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

  • Subject: Ontology Registry and Repository Technology & Infrastructure Landscape
  • 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)

Conference Call Details

  • Date: Thursday, February 28, 2008
  • Start Time: 10:30am PST / 1:30pm EST / 18:30 UTC
  • Expected Call Duration: 2.0~2.5 hours
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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

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 Ontology Summit 2008 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 - Leo Obrst / Frank Olken
    • 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) - Bruce Bargmeyer, Mike Dean, Mark Musen, Farrukh Najmi & Peter P. Yim
    • 5. Q & A and Open discussion by all participants (30~45 minutes) - All
    • 6. Summary / Conclusion / Follow-up-actions by the Session co-chairs - Leo Obrst / Frank Olken

Title: Ontology Registry and Repository Technology & Infrastructure Landscape

Abstracts:

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 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 - Mark Musen
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 [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 - Peter P. Yim
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

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

Questions, Answers & Discourse

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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

John Bateman: question to Frank Olken: what does the "(mostly)" in NSF funding

'Eligibility: U.S. based academic researchers (mostly)' mean?!?

Mike Dean: we should also mention the recent OMG Ontology SIG work on repositories - perhaps as

the first item during the discussion phase

Susan Turnbull: 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?

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

John Bateman: Q for Mark: are the mappings (e.g., with Prompt) only term-to-term based or anything

more complex? Formal basis?

Arturo Sanchez: Question for Dr. Musen: How are different versions of mappings and versions of

annotations managed?

Michelle Raymond: 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?

Mike Dean: annual workshop and competition for automated ontology matching tools at

http://ontologymatching.org

Arturo Sanchez: Question for Dr. Musen: are there papers from your group which describe in

more detail the community-based approach you mentioned?

John Bateman: Q: for Mark wrt Arturo Sanchez: very good point! Versioning is also a critical issue.

Anything beyond Subversion? Papers?

Michelle Raymond: Q re "mapping" to all panelists - when mapping between ontologies, what mechanisms

do you recommend for scoping that map?

Ravi Sharma: Michelle

Ravi Sharma: 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.

Ravi Sharma: 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.

Mike Dean: open source Snoggle tool for OWL-to-OWL ontology mapping using SWRL

http://snoggle.projects.semwebcentral.org/

Peter P. Yim: 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?

Peter P. Yim: Ref. the versioning questions, one might want to check out Werner Ceusters 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

John Bateman: 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

  • To download the audio recording of the session, click here
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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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