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

Conference Call Details    (1SIQ)

Attendees    (1SJQ)

Agenda Ideas    (1SK0)

Panel Session: Getting OOR Development Off the Ground (Take-2): the work begins ...    (1TG4)

Agenda & Proceedings:    (1TG5)

Briefing Abstracts    (1TGH)

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.    (1TJD)

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.    (1TJE)

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.    (1THF)

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.    (1THG)

Questions, Answers & Discourse:    (1TGI)

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

Unedited chat transcript:    (1TGM)

 PeterYim: Welcome to the Joint Ontolog-OOR Panel Discussion - Thu 19-February-2009    (1UO1)
 * Subject: Getting OOR Development Off the Ground (Take-2): the work begins ...    (1UO2)
 * Session Chair: Dr. ToddSchneider (Raytheon) - "The OOR Initiative in Review"    (1UO3)
 * Panelists / Briefings:    (1UO4)
  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"    (1UO5)
 anonymous morphed into Todd Schneider    (1UO6)
 anonymous1 morphed into Natasha Noy    (1UO7)
 PeterYim: see details on session page at:  http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_02_19    (1UO8)
 Forest morphed into Forest(Zhang, Lin)    (1UO9)
 anonymous1 morphed into Mark Musen    (1UOA)
 anonymous1 morphed into Luis Bermudez    (1UOB)
 anonymous morphed into Benjamin Dai    (1UOC)
 anonymous morphed into Trish Whetzel    (1UOD)
 anonymous morphed into Paul Alexander    (1UOE)
 anonymous morphed into CarlosRueda    (1UOF)
 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?    (1UOG)
 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?    (1UOH)
 MathieuDaquin: to Todd: why looking only at metadata and not to the content of ontologies for search/discovery?    (1UOI)
 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?    (1UOJ)
 anonymous morphed into SteveRay    (1UOK)
 DougHolmes: @Todd: what is the rationale for no including instances? That constraint seems to exculde, for example, DBPedia, WordNet and similar reference ontologies.    (1UOL)
 RaviSharma: Mark How well have different ontologies started to interoperate, both in terms of transfer ofr artefacts as well as semantically (overlap of concepts)?    (1UOM)
 RaviSharma: Mark    (1UON)
 RaviSharma: you did address some of these in last slides.    (1UOO)
 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    (1UOP)
 PeterYim: Our first "sandbox" instance of OOR powered by the NCBO BioPortal is now available at: http://oor-01.cim3.net    (1UOQ)

Audio Recording of this Session    (1TGO)

Resources    (1SK2)

For the record ...'    (1TJV)

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