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Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 28-February-2008     (1)

  • Subject: Ontology Registry and Repository Technology & Infrastructure Landscape     (1A)

  • Shared-screen support (VNC session) will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (1E5)
    • view-only password: "ontolog"     (1E5A)
    • 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.     (1E5B)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides below and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (1E5C)
  • 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.     (1E10)

Attendees     (1F)

Background     (1H)

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.     (1H1)

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.     (1H2)

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.     (1H3)

Agenda & Proceedings     (1I)

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

Title: Ontology Registry and Repository Technology & Infrastructure Landscape     (1J)

Abstracts:     (1J1)

The XMDR project is making proposals for the next edition of ISO/IEC     (1J3)

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.     (1J4)

The XMDR has developed use cases, an architecture, and a prototype     (1J5)

implementation to demonstrate the workability of the proposals.     (1J6)

The talk will briefly overview the effort and proposals. Much can be found     (1J7)

on our web site at http://XMDR.org.     (1J8)

The DAML Ontology Library was created in 2000. This talk will cover     (1J10)

our experiences, lessons learned, and suggestions for OOR. We'll also discuss some related ontology registry/repository efforts including Swoogle, Ontaria, and SchemaWeb.     (1J11)

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.     (1J13)
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.     (1J14)
ebXML RegRep [1] is an open standard for Registry and Repositories.     (1J16)

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.     (1J17)

ebXML RegRep provides a minimal and extensible metadata information model     (1J18)

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.     (1J19)

A royalty-free open source implementation of RegRep is available [3].     (1J20)

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].     (1J21)

The talk will provide an brief overview of ebXML RegRep and how it may serve     (1J22)

as the core Repository Server for OOR.     (1J23)

... see below for the references cited by Farrukh in the above abstract.     (1J24)

Peter will mainly be talking about the hardware and network     (1J26)

infrastructure that he and his company (CIM3) can bring to the table, through various use cases, like:     (1J27)

(a) the CWE (collaborative work environment) - as in the Ontolog-CWE,     (1J28)

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/     (1J29)

(b) the subversion repository currently being used for the joint     (1J30)

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/     (1J31)

(c) the OntologyPortal.org [[SigmaKEE]] (Sigma Knowledge Engineering     (1J32)

He will explore how that infrastructure and the experience gained through their development and operations can be leveraged for the OOR initiative.     (1J34)

Resources     (1J35)

Questions, Answers & Discourse     (1J36)

  • (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when the talk is in progress. To un-mute, press "*3"     (1J36A)
  • If you want to speak or have questions or remarks to make, please "raise your hand (virtually)" by pressing "11" on your phone keypad. You may speak when acknowledged by the speaker or the session moderator. Test your voice and introduce yourself first before proceeding with your remarks, please.     (1J36B)
  • You can also type in your questions or comments through the browser based chat session by:     (1J36C)
  • For those who have further questions or remarks on the topic, please post them to the [ontology-summit] forum so that everyone in the community can benefit from the discourse. (One needs to be subscribed to this archived mailing list first before posting. See subscription details here.)     (1J36D)

Questions and Discussion captured from the chat session     (1J37)

VNC2: Welcome to the: Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session     (1J37A)

- Thu 28-February-2008     (1J37B)

John Bateman: question to Frank Olken: what does the "(mostly)" in NSF funding     (1J37C)

'Eligibility: U.S. based academic researchers (mostly)' mean?!?     (1J37D)

Mike Dean: we should also mention the recent OMG Ontology SIG work on repositories - perhaps as     (1J37E)

the first item during the discussion phase     (1J37F)

Susan Turnbull: Q for Dean, slide 4, Could use of light-weight XML instance document (i.e. http://et.gov)     (1J37G)

support distributed, sustainable curation of the DAML-related repository you described?     (1J37H)

Arturo Sanchez: Question for Dr. Musen: How is the "mapping" relation formally defined?     (1J37I)

John Bateman: Q for Mark: are the mappings (e.g., with Prompt) only term-to-term based or anything     (1J37J)

more complex? Formal basis?     (1J37K)

Arturo Sanchez: Question for Dr. Musen: How are different versions of mappings and versions of     (1J37L)

annotations managed?     (1J37M)

Michelle Raymond: Q to BioPortal - Mappings seem to be made at the terminology level between Ontologies.     (1J37N)

Is their quality checking that the terms matched also have appropriate relationships if     (1J37O)

one term follows the relationships of terms in the other Ontology?     (1J37P)

Mike Dean: annual workshop and competition for automated ontology matching tools at     (1J37Q)

Arturo Sanchez: Question for Dr. Musen: are there papers from your group which describe in     (1J37S)

more detail the community-based approach you mentioned?     (1J37T)

John Bateman: Q: for Mark wrt Arturo Sanchez: very good point! Versioning is also a critical issue.     (1J37U)

Anything beyond Subversion? Papers?     (1J37V)

Michelle Raymond: Q re "mapping" to all panelists - when mapping between ontologies, what mechanisms     (1J37W)

do you recommend for scoping that map?     (1J37X)

Ravi Sharma: The mechanism that would integrate ODM, OWL, and Other major notations, metamodels     (1J37Z)

of various ontologies but leave the integration to the ontology presentation engines.     (1J37AA)

This is only possible where we can create metamodels for ontologies i.e. open repositories     (1J37AB)

can abstract common and unique requirements for storing onto artifacts but we would not be     (1J37AC)

responsible for their integration, onto-engines would.     (1J37AD)

Ravi Sharma: Please treat my response to michelle as also another comment for panelists to validate.     (1J37AE)

These kinds of consensus will take us to realize use cases at Arch levels similar to what     (1J37AF)

Farrukh did.     (1J37AG)

Mike Dean: open source Snoggle tool for OWL-to-OWL ontology mapping using SWRL     (1J37AH)

Peter P. Yim: Q for the panel and all participants - what can the OOR deliver at the     (1J37AJ)

Summit F2F workshop (Apr-2 that could make a good milestone for the team as a whole?     (1J37AK)

Peter P. Yim: Ref. the versioning questions, one might want to check out Werner Ceusters talk on     (1J37AL)

"Realism-based Change Management for Quality Assurance in Ontologies and Data Repositories"     (1J37AM)

as part of the "Ontology Measurement & Evaluation" Mini-Series events ... Please refer to     (1J37AN)

details at the session wiki page,     (1J37AO)

John Bateman: Comment to the mapping and versioning points: getting access to the scoping of     (1J37AQ)

mappings requires more structure in the ontology definitions: we treat these as     (1J37AR)

logical theories + structure. Characterisation of possible mapping relations were     (1J37AS)

described in our Ontolog talk     (1J37AT)

Michelle Raymond: Q for all panelists - what do you see as a "show stopper" (and/or "pet")     (1J37AV)

research question that MUST be addressed to really make a big usefulness or feasibiltiy     (1J37AW)

impact in Ontology Repositories?     (1J37AX)

All Panelists: ... Quality ... Life Cycle Management ... Governance ... Interoperability ... Federation ... Mapping     (1J37AY)

Audio Recording of this Session     (1K)


This page has been migrated from the OntologWiki - Click here for original page     (1K7)