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Joint Ontolog-OOR Panel Discussion - Thu 19-February-2009     (1)

  • Subject: Getting OOR Development Off the Ground (Take-2): the work begins ...     (1A)
  • Session Chair: Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review" - [ slides ]     (1B)

  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (1E5)
    • view-only password: "ontolog"     (1E5A)
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  • Q&A and Discussion:     (1E6)
    • we will hold off Q&A and discussion until all presenters have finished their briefings.     (1E6A)
    • (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"     (1E6B)
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      • 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.     (1E6D1)
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  • 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.     (1E7)
  • 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.     (1E11)

Attendees     (1G)

Agenda Ideas     (1G5)

Panel Session: Getting OOR Development Off the Ground (Take-2): the work begins ...     (1H)

Agenda & Proceedings     (1I)

  • Session Format: this is a virtual session conducted over an augmented conference call.     (1I1)

Briefing Abstracts     (1J)

  • Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review"     (1J1)
    • 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.     (1J1A)
  • Professor MarkMusen (NCBO, Stanford-BMIR) - "BioPortal-OOR"     (1J2)
    • 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     (1J2A)
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.     (1J4A)
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.     (1J4B)
  • Mr. MikeDean (BBN) - "Aligning the OOR Software Architecture for Collaboration"     (1J5)
    • Abstract: ... an overview of how we can go forward from here, in terms of open software development for OOR.     (1J5A)

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.     (1J7)

NeOn is developing a reference architecture for semantic applications, based     (1J9A)

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.     (1J10)

In this presentation, I will describe some of these components (e.g. Wayson,     (1J11A)

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.     (1J12)

  • Professor KenBaclawski (Northeastern University) - "Multilingual (and Other) Considerations in our OOR Implementation"     (1J13)
    • 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.     (1J13A)
  • Professor MichaelGruninger (University of Toronto) - "COLORE: Common Logic Ontology Repository"     (1J14)
    • 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.     (1J14A)

Questions, Answers & Discourse     (1K)

Q & A and Discussion captured from the chat session     (1L)

Unedited chat transcript:     (1L1)

Peter P. Yim: Welcome to the Joint Ontolog-OOR Panel Discussion - Thu 19-February-2009     (1L2)

  • Subject: Getting OOR Development Off the Ground (Take-2): the work begins ...     (1L3)

o Professor Mark Musen (NCBO, Stanford-BMIR) - "BioPortal-OOR"     (1L6)

o Dr. Natasha Noy (Stanford-BMIR, NCBO) - "Representing Metadata in NCBO BioPortal"     (1L7)

o Mr. Mike Dean (BBN) - "Aligning the OOR Software Architecture for Collaboration"     (1L8)

o Dr. Paul Buitelaar / Mr. Andreas Harth (DERI, Galway) - "From OntoSelect towards OntoSelect-SWSE"     (1L9)

o Dr. Mathieu d'Aquin (Open University, UK) - "NeOn support for sharing and reusing ontologies (and related things)"     (1L10)

o Professor Ken Baclawski (Northeastern University) - "Multilingual (and Other) Considerations in our OOR Implementation"     (1L11)

o Professor Michael Grüninger (University of Toronto) - "COLORE: Common Logic Ontology Repository"     (1L12)

anonymous morphed into Todd Schneider     (1L13)

anonymous1 morphed into Natasha Noy     (1L14)

Forest morphed into Forest(Zhang, Lin)     (1L16)

anonymous1 morphed into Mark Musen     (1L17)

anonymous1 morphed into Luis Bermudez     (1L18)

anonymous morphed into Benjamin Dai     (1L19)

anonymous morphed into Trish Whetzel     (1L20)

anonymous morphed into Paul Alexander     (1L21)

anonymous morphed into Carlos Rueda     (1L22)

Ravi Sharma: 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?     (1L23)

Ravi Sharma: 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?     (1L24)

Mathieu Daquin: to Todd: why looking only at metadata and not to the content of ontologies for search/discovery?     (1L25)

Ravi Sharma: 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?     (1L26)

anonymous morphed into Steve Ray     (1L27)

Doug Holmes: @Todd: what is the rationale for no including instances? That constraint seems to exculde, for example, DBPedia, WordNet and similar reference ontologies.     (1L28)

Ravi Sharma: Mark How well have different ontologies started to interoperate, both in terms of transfer ofr artefacts as well as semantically (overlap of concepts)?     (1L29)

Ravi Sharma: you did address some of these in last slides.     (1L31)

Ravi Sharma: Mike Dean 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     (1L32)

Peter P. Yim: Our first "sandbox" instance of OOR powered by the NCBO BioPortal is now available at: http://oor-01.cim3.net     (1L33)

  • 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.)     (1L34)

Audio Recording of this Session     (1M)

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Resources     (1N)


For the record ...'     (1N11)

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



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