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Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - Thu 27-March-2008

  • Subject: An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1
  • Session co-chairs:
    • Dr. LeoObrst (MITRE) &
    • Dr. FabianNeuhaus (NIST)

Conference Call Details

  • Date: Thursday, March 27, 2008
  • Start Time: 10:30am PDT / 1:30pm EDT / 17:30 UTC
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Attendees

  • Other Expected Attendees who may have joined after our 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:
    • Cory Casanave (will check out the audio archive later)
    • Suzi Lewis (unfortunately Suzi, who was traveling, was in a remote place which lost Internet connectivity. She was, hence, unable to join us. We will try to re-schedule her participation in this discussion as best we can. =ppy)

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 first of two panel discussion sessions on "Open Ontology Repository: Rationale, Expectations & Requirements." We are attemptig to bring together some of the world's top ontological content custodians and researchers, 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.

Title: An Open Ontology Repository: Rationale, Expectations & Requirements

Abstracts:

  • Panelists - "Title" - [ OOR-content ]
    • BillBug - "Driving large-scale neuroscience data federation by wrestling complex semantic domains to the ground (or foundation)" - [ BIRNlex] and [ NIFSTD]
      • Resource(s) - Both BIRNLex (OWL-DL ontology for the BIRN project) and NIFSTD (OWL-DL ontology for the Neuroscience Information Framework [NIF] project) are split up into separate, re-usable domain ontologies (e.g., neuroanatomy, organisms, nerve cells, etc.) which are collectively imported into a base OWL file. NIFSTD actually imports all of BIRNLex and adds a few additional domains. The files are available respectively at:
    • EvanWallace - "Thoughts on hosting an Ontology and Vocabulary Repository at OMG"
      • Remarks (--EvanWallace / 21 Mar 2008 17:43:09 -0400): regarding OOR-content - Specific content for this repository is to be determined. The intent is to provide reliable availability of reusable semantic models in various forms related to OMG standards. These would be include:
        • ontologies based on any of the logic languages supported by ODM metamodels such as Common Logic, OWL, and RDFS;
        • vocabularies based on the Semantics for Business Vocabularies and Rules specification and Topic Maps; and
        • conceptual models based on UML.
      • See our appraoch towards the issue in the recently released OMG RFP & RFI document:

from OMG members) &

    • JohnLMcCarthy - "Standard & Prototype Starting Point for An Open Ontology Repository: The Extended Metadata Registry Project"
    • KenBaclawski - "Enhancing Organism Based Disease Knowledge Using Biological Taxonomy, and Environmental Ontologies" - [ Medline, Agricola, GBIF, ProMED, WHO Health Reports, GENBANK and the Encyclopedia of Life ]
      • Remark: This is joint work with Neil Sarkar of the Marine Biological Laboratory. Neil is the Principal Investigator.
    • PeterBenson - "NATO codification system as the foundation for the eOTD, ISO 22745 and ISO 8000"
    • RexBrooks - "Content Provider-Repository Builder Focus on Architecture, Registry-Repository & Emergency Data Exchange Language Reference Information Model (EDXL-RIM)" - [EDXL-RIM]
      • Remarks: EDXL-RIM is the content that will be produced by the OASIS Emergency Management Technical Committee, EDXL-RIM Subcommittee (under formation now). EDXL-RIM will have three representations: XMl Schema, RDF Schema and OWL-DL Ontology.
    • SuziLewis - "How the Gene Ontology led directly to the Open Biomedical Ontology Foundry, or How I learned to stop worrying and love standards" - see: regrets

Resources

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

Questions, Answers & Discourse

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Questions and Discussion captured from the chat session

Ravi Sharma: Q For William Bug: How is the usage of BIRN work by 1. research 2. operaional practitioners

progressing especially in adoption of common or cross discipline concepts and vocabularies

and Other collaborative features?

Leo Obrst: Question to Bill Bug: Biomedicine is changing so quickly. How do you integrate working hypotheses

(not yet firm) with fairly established theories (ontologies)? Is this very fast changeability a

hard problem? How do you keep up?

Ravi Sharma: Q for Evan Wallace, can we think of a combined collaborative OOR Repository &/or Registry

definition or Repository &/ or Registry implementation RFPs in OMG framework. How does

implementation funding model work in OMG?

Leo Obrst: Question to Evan Wallace: Would a conceptual model -> ontology (logical theory) translation service

be desired (e.g., along the line of ODM), and an ontology -> conceptual model translation service,

for an OOR?

JohnLMcCarthy: Q for Bill Bug: slide 9 mentions reuse and coordination with other health semantic info

efforts; is there any specific relationship to semantics in the National Cancer

Institute (NCI) Enterprise Vocabulary Services (EVS)?

Peter P. Yim: Question to JohnLMcCarthy: what "services" are available after a certain ontological artifact is

"loaded" into XMDR now ... is it consistent across different artifacts?" which I assume the answer

is "no." the real question is how are the XMDR folks trying to address that?

Kevin Keck: @PeterYim: A partial answer is, that the API supports text search and SPARQL query of the

registry: https://xmdr.lbl.gov/mediawiki/index.php/Core_APIs

Kevin Keck: @PeterYim: But in a broader sense, another "service" the registry provides is a metamodel

for description of shared and related meanings, both between ontologies and between ontologies

and data.

JohnLMcCarthy: @PeterYim: to add to Kevin's response, the text and SPARQL query interfaces treat loaded

artifacts consistently, in the sense that users can specify queries restricted to particular

metadata attributes that are used to characterize the artifacts in a consistent way. When we

load metadata (including the individual concept components of ontologies), each component gets

mapped into a particular class and attribute of the underlying metamodel.

Leo Obrst: Question to JohnLMcCarthy: How come it took so long to load Omega? What format was it in: OWL, etc.?

A week: 4 million files, so ~250,000/24 hrs? Is this a limitation of the incoming ontology format

or an issue with XMDR? How does this compare, e.g., with various RDF triple stores?

Kevin Keck: @LeoObrst: the issue was the engine we've been using to support SPARQL, namely Jena. We have

since mitigated this by using Jena differently (grouping files into much larger models in the

Jena store).

Michelle Raymond: For Evan Wallace (then other panelists): What are your requirements for (recommendations

for) the ontology repository architecture to best aid in inclusion of support material for

both the stored "Ontology(ies)" and the "Ontology(ies)" inter-relations? Example in

standards/schema: In working with BPMN, XPDL, BPEL ... (BPMD) - the issues haven't been in

the viability of usage (i.e. schemas can be extended, instances can be generated, they tie

together...). The issues have been lack of explanatory documentation, cookbooks of good

usage examples and libraries, (the things that aid in adoption of the standards.)

Leo Obrst: Question to Peter Benson: Given yesterday's story about nuclear missile detonators being

delivered to Taiwan, rather than the helicopter batteries they were supposed to be: how

can ontologies and an OOR assist in preventing this kind of logistics snafu in the future?

Peter Benson: answer to Leo Obrst: I suspect that the problem was a disconnect between the data and the

physical object that could be solved by embedding identifiers in objects and resolving the

identifiers to metadata from the authoritative source i.e. the manufacturer. This process

is used in MSDS where a manufacturer must make available an MSDS for every chemical product

they supply.

Peter Benson: correction I meant to say identifiers to master data

Ravi Sharma: Q for Dr. KenBaclawski. From this varied set of ontologies in allied disciplines, unless

we want to overload search engines with SPARQL type Queries, we need to either map namespaces

and concepts that are equivalent among ontoloies or look for other efficiencies in IT tools?

Ken Baclawski: In response to RaviSharma. The mappings are often quite complicated. Species and genus

names change over time in many ways, both the classification and the terminology. There

are also several competing taxonomies. One also has many inconsistencies among the ontologies

that have to be resolved.

JohnLMcCarthy: Q for Rex Brooks: XMDR has tried to represent metadata (including concepts) in a way that

conforms to both an XML Schema and a corresponding OWL spec. We wanted to generate one

from the other, but that was a challenge. Does ebXML generate one from the other, or are

they more loosely linked?

Rex Brooks: I wish that were true John. However, the closest I've been able to get is with XMI and that

is not especially faithful to either specification.

Rex Brooks: We are specifically asking for jurisdictions using EDXL use XMDR to create their own "citable"

lists for things like organisational roles, events types, equipment, etc.

Rex Brooks: What we are planning to do is to make our own specific mappings and publish them along with

the specification representations themselves.

Peter P. Yim: Q for Bill Bug, Ken Baclawski, Son Doan (and Suzi Lewis, Chris Chute, Mark Musen ... etc. if they are on this call too)

... how do you see the OOR effort help "normalize" work that among all these related work in

the biomedical informatics domain?

Ken Baclawski: Response to PeterYim. Can you clarify what "normalize" means?

Ravi Sharma: Q for RexBrooks. How do you use decision rules if intended resources are not available?

especially for the last slide shown, I can not open it.

Son Doan: Q for Dr. KenBaclawski. I has a small question about Environmental ontology (EnvO) and

Geo-location instance hierarchy (Gaz). Are they public and how we can access to them ? Thanks.

Ken Baclawski: Response to SonDoan. Both are public. I will make links available.

Michelle Raymond: For Bill Bug: How do the "users' needs" lead to adding relationship's accross taxonomies? -

Question based on paraphrased statement, "Given the multiple taxonomies, the relationships

are added - as driven by what the user community expresses as a need.", when speaking on

slide 11 titled 'Objective: represent complex neuroscience domains: Using shared

community ontologies'

Ann Wrightson: Complementary question to Michelle's, relating to discussion on the [Quality] list: Do

participants here have criteria for ontology characteristics that could or should admit

or exclude an ontology from an OOR?

Leo Obrst: Question to all: What is the most important service that an OOR could provide to you, as a

content provider? What is the next most important? and the next? ... namely the top 3 services.

(partially transcribed.)

Ann Wrightson: Answer to Leo: a) enabling me to know what ontology-analysis work has already been done

in a knowledge-domain (eg in which I have a new project) irrespective of access rules etc;

b) characteristics of these existing efforts that enable me to evaluate their potential

utility and cost of use/implementation

Peter Benson: A to Leo Obrst: 1. Protection from claims of "joint work" 2. Mapping 3. Persistance.

Taken together beyond unambigious basically data portability and data preservation

Son Doan: Answer to LeoObrst. I think the most important service as content provider is how to

control the content of ontology. The next is mechanism to allow verify it.

Evan Wallace (transcribed): Answer to Leo. (1) persistence (availability), (2) maintenance,

and (3) support for discovery

Peter P. Yim (transacribed): Answer to Leo. ... I guess that will have to be the basics in "open, "ontology" and "repository"

(1) that the OOR being *truly* "open",

(2) that it does serve *all* sorts of ontological artifacts (not just some, and not others), and

(3) that it does provide a *high available* persistent store for those artifacts.

Ken Baclawski: A to Leo: It is hard to decide which of the requirements is the most important. The ability

to browse, query and make inferences across several heterogeneous ontologies efficiently is

certainly one of the most important. We can do this now to some degree, but the protocols

and formats differ and require ad hoc processing.

Son Doan: Additional to Leo. We are developing the Bio Caster ontology of infectious disease. There are

some experts like epidemiologists, linguists, and anthropologists in US, Japan, Thai, etc involved.

For our case it is important to collaborate with others. I think CODS is quite useful. (Thank you

very much to Peter P. Yim for hosting our ontology). Also I have a small comment about infrastructure

that it would best if it is faster. For our case it takes long time to open ontology.

Ken Baclawski: Let me second Son's point. The users lose patience with an ontology based retrieval if it

does not have good performance.

Peter P. Yim: to Doan -- performance (on the load time for multiuser protege) issue duly noted. In fact,

that was a compromise on the part of the protege team to get runtime performance ... I believe

some significant improvements is on the way (from the Protege team)

Michelle Raymond: For online discussion thread: Given that we are noting as different "levels"

- Dictonary, Taxonomy, Ontology, Ontology+, Ontology++, ... is there a different way

to manage these within the repository where their "handling" and placement are appropriate

for that level? or are all levels just "files" of various quality vectors and should

be handled the same?

Ken Baclawski: To Michelle: While it might be useful for the repository to use different strategies internally,

it would not be a good idea for the interface to have diversity. That is one of the problems we

now have and that the OOR should help solve.

Ann Wrightson: Question, relating to discussion on the [Quality] list: Do participants here have criteria

for ontology characteristics that could or should admit or exclude an ontology from an OOR?

Ravi Sharma: Response to Peter Benson, there are case based reasoning CBR tools for navigating the FAQs

to right professional level of curiosity that can be plugged with search and query tools.

This would satisfy and provide answers at appropriate professional levels including the

filtering of amateurs' questions at starting levels.

Leo Obrst: Question to Rex Brooks: I am involved in an event management framework effort which is trying to

develop a set of ontologies for emergency events. It sounds like EDXL could greatly help in this:

where can I get more information? Is there an EDXL ontology or set of ontologies?

Rex Brooks: Answer to Leo: We are working on this now. As of now we don't have an ontology for this.

I can get more information for you by next week.

Rex Brooks: We are tasking ourselves with developing an EDXL-specific ontology, but we will need to include

the work of others: ISCRAM, EIC, DHS, NIEM, DNDO, and several European and Asian communities

and organisations as well.

Rex Brooks: Perhaps we can discuss this offline, Leo?

Todd Schneider (previously anonymous1): I would suggest that 'good' engineering practices should be employed

in building ontologies. So that backing evidence or requirements should always be part of

the ontology: DOCUMENTATION.

Todd Schneider: Another point associated with 'documentation'. It seems to be that many people think that

the use of ontologies provides a well-founded (i.e. no infinite descending chains) basis

for knowledge representation. I don't see that the use of ontologies provides this 'attribute'.

If I'm wrong, please let me know (it's happened before). If not, then rigorous documentation

is vital. And documentation should include both references and design decisions (formalized

if possible). This sort of information will be/is crucial when it comes time to mediate different

terminologies for the same domain.

Peter Benson: Who was asking about UDEF?

Peter P. Yim: to Peter Benson, it was Thomas Brunner that was asking JohnLMcCarthy about UDEF and ISO 11179, to which

both I and Frank Olken responded.

Audio Recording of this Session

  • To download the audio recording of the session, click here
    • the playback of the audio files require the proper setup, and an MP3 compatible player on your computer.
  • Conference Date and Time: 27-Mar-2008 10:46am~1:26pm PDT
  • Duration of Recording: 2 Hour 32 Minutes
  • Recording File Size: 17.4 MB (in mp3 format)
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Join us at part 2 of 2 of this OOR-Panel Discussion - see: ConferenceCall_2008_04_03 !



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