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Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 10-April-2008

  • Subject: Developing an Ontology of Ontologies for OOR
  • Session co-chairs:
    • Professor BarrySmith (NCOR; University at Buffalo) &
    • Professor MichaelGruninger (University of Toronto)
  • Panelists:
    • Professor MichaelGruninger (U of Toronto) - "A Framework for an Ontology of Ontologies"
    • Dr. PeterHaase (AIFB, U of Karlsruhe; Project NeOn) - "The OMV Ontology Metadata Vocabulary"
    • Dr. NatashaNoy (Stanford-BMIR) - "Ontology metadata in NCBO's BioPortal"
    • Ms. ElisaKendall (OMG; Sandpiper Software) - "Metadata Support for OMG's Emerging Ontology and Vocabulary Management Initiative"

Conference Call Details

  • Date: Thursday, April 10, 2008
  • Start Time: 10:30am PDT / 1:30pm EDT / 7:30pm CEST / 17:30 UTC
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Attendees

  • Other Expecting Attendees (who may have joined us after the roll call):
    • ... 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 <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...
  • Regrets:
    • Leo Obrst (will be at an off-site; but will try to call in, if at all possible)
    • Ed Dodds

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

  • This is the last of the four OOR-panel discussion sessions taht has been scheduled to explore various aspects of an "Open Ontology Repository (OOR)." In this session, the focus will be on the incorporation and development of an Ontology of Ontologies that would be of value (probably crucial) to an well designed and implemented OOR. Again, We are attemptig to bring together some of the world's top experts who has done related work to participate in this panel discussion sessions. Besides hearing from the panelists, we are setting aside ample time (~45 minutes) after their briefings, for some good Q&A and discussions among all who will be participating in this sessions.
  • Session Format: this is a virtual session conducted over an augmented conference call.

Topic: Developing an Ontology of Ontologies for OOR

Panelists' Presentation Titles and Abstracts:

A Framework for an Ontology of Ontologies - MichaelGruninger

[ slides ]

Under the appellation of "ontology" are found many different types of artifacts created and used in different communities to represent entities and their relationships for a wide range of purposes.The Ontology Summit 2007 "Ontology, Taxonomy, Folksonomy: Understanding the Distinctions," was an attempt to bring together various communities having a different understanding of what is an ontology, and to foster dialog and cooperation among these communities.
The results of the Summit identified a limited number of key dimensions along which ontologies can be characterized and to provide operational definitions for these dimensions.
This talk will give an overview of the framework that is constituted by these dimensions.

The OMV Ontology Metadata Vocabulary - PeterHaase

[ slides ]

In my presentation I will talk about OMV, a proposal for an Ontology

Metadata Vocabulary that has been originally developed within the Knowledge Web project and is now maintained by the OMV consortium. I will explain the coverage and scope of OMV, some basic design rationales as well as applications. In particular, I will talk about uses and tool support for OMV developed in the NeOn project.

Ontology metadata in NCBO's BioPortal - NatashaNoy

[ slides ]

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. BioPortal is accessible at http://bioportal.bioontology.org. Users can access the BioPortal content interactively via their Web browsers or programmatically via Web services. An alpha version of the next BioPortal release, which is available at http://alpha.bioontology.org supports 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.
I will discuss the metadata requirements for BioPortal and our approach for representing metadata about ontologies, maintaining the metadata as the ontologies evolve, and encouraging users to provide metadata both on the ontologies that they author and the ones that they use in their own projects.

Metadata Support for OMG's Emerging Ontology and Vocabulary Management Initiative - ElisaKendall

[ slides ]

As presented in EvanWallace's talk in the OOR-Panel Session (ConferenceCall_2008_03_27), the OMG is exploring what it would take to host a repository to manage standard ontologies and vocabularies. An initial request for information was issued at the recent OMG Technical Meeting in Washington, DC. (http://www.omg.org/cgi-bin/doc?ontology/08-03-02.pdf, Ontology and Vocabulary Management RFI). Searchable metadata is a critical aspect of this anticipated facility, and as such, we are actively investigating and seeking input on ontology management metadata.
Potential starting points include, but are certainly not limited to: the OMV Ontology Metadata Vocabulary augmented via lessons learned in developing the BioPortal, current work in the ISO JTC1 SC32 WG2 effort to update the ISO 11179 Metadata Registry standard to include concept systems, vocabularies, and ontologies, and lessons learned in provenance and trust research by Dr. DeborahMcGuinness and her colleagues. I will briefly present some of the requirements and challenges we have identified for a successful ontology management capability at OMG, and look forward to active discussion and input from this community.

( more details coming! ) - see: developing details

Resources

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

Questions, Answers & Discourse

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  • 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.)

Questions and Discussion captured from the chat session

Peter P. Yim: Welcome to the Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 10-April-2008

  • Subject: Developing an Ontology of Ontologies for OOR
  • Session co-chairs: (1D3L)

o Professor Barry Smith (NCOR; University at Buffalo) &

o Professor Michael Grüninger (University of Toronto)

  • Panelists:

o Professor Michael Grüninger (U of Toronto) - "A Framework for an Ontology of Ontologies"

o Dr. Peter Haase (AIFB, U of Karlsruhe; Project NeOn) - "The OMV Ontology Metadata Vocabulary"

o Dr. Natasha Noy (Stanford-BMIR) - "Ontology metadata in NCBO's BioPortal"

o Ms. Elisa Kendall (OMG; Sandpiper Software) - "Metadata Support for OMG's Emerging Ontology and Vocabulary Management Initiative"

Arturo Sanchez: Question for Michael Grüninger: why limit the formalisms used to express semantics to Model Theory (slide 9)?

Arturo Sanchez: For Michael Grüninger and Peter Haase: how would you characterize OMV according to the

Ontology Summit 2007 model?

Rex Brooks: For Michael Grüninger: Could we have some examples of Semi-Structured Ontologies?

Rex Brooks: For Michael Grüninger: I would also like to have some examples of descriptive v. prescriptive

ontologies, and how we can capture that in metadata, to avoid inadvertent misuse.

John Graybeal: For Michael Grüninger: On slide 17, is it really the Design Methodology that you care about,

or the validation/review characteristics of the result? The important thing would seem to be

whether an ontology has been established as consistent or conformant along various axes,

not how it got to that state.

Todd Schneider: In general we should assume we will not know all of the 'items' that will need to be

represented in the metadata associated with an artifact and design for this.

John Graybeal: For Michael Grüninger: The characterization of WordNet during slide 11 (Level of Structure)

lost me a little, I'd like to hear that again. (An example table, showing how a number of

ontologies fits into these various dimensions, would be quite helpful.)

Arturo Sanchez: For John Graybeal: see http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Population_Session

and search for Population-spreadsheet, various ontologies where mapped to the model

during the summit

John Graybeal: For Arturo Sanchez: This is brilliant, though the copy I found is largely empty.

Where can I find one that integrates all the results?

Arturo Sanchez: For John Graybeal: if you look under "Breakout Group Task:" you will find the

various results from all the groups. In particular, the link to the document

about WordNet is http://ontolog.cim3.net/file/work/OntologySummit2007/workshop/Population-spreadsheet_WordNet-as-ontology_20070423b.doc

Peter P. Yim (added subsequently): to John Graybeal: you can also look under

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Communique_Session#nid108F

... check out the various breakout groups' work products as well as

OlivierBodenreider's "Framework Dimensions Sorted" piece

at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Communique_Session#nid10PD

Ken Baclawski: With one of my students, I have evaluated 40 large ontologies using the Ontology Summit 2007

Framework Dimensions. I have written up some conclusions about the results and could

present them at some point.

Rex Brooks: For Peter Haase: Small note on "Party," don't you think we need a category for "Agent"

which can be a subtype of either "Organisation" or "person," as well as a "party" in its

own right, e.g. a spider/webcrawler bot?

Peter Haase: to Rex Brooks: I believe the concept Party captures what you propose as Agent

Peter Haase: we did not want to call it agent as the term is so overloaded

Rex Brooks: Thanks PeterHaase. It may require a qualifier or another term to be able to specify

the Party as some kind of software agent v. an organisation or person. I will need

to take a good look at OMV.

Mala Mehrotra: For Natasha Noy: Are the mappings being stored as metadata? Slide 5.

Natasha Noy: For Mala Mehrotra: Yes, mappings are also metadata (and have the same issues,

such as versioning, contributions from communities, etc.)

Mala Mehrotra: For Natasha Noy: SO what language - or what level of expressivity - are you

all requiring in the BioPortal for mappings?

Arturo Sanchez: For Natasha Noy: what is the definition of "validity"? without a formal definition

it is not possible to check for such property ...

Arturo Sanchez: For Natasha Noy: so, by allowing ontology versioning by creating brand new ontologies

from existing ones, that means interoperability among versions might not be possible

... any comments?

John Graybeal: Awesome lineup, Peter. Must leave now, will catch up later.

Todd Schneider: For Peter Haase: Does OMV support a distributed structure (e.g. P2P)?

Rex Brooks: For Peter Haase: Would OMV be capable of being used as a "Classification Scheme"

in ebXML RIM, if you happen to know?

Peter Haase: to Rex Brooks: The OMV API for the registry that I mentioned is actually an

"OMV Specialized ebXML Registry"

Peter Haase: so we used the extension mechanisms of ebXML

Rex Brooks: Thanks Peter Haase, that is terrific for the groups I work with.

Peter Haase: we have P2P-like applications that make use of OMV and have a P2P extension to describe

the peers, but there is nothing P2P specific in OMV itself

Peter Haase: what kind of structures were you thinking about?

Peter Haase: regarding the ebXML registry, you may want to look at " D6.4.1: Realisation &

early evaluation of NeOn service-oriented registry and repository " under

http://www.neon-project.org/web-content/index.php?option=com_weblinks&catid=17&Itemid=67

Peter Haase: what we also do have is the separation between logical identifiers of

ontologies (ontology URI) and their physical location, this can be used to support

replication and caching

Todd Schneider: To Peter Haase: In that case (i.e. the ontologies are maintained locally),

is OMV being used more for a registry? If so, can there be multiple registries

(i.e.distributed)? For example, different COP's maintaining their own 'instances'

of thier OMV registry for their domain/COP.

Peter Haase: yes, we have both registries and repositories using OMV. They can be distributed,

in fact, the Oyster system I mentioned is such a distributed system

Peter Haase: it also supports the propagation and synchronization of the metadata

Rex Brooks: To all panelists: This is really terrrific as the groups I work with head directly

into building registry-repositories and ontologies. Thanks All!

Rex Brooks: My question is for Peter Haase: Could you elaborate on the difference, with examples,

if you can, between prescriptive and descriptive ontologies?

Peter Haase: I am afraid I cannot, Michael Grüninger brought this distinction up, perhaps he can

better answer [--ed. which Michael Grüninger did answer to verbally. Refer to the audio archive.]

Evan Wallace: I don't understand this distinction in this context.

Ann Wrightson: I'm uncomfortable with the use of "structured" to apparently mean "logically clean".

Surely these are different notions? An "unstructured" ontology in the expression-sense

stated in slide 11 could have in fact a considerable amount of structure in the usual sense

of the word (eg follow a component-assembly-structure defined in EXPRESS)

[--ed. which Michael Grüninger did answer this verbally when Ann Wrightson posed the

question again (below). Refer to the audio archive.]

Ann Wrightson: My question: To Michael Grüninger, regarding Structure. I'm thinking in particular of

the HL7v3 RIM (Reference Information Model) that is used as a theory-of-what-there-is

(a semi-formal upper ontology) to both describe and prescribe the kinds of things

can be said in a largish family of derivative standards. The RIM has internal structure,

and the related set of standards has structure (that could be expressed eg using

STEP concepts). How would/should this kind of structure be handled in our dialogue,

distinct from the quality of being "structured" that is present in MichaelGruninger's slide 11?

Evan Wallace: For some content in some ontology language forms, some metadata could be

Evan Wallace: automatically generated (DL expressivity, satisfiability, etc.).

Evan Wallace: I believe that some OMV tools do this already for OWL DL ontologies.

Peter Haase: yes, this is what e.g. Watson does, it generates/extracts most metadata automatically

Evan Wallace: Peter Haase: Does OMV or Watson provide any support for Common Logic or some other FOL form?

Peter Haase: in principle it can capture metadata about ontologies in any ontology language

Ann Wrightson: Following on from the response just now, and thinking back to the NASA presentation

on ConferenceCall_2008_03_20: though we shouldn't expect the OOR to provide or perform

configuration management of ontologies, I guess there should be guidance concerning

provision of versioning infomration that will support users who want to reuse ontologies

within a strong configuration management or product line development environment.

Chaim Zins: Just a short remark: We need to diferentiate between the topic "Ontology of ontologies"

and metadata issues related to the field of ontology study.

[--ed. to which Barry Smith did answer, verbally. Refer to the audio archive.]

Arturo Sanchez: For Peter Haase: Good point ... so, metadata management is informed (so to say) by

the semantics of your model, using which concepts such as "validity", "extensions",

"editing", "refinement" can be equally formally defined (in theory, at least ) Thanks.

Todd Schneider: To Barry Smith: Perhaps we need a variant or sub-repository of the Open Repository that

would support a peer review process to meet higher quality standards?

Peter Haase: to Arturo Sanchez: yes, in theory and to some extent already in practice

Chaim Zins: I agree with your remark.

Evan Wallace: BarrySmith's comment just underlines my opinion that the term Ontology

Chaim Zins: The first question is "what is ontology?"

Evan Wallace: of Ontologies is not a good term for describing ontology metadata needed for a repository.

Evan Wallace: Cute terms are great for slideset titles but bad for describing discussion topics.

Arturo Sanchez: Ontology of Ontologies in this context is: using the metadata approach to represent the

knowledge about ontologies. Therefore, applications will be inherently limited by the models

used to characterized ontologies. For instance, consider the example for which the ontology

used to characterize ontologies in the repository has less "expressive power" than ontologies

it is trying to define

Michelle Raymond: Ann Wrightson mentions that (paraphased) 'in product line development environments

strong configuration management is required.' Currently, there are industry product

providers that very much MUST point to the exact ontology AND the associated metadata

for that ontologies when providing a product release. To do this now, sometimes

the "real" standard can't be linked in, as there is concern that it has remained static

or at least a needed level of consistency. Thus, the vendor includes a copy of

the ontology and associated metadata, files, documents and the like in their

product release and does not encourage customers to visit the "real" source. This can be

a legal issue of "fair use" when a copy is made. It is also disassociating the product

from the further value potentially available in the "real" ontology and the repository

that holds it. I believe we need to address this issue both in firm rules that SHALL NOT

allow revision of a "status-final" ontology and that we must further consider requiring

some meta-data associated with an ontology as also being "status=final." Comments about

my statements are very much desired as is turning this into a conversational thread.

Evan Wallace: We should start a thread about versioning on one of the email lists which captures both

AnnWrightson's and MichelleRaymond's comments on today's chat session. Would one of you

do it or should I?

--ed. see: follow-up discussion thread started by EvanWallace

Audio Recording of this Session

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  • Conference Date and Time: 10-Apr-2008 10:36am~12:57pm PDT
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Join us at the Ontology Summit 2008 workshop, April 28~29, 2008; either on-site at NIST, Gaithersburg, Maryland, USA or participate remotely! - see deails here.



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