ConferenceCall 2008 02 28

= Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 28-February-2008 =


 * Subject: Ontology Registry and Repository Technology & Infrastructure Landscape


 * Session co-chairs:
 * Dr. LeoObrst ([[OpenOntologyRepository]]; MITRE) &
 * Dr. FrankOlken (OntologySummit2008; NSF)


 * Panelists:
 * Mr. BruceBargmeyer (XMDR, LBL),
 * Mr. MikeDean (DAML, BBN, W3C),
 * Professor MarkMusen (Stanford-BMIR),
 * Mr. FarrukhNajmi ( OASIS ebXML RegRep TC, Wellfleet Software) &
 * Mr. PeterYim (Ontolog, CIM3)


 * Archive:
 * slides: 0-Olken, 1-Bargmeyer, 2-Dean, 3-Musen, 4-Najmi, 5-Yim ... and,
 * audio recording of the session (mp3)
 * transcript of the online chat session during the panel discussion

Conference Call Details

 * Date: Thursday, February 28, 2008 
 * Start Time: 10:30am PST / 1:30pm EST / 18:30 UTC
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 * Acknowledgment: we want to thank the OOR teams members who brought about this panel session, idea of which came about during their 2008.02.13 meeting discussion).

Attendees

 * Registered Particpants & Attendees:
 * LeoObrst
 * FrankOlken
 * BruceBargmeyer
 * MikeDean
 * MarkMusen
 * FarrukhNajmi
 * PeterYim
 * SteveRay
 * MichelleRaymond
 * Louis Roberts (Boeing)
 * RaviSharma
 * MustafaJarrar
 * CoryCasanave
 * Onnalee Gomez (CDC/CCHIS/NCPHI)
 * Jaime Ramirez (Boeing)
 * EvanWallace
 * AzamatAbdoullaev
 * SusanTurnbull
 * Elgar Pichler (Astra Zeneca)
 * HerbBasik
 * DavidMartin
 * KenBaclawski
 * Neil Custer (CSC)
 * ArturoSanchez
 * BenjaminDai
 * DougHolmes
 * Yung S Kim (Boeing)
 * Thomas Brunner (Novartis Pharmaceuticals)
 * Rob Frost (BEA Systems, Inc.)
 * Rajesh Tavva (IIIT, Hyderabad, India )
 * Kevin Keck (Lawrence Berkeley National Laboratory)
 * BruceBray
 * MalaMehrotra
 * RobertoRocha
 * MichaelGruninger
 * JieBao
 * DeanSpik
 * Xixi Luo (Tetherless World Constellation, RPI)
 * Harold Solbrig (Apelon)
 * JohnBateman
 * Susan Matney (U of Utah)
 * Line Pouchard (Oak Ridge National Lab)
 * FabianNeuhaus
 * Peter Schad (NIH/NCI, SAIC)
 * ... to register for participation, please add your name (plus your affiliation, if you aren't already a member of the community) above, or e-mail  so that we can reserve enough resources to support everyone's participation. ...
 * ... to register for participation, please add your name (plus your affiliation, if you aren't already a member of the community) above, or e-mail  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * AntoinetteArsic
 * AmandaVizedom
 * MarciaZeng (May join between 12:00-1:30 pm)
 * ElisaKendall
 * DagobertSoergel (couldn't get into the conference line)

Background
Two parallel initiatives are ongoing in the community, revolving around the theme of "Open Ontology Repository". On the one hand, a working group under the auspices of the OpenOntologyRepository Initiative, and on the other, the discourse (and essentially a discussion group that culminates in a two-day workshop) conducted as the main focus for OntologySummit2008.

It is at the intersection of these two initiatives that this panel discussion session is being held. The OpenOntologyRepository team is taking the opportunity to have some of its members who are bringing technology and infrastructure to the table to present them side-by-side, and to discuss how these can all fit nicely together. The OntologySummit2008 folks, on the other hand would want to take the opportunity to survey (at least a subset of) the technology & infrastructure landscape to gain insight into the state-of-art in Ontology Registry and Repository.

Besides hearing from the panelists, we are setting aside ample time after their briefings, for some good Q&A and discussions among all who are participating in this session.

Refer to details at the respective project homepages of the two initiatives at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository. & . http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008

Agenda & Proceedings:

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


 * Agenda:
 * 1. Opening by the Session co-chairs - LeoObrst / FrankOlken
 * 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. Panelists' Briefings (12~15 min. each) - BruceBargmeyer, MikeDean, MarkMusen, FarrukhNajmi & PeterYim
 * 5. Q & A and Open discussion by all participants (30~45 minutes) - All
 * 6. Summary / Conclusion / Follow-up-actions by the Session co-chairs - LeoObrst / FrankOlken

Title: Ontology Registry and Repository Technology & Infrastructure Landscape
Abstracts:


 * The eXtended Metadata Registry Project (XMDR) - BruceBargmeyer


 * The XMDR project is making proposals for the next edition of ISO/IEC

11179-Metadata Registries. We are developing a UML model and text. The direction of the work is to register any semantic artifact useful in managing data. The intension is to link concepts found in concept systems (thesauri, taxonomies, ontologies, etc.) to concepts in metadata, to concepts in data.


 * The XMDR has developed use cases, an architecture, and a prototype

implementation to demonstrate the workability of the proposals.


 * The talk will briefly overview the effort and proposals. Much can be found

on our web site at http://XMDR.org.


 * The DAML Ontology Library - MikeDean


 * The DAML Ontology Library was created in 2000. This talk will cover

our experiences, lessons learned, and suggestions for OOR. We'll also discuss some related ontology registry/repository efforts including Swoogle, Ontaria, and SchemaWeb.


 * The NCBO BioPortal  - MarkMusen


 * The National Center for Biomedical Ontology (NCBO; see http://bioontology.org) is developing  BioPortal , an open-source repository of ontologies, terminologies, and thesauri of importance in biomedicine. An early version of BioPortal is accessible at http://bioportal.bioontology.org.  Users can access the BioPortal content interactively via their Web browsers or programmatically via Web services.  The version of BioPortal currently under development includes facilities for visualizing ontologies, for creating mappings between ontologies, and for adding "marginal notes" through which the user community can comment on ontologies and discuss modeling decisions. An active BioPortal user group is providing feedback on these new features and guiding our future development work.


 * BioPortal will contribute to the OOR initiative by providing a framework with which to experiment with community-based interaction with an ontology repository, and to explore metadata for capturing mappings, annotations, and user dialogs about ontology content. Our interest is not only in developing computational technology to support community involvement in the use of ontologies, but also in studying the way in which this technology can promote the use of ontologies within the biomedical enterprise.  We anticipate that our work will provide models for the dissemination and use of ontologies in e-science broadly, and may generalize to other kinds of professional communities.


 * ebXML RegRep as an OOR Server - FarrukhNajmi


 * ebXML RegRep [1] is an open standard for Registry and Repositories.

It has been approved by OASIS and ISO (ISO 15000 part 3, 4). Its origins are based upon ISO 11179. Its basic function is to provide end-to-end management and discovery of any type of content and associated metadata.


 * ebXML RegRep provides a minimal and extensible metadata information model

and extensible services and protocols for publishing and discovering content. It has a flexible query feature that allows virtually any type of discovery. Its numerous features include subscription and notification, automatic validation and cataloging of content, lifecycle support, change history, fine-grained role based access control and federation support including federated queries. The RegRep TC [2] at OASIS is actively working on version 4.0 of the standard which provides many new features such as REST support via OpenSearch and ATOM bindings and enhanced type extensibility.


 * A royalty-free open source implementation of RegRep is available [3].

Because of its extensibility features, ebXML RegRep is being adopted in many vertical and organizations [4]. The specification is also being profiled by several other standard [5] including a profile for OWL Lite [6].


 * The talk will provide an brief overview of ebXML RegRep and how it may serve

as the core Repository Server for OOR.

... see below for the references cited by Farrukh in the above abstract.


 * A Hardware and Network Infrastructure for Open Ontology Community Support - PeterYim


 * Peter will mainly be talking about the hardware and network

infrastructure that he and his company (CIM3) can bring to the table, through various use cases, like:


 * (a) the CWE (collaborative work environment) - as in the Ontolog-CWE,

ProtegeWiki & ProjectWiki [which supports communities of practice and open collaboration.] ... Ref. http://ontolog.cim3.net/ , http://protege.cim3.net/wiki/ & http://project.cim3.net/wiki/


 * (b) the subversion repository currently being used for the joint

Stanford-BMIR/CIM3 CODS (Collaborative Ontology Development Service & Infrastructure) initiative. [which supports the Protege frame-based ontologies, RDF and OWL ontology development.] ... Ref. http://protege.cim3.net/cgi-bin/wiki.pl?CODS .. http://protege1.cim3.net/svn1/ & http://protege1.cim3.net/svn2/


 * (c) the OntologyPortal.org SigmaKEE (Sigma Knowledge Engineering

Environment) work. [where SUO-KIF based, First Order Logic ontology development is supported.] ... Ref. http://sigma.ontologyportal.org:4010/sigma/Browse.jsp?kb=SUMO&lang=EnglishLanguage & http://ontolog.cim3.net/file/work/ontology/UBLONT/CCTONT-worksheet-v0-4.html

He will explore how that infrastructure and the experience gained through their development and operations can be leveraged for the OOR initiative.

Resources

 * Our panel's prepared slides can be accessed by clicking on each of the title links below:
 * 0 - FrankOlken - "Ontology Registry and Repository Technology & Infrastructure Landscape - Session Opening"
 * 1 - BruceBargmeyer - "The eXtended Metadata Registry Project (XMDR)"
 * ref. http://xmdr.org/overview.html
 * 2 - MikeDean - "The DAML Ontology Library"
 * ref. http://www.daml.org/ontologies/
 * 3 - MarkMusen - "The NCBO BioPortal"
 * ref. http://bioportal.bioontology.org
 * Mark's recent Ontolog talk: "If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies" ... details at: ConferenceCall_2007_12_06
 * 4 - FarrukhNajmi - "ebXML [[RegRep] as an OOR Server]" - references:
 * [1] What Is ebXML RegRep - http://ebxmlrr.sourceforge.net/wiki/index.php/Overview#What_is_ebXML_Registry-Repository
 * [2] ebXML RegRep TC - http://www.oasis-open.org/committees/regrep
 * [3] freebXML Registry Open Source Project - http://ebxmlrr.sourceforge.net
 * [4] ebXML RegRep Adoption - http://ebxmlrr.sourceforge.net/wiki/Showcase
 * [5] ebXML RegRep Profiles - http://ebxmlrr.sourceforge.net/wiki/Overview#Profiles_of_ebXML_Registry_Standard
 * [6] ebXML Registry Profile for OWL Lite - http://docs.oasis-open.org/regrep/v3.0/profiles/owl/
 * 5 - PeterYim - "A Hardware and Network Infrastructure for Open Ontology Community Support"
 * CIM3 infratsructure pictures: facility, servers-1f & servers-1r


 * To participate in the online discourse to further explore the subject matter, please subscribe to our open archived discussion forums as appropriate:
 * to participate in the OpenOntologyRepository Initiative - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YX
 * to participate in the OntologySummit2008 Initiative - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008#nid18V7


 * additional resources:
 * (... to be added by the panel)

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Questions and Discussion captured from the chat session:
VNC2: Welcome to the: Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 28-February-2008

JohnBateman: question to Frank Olken: what does the "(mostly)" in NSF funding 'Eligibility: U.S. based academic researchers (mostly)' mean?!?

MikeDean: we should also mention the recent OMG Ontology SIG work on repositories - perhaps as the first item during the discussion phase

SusanTurnbull: Q for Dean, slide 4, Could use of light-weight XML instance document (i.e. http://et.gov) support distributed, sustainable curation of the DAML-related repository you described?

ArturoSanchez: Question for Dr. Musen: How is the "mapping" relation formally defined?

JohnBateman: Q for Mark: are the mappings (e.g., with Prompt) only term-to-term based or anything more complex? Formal basis?

ArturoSanchez: Question for Dr. Musen: How are different versions of mappings and versions of annotations managed?

MichelleRaymond: Q to BioPortal - Mappings seem to be made at the terminology level between Ontologies. Is their quality checking that the terms matched also have appropriate relationships if one term follows the relationships of terms in the other Ontology?

MikeDean: annual workshop and competition for automated ontology matching tools at http://ontologymatching.org

ArturoSanchez: Question for Dr. Musen: are there papers from your group which describe in more detail the community-based approach you mentioned?

JohnBateman: Q: for Mark wrt Arturo Sanchez: very good point! Versioning is also a critical issue. Anything beyond Subversion? Papers?

MichelleRaymond: Q re "mapping" to all panelists - when mapping between ontologies, what mechanisms do you recommend for scoping that map?

RaviSharma: Michelle

RaviSharma: The mechanism that would integrate ODM, OWL, and Other major notations, metamodels of various ontologies but leave the integration to the ontology presentation engines. This is only possible where we can create metamodels for ontologies i.e. open repositories can abstract common and unique requirements for storing onto artifacts but we would not be responsible for their integration, onto-engines would.

RaviSharma: Please treat my response to michelle as also another comment for panelists to validate. These kinds of consensus will take us to realize use cases at Arch levels similar to what Farrukh did.

MikeDean: open source Snoggle tool for OWL-to-OWL ontology mapping using SWRL http://snoggle.projects.semwebcentral.org/

PeterYim: Q for the panel and all participants - what can the OOR deliver at the Summit F2F workshop (Apr-2 that could make a good milestone for the team as a whole?

PeterYim: Ref. the versioning questions, one might want to check out WernerCeusters talk on "Realism-based Change Management for Quality Assurance in Ontologies and Data Repositories" as part of the "Ontology Measurement & Evaluation" Mini-Series events ... Please refer to details at the session wiki page, at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_01_11

JohnBateman: Comment to the mapping and versioning points: getting access to the scoping of mappings requires more structure in the ontology definitions: we treat these as logical theories + structure. Characterisation of possible mapping relations were described in our Ontolog talk from: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2008_01_31.

Michelle Raymond: Q for all panelists - what do you see as a "show stopper" (and/or "pet") research question that MUST be addressed to really make a big usefulness or feasibiltiy impact in Ontology Repositories?

All Panelists: ... Quality ... Life Cycle Management ... Governance ... Interoperability ... Federation ... Mapping

Audio Recording of this Session

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 * Conference Date and Time:	28-Feb-2008 10:40am~12:48pm PST
 * Duration of Recording:	2 Hour 07 Minutes
 * Recording File Size:	       14.5 MB (in mp3 format)
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