitelaar
 * AndreasHarth
 * LuisBermudez
 * CarlosRueda
 * PeterEirich
 * SusanTurnbull
 * DougHolmes
 * LinZhang
 * RaviSharma
 * PaulAlexander
 * SteveRay
 * RexBrooks
 * LeoObrst
 * Stuart Turner
 * GaryBergCross
 * BruceBray


 * Expecting:
 * KatherineGoodier
 * CameronRoss
 * Timothy Williams (CAP SNOMED Terminology Solutions)
 * BobbinTeegarden
 * Rich Cooper (The English Logic Kernel)
 * AlexGarcia
 * Carl Singer
 * (please add yourself to the list if you are already an OOR team member, or rsvp to )
 * (please add yourself to the list if you are already an OOR team member, or rsvp to )


 * Regrets:

Agenda Ideas

 * Review of existing work; requirements analysis; Draft prioritization
 * announce a first public "sandbox" instance of OOR
 * coordinate integration of existing efforts
 * develop a short/medium term action plan
 * use of TRAC to connect to subversion repository and wiki

Agenda & Proceedings:

 * Session Format: this is a virtual session conducted over an augmented conference call.


 * Agenda:
 * 1. Opening by the Session chair - ToddSchneider
 * 2. we'll go around with a self-introduction of participants (15~20 minutes) - All - we'll skip this if we have more than 25 participants (in which case, it will be best if members try to update their namesake pages on this wiki prior to the call so that everyone can get to know who's who more easily.)
 * 3. Briefings from the Panelists - MarkMusen, NatashaNoy, MikeDean, MathieuDaquin, PaulBuitelaar / AndreasHarth, KenBaclawski, MichaelGruninger (10 min. for each briefing)
 * 4. [ Q & A and Open discussion] by all participants (~30 minutes) - All, via the conference call and the IM chat session.
 * 5. Reducing the discussion to actionable items and commitments - All (15 min.)
 * 6. Summary / Follow-up plans & actions / Conclusion - session chair


 * To join the team and participate in the OOR effort or to further explore the subject matter, please subscribe to our open archived discussion forum - [oor-forum] - see details at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YX
 * To join the development team and contribute software and technology, please subscribe to our open archived discussion list - [oor-dev] and sign up at the OOR project site at SemWebCentral - see details under: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YX

Briefing Abstracts

 * Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review"
 * Abstract: ... we will take a look at where things stand with the OOR Initiative (founded 23-Jan-2008), a year after it has coming into being.


 * Professor MarkMusen (NCBO, Stanford-BMIR) - "BioPortal-OOR"
 * Abstract: ... this is an update on the latest development in the NCBO BioPortal, and the collaboration that is being forged between the BioPortal developers and the OOR developers. The now publicly available first instance of the OOR, powered by the NCBO BioPortal technology will serve to help jumpstart OOR's software development work. Take a look at this first "sandbox" instance of OOR at: http://oor-01.cim3.net


 * Dr. NatashaNoy (Stanford-BMIR, NCBO) - "Representing Metadata in NCBO BioPortal"
 * Abstract:


 * The National Center for Biomedical Ontology (NCBO) is developing BioPortal, a Web-based repository for biomedical ontologies. BioPortal supports not only the technical requirements for access to biomedical ontologies either via Web browsers or via Web services, but also community-based participation in the evaluation and evolution of ontology content. While the installation of BioPortal at the NCBO contains only biomedical ontologies, the BioPortal implementation itself is domain-independent. We have deployed the BioPortal code as the first public OOR instance.
 * Metadata plays critical role in BioPortal. In this presentation, we will discuss the different types of BioPortal metadata, including pertinent ontology information, notes, reviews, and other user-provided content, mappings between ontology terms and metadata on mappings. We will give a brief overview of the ontology-based representation of metadata and discuss the relation between the BioPortal Metadata ontology and other metadata vocabularies, such as OMV.


 * Mr. MikeDean (BBN) - "Aligning the OOR Software Architecture for Collaboration"
 * Abstract: ... an overview of how we can go forward from here, in terms of open software development for OOR.

earlier OOR panel]]. Current development of OntoSelect however changed from DFKI to DERI at the National University of Ireland, Galway. At DERI we are working towards the integration of OntoSelect in the SWSE (Semantic Web Search Engine) platform. SWSE allows for efficient crawling, indexing and retrieval of semantic web data. OntoSelect-SWSE is currently implemented as a special SWSE instance that will be extended to offer the same search and browse functionality as OntoSelect, but with a more extensive dataset, a richer set of metadata associated with ontologies and ranking based (also) on ontology use.
 * Dr. PaulBuitelaar / Mr. AndreasHarth (DERI, Galway) - "From OntoSelect towards OntoSelect-SWSE"
 * Abstract: ... We briefly recap the functionality of OntoSelect as [[ConferenceCall_2008_12_04|presented at an


 * Dr. Mathieu d'Aquin (Open University, UK) - "NeOn support for sharing and reusing ontologies (and related things)"
 * Abstract:


 * NeOn is developing a reference architecture for semantic applications, based

on a number of infrastructure components, designed to facilitate the collaborative development of ontologies, as well as their reuse, exploitation and combination in various systems and applications. As such, most of these components are relevant to the tasks of sharing and reusing ontologies, which are essential activities realized by an ontology repository.
 * In this presentation, I will describe some of these components (e.g. Wayson,

Oyster2, the Alignment server, etc.) and how they can contribute to the implementation of an ontology repository. An important aspect to be considered is the way such components are combined to provide, on the one hand, a better user experience and, on the other hand, efficient support for applications developers. I will describe ongoing work realized in this direction, to finally emphasize the importance in this context of a proper community building effort, besides the necessary development effort.


 * Professor KenBaclawski (Northeastern University) - "Multilingual (and Other) Considerations in our OOR Implementation"
 * Abstract: This briefing introduces some of the localization considerations that are being addressed by two medical projects related to the OOR. The first is concerned with repositories of biological materials (biobanks), and the second is concerned with biodiversity and disease.


 * Professor MichaelGruninger (University of Toronto) - "COLORE: Common Logic Ontology Repository"
 * Abstract: This talk will outline a project to construct a repository of first-order ontologies (specified using Common Logic) that will serve as a testbed for ontology evaluation and integration techniques, and that can support the design, evaluation, and application of ontologies in first-order logic. The near-term objective is to incorporate these ontologies into the OOR architecture.

Questions, Answers & Discourse:

 * see process above

Q & A and Discussion captured from the chat session:
Unedited chat transcript: 

PeterYim: Welcome to the Joint Ontolog-OOR Panel Discussion - Thu 19-February-2009


 * Subject: Getting OOR Development Off the Ground (Take-2): the work begins ...


 * Session Chair: Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review"


 * Panelists / Briefings:

o Professor MarkMusen (NCBO, Stanford-BMIR) - "BioPortal-OOR" o Dr. NatashaNoy (Stanford-BMIR, NCBO) - "Representing Metadata in NCBO BioPortal" o Mr. MikeDean (BBN) - "Aligning the OOR Software Architecture for Collaboration" o Dr. PaulBuitelaar / Mr. AndreasHarth (DERI, Galway) - "From OntoSelect towards OntoSelect-SWSE" o Dr. Mathieu d'Aquin (Open University, UK) - "NeOn support for sharing and reusing ontologies (and related things)" o Professor KenBaclawski (Northeastern University) - "Multilingual (and Other) Considerations in our OOR Implementation" o Professor MichaelGruninger (University of Toronto) - "COLORE: Common Logic Ontology Repository"

anonymous morphed into Todd Schneider

anonymous1 morphed into Natasha Noy

PeterYim: see details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19

Forest morphed into Forest(Zhang, Lin)

anonymous1 morphed into Mark Musen

anonymous1 morphed into Luis Bermudez

anonymous morphed into Benjamin Dai

anonymous morphed into Trish Whetzel

anonymous morphed into Paul Alexander

anonymous morphed into CarlosRueda

RaviSharma: Todd Are we insisting that Instances be not stored in repository or are we saying these are not generally stored and lead to them through metadata or semantic discoveries?

RaviSharma: Todd - the metadata should be semantically meaningful as contrasted with simple taxonomy or heirarchical metadata or justt dataset description attributes as metadata. At least these should be tagged and have meaning of Metadata terms and vocabularies?

MathieuDaquin: to Todd: why looking only at metadata and not to the content of ontologies for search/discovery?

RaviSharma: Todd - further we could have in addition to what you suggest an associated OWL or such file that will tie together the use of metadata for a given instance of Ontology whether in the OOR or in a separate URL?

anonymous morphed into SteveRay

DougHolmes: @Todd: what is the rationale for no including instances? That constraint seems to exculde, for example, DBPedia, WordNet and similar reference ontologies.

RaviSharma: Mark How well have different ontologies started to interoperate, both in terms of transfer ofr artefacts as well as semantically (overlap of concepts)?

RaviSharma: Mark

RaviSharma: you did address some of these in last slides.

RaviSharma: MikeDean and BenjaminDai - Mike remeber my inputs for documentation offered, should I now contribute them on the NCBO Wiki?http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development

PeterYim: Our first "sandbox" instance of OOR powered by the NCBO BioPortal is now available at: http://oor-01.cim3.net


 * For those who have further questions or remarks on the topic, please post them to the [oor-forum] listserv so that everyone on the team can be kept in sync. (One needs to be subscribed to this archived mailing list first before posting. See subscription details here.)

Audio Recording of this Session

 * To download the audio 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:	19-Feb-2009 10:38am~1:00pm PST
 * Duration of Recording:	2 Hour 18 Minutes
 * Recording File Size:	       15.8 MB (in mp3 format)


 * suggestions:
 * its best that you listen to the session while having the respective presentations opened in front of you. You'll be prompted to advance slides by the speaker.
 * 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.)

Resources

 * ref. our discussion during the OOR team meeting on 2009.02.06 - http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2009_02_06#nid1T0X
 * "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" Panel session (2008.08.22) proceedings - see: ConferenceCall_2008_08_22
 * [oor-forum] OOR-team discussion (mailing list) archives - http://ontolog.cim3.net/forum/oor-forum/
 * [oor-dev] development discussion (mailing list) archives - http://ontolog.cim3.net/forum/oor-dev/
 * OntologySummit2008 homepage and the OntologySummit2008_Communique
 * OOR Charter - To promote the global use and sharing of ontologies by: 1. establishing a hosted registry-repository; 2. enabling and facilitating open, federated, collaborative ontology repositories; 3. establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.
 * OOR (Software Development) Project site at SemWebCentral - http://oor.projects.semwebcentral.org
 * OpenOntologyRepository homepage - http://OpenOntologyRepository.org
 * The OOR team's key content pages: (contribution from team members solicted)
 * OpenOntologyRepository_Scope
 * OpenOntologyRepository_Organization
 * OpenOntologyRepository_Process
 * OpenOntologyRepository_Policy
 * OpenOntologyRepository_IPR
 * OpenOntologyRepository_Requirement
 * OpenOntologyRepository_UseCases
 * OpenOntologyRepository_Architecture
 * OpenOntologyRepository_Approach
 * OpenOntologyRepository_Roadmap
 * OpenOntologyRepository_Plan
 * OpenOntologyRepository_Funding
 * OpenOntologyRepository_ResearchIssues
 * Our first "sandbox" instance of OOR powered by the NCBO BioPortal: http://oor-01.cim3.net

For the record ...'

How To Join (while the session is in progress)

 * 1. Dial in with a phone: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19#nid1SIV
 * 2. Open chat in a new browser window: http://webconf.soaphub.org/conf/room/ontolog_20090219
 * 3. Download presentations for each speaker here: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19#nid1SIN
 * or, 3.1 Open VNC (shared screen) session in a new browser window: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19#nid1SJ9