Actions

Ontolog Forum

Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009

Title: BioPortal and related Ontology Repository Implementations and Development

Session Chair: Dr. NatashaNoy (Stanford) - [ opening slides ]

Panelists:

  • Dr. Carlos Rueda, Mr. Paul Alexander & Mr. JohnGraybeal (MBARI) - "MMI Ontology Registry and Repository" - [ slides ]
  • Mr. MikeDean (BBN) - " OOR Progress, Federation, and Other Thoughts" - [ slides ]
  • Mr. StephenGranite (Johns Hopkins) - "Utilizing NCBO Tools to Develop & Use an ECG Ontology" - [ slides ]
  • Dr. AlexGarcia (Bremen) - "The Ontology Repository for Assistive Technologies, ORATE" - [ slides ]
  • Professor KenBaclawski (Northeastern) - "OOR at Northeastern" - [ slides ]
  • Professor MichaelGruninger (Toronto) - "Common Logic Ontology Repository" - [ slides ] (in absentia)

Archives

Conference Call Details

  • Date: Thursday, July 30, 2009
  • Start Time: 10:30am PDT / 1:30pm EDT / 7:30pm CEST / 6:30pm BST / 17:30 UTC
  • Expected Call Duration: ~2.0 hours
  • Dial-in Number:
    • from a US telephone (US): +1-218-844-8060 (domestic long distance cost will apply)
    • When calling in from a phone, use Conference ID: "4389979#"
    • from Europe, call:
      • Austria 0820-4000-1577
      • Belgium 070-35-9992
      • France 0826-100-280
      • Germany 01805-00-7642
      • Ireland 0818-270-037
      • Italy 848-390-179
      • Spain 0902-886-056
      • Switzerland 0848-560-327 or 0848-414-110
      • UK 0870-738-0765
    • callers from other countries please dial into either one of the US or European numbers
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • view-only password: "ontolog"
    • 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.
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides above and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • Discussions and Q & A:
    • (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when a presentation is in progress. To un-mute, press "*3"
    • You can type in your questions or comments through the browser based chat session by:
    • or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20090730
      • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
    • (when everyone is muted) If you want to speak or have questions or remarks to make, please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)
    • thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ontolog_20090730@soaphub.org ... Handy for mobile devices!
  • Please note that this session will be recorded, and the entire proceedings including the audio archives are expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

Abstract

Title: BioPortal and related Ontology Repository Implementations and Development
This session will cover issues related to development efforts that are going into the BioPortal and the initial implementation of the OOR; particularly as it relates to software efforts as a contribution to the codebase of our first instance of the OOR that is built upon the NCBO BioPortal technology. - Chair: Natasha Noy - [ opening slides ]
Here are the abstracts of the briefings from our panelists that will seed our discussion:
  • "MMI Ontology Registry and Repository" - by Carlos Rueda, Paul Alexander & John Graybeal - [ slides ]
    • Abstract: We will share our technical approach and experience using NCBO BioPortal, both back- and front-end, as a supporting system for the MMI Ontology Registry and Repository. After briefly describing our driving requirements, we will show the main features and APIs provided by BioPortal that we use and also the additional mechanisms that were necessary to implement for more flexible access and manipulation of the registered ontologies as well as the integration of new modules.
  • " OOR Progress, Federation, and Other Thoughts" - by Mike Dean - [ slides ]
    • Abstract: I appreciate OOR progress to date. One of my interests in federation of registries/repositories. I'll present some thoughts on federating OOR with knoodl and Semantic MediaWiki+. I also have some thoughts and questions regarding how to best handle multi-file ontologies.
  • "Utilizing NCBO Tools to Develop & Use an ECG Ontology" - by StephenGranite - [ slides ]
    • Abstract: The CardioVascular Research Grid (CVRG) project uses emerging standards for describing diverse types of biomedical data. However, the medical community has no comprehensive ontology or data model in use at the current time to describe the most commonly collected biomedical time-series data type in modern health care, the electrocardiogram (ECG). To address this need, the CVRG team leads a Driving Biomedical Project for the National Center for Biomedical Ontologies (NCBO), using NCBO tools to develop an ECG ontology. To help in this process, the CVRG team developed a tool for searching NCBO managed ontologies to discover ECG-related concepts. The tool uses NCBO Representation State Transfer (REST) services. The tool appends discovered concepts to an OWL file containing the ontology. The user reviews the OWL file in Protégé and selects the concepts to be incorporated. The CVRG has also developed a Web 2.0 prototype to visualize and annotate ECG waveforms. The prototype uses the Google Web Toolkit (GWT) and its Visualization API. The prototype leverages the NCBO REST services real-time, retrieving an ontology concept and its definition, to insert into the annotation. Information on these tools is available through the CVRG Home Page (http://www.cvrgrid.org).
  • "The Ontology Repository for Assistive Technologies, ORATE" - by AlexGarcia - [ slides ]
    • Abstract: We are currently extending Bioportal and Protégé in order to support a specific community, assistive technologies. We are interested in two aspects: interoperability and collaboration. We are actively working on ontology engineering methodologies so that we can support the collaboration, facilitate the participation of domain experts and deliver ontologies that have some degree of interoperability. We are also interested in making a practical use of the e-connections idea, we see the mappings as baseline e-connections.
  • "OOR at Northeastern" - by Ken Baclawski - [ slides ]
    • Abstract: This is a report on some of the OOR activities at Northeastern University. They include (a) Research on OOR web service interfaces, (b) Integration of OOR with semantic wikis, (c) OOR testing activities; and the outlook, as more students will be able to participate in the upcoming Fall.
  • "Common Logic Ontology Repository" - by Michael Grüninger - [ slides ]
    • Abstract: This briefing introduces the COLORE project, which will construct a repository of Common Logic ontologies that will serve as a testbed for ontology evaluation and integration techniques, and that can support the design, evaluation, and application of ontologies in first-order logic.

Resources

Agenda

1. Opening by session Chair (NatashaNoy)

2. Briefings from Panelists -- Carlos Rueda et al., StephenGranite, AlexGarcia, Katherine Goodier, Ken Baclawski, Michael Grüninger & Mike Dean

3. Q & A and Open Discussion (All) -- please refer to process above

4. Summary and Next Steps (NatashaNoy)

Proceedings

Please refer to the archives above

IM Chat Transcript captured during the session

(The chat transcript below has been lightly edited to help improve on clarity of the conversation.)

Peter P. Yim: Welcome to: Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009

Title: BioPortal and related Ontology Repository Implementations and Development

Session Chair: Dr. Natasha Noy (Stanford)

Panelists:

  • Mr. Mike Dean (BBN) - " OOR Progress, Federation, and Other Thoughts"
  • Mr. StephenGranite (Johns Hopkins) - "Utilizing NCBO Tools to Develop & Use an ECG Ontology"
  • Dr. AlexGarcia (Bremen) - "The Ontology Repository for Assistive Technologies, ORATE"

Peter P. Yim: session page is at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_30

Peter P. Yim: slides are at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_30#nid204D

anonymous morphed into Randy Kerber

anonymous1 morphed into Rex Brooks

anonymous morphed into Stuart Turner

anonymous morphed into MichaelDorf

anonymous1 morphed into MyCoyne

anonymous morphed into Kurt Conrad

anonymous morphed into Arturo Sanchez

anonymous morphed into StephenGranite

anonymous1 morphed into AlexGarcia

anonymous morphed into Pavithra Kenjige

Paul Alexander: The BioPortal GUI deployment document I was referring to is located

here: http://www.bioontology.org/wiki/images/3/32/Bioportal_GUI_Deployment.doc

Ravi Sharma: Mike Dean, What is the OMV, ontology metadata view? based on what?

AlexGarcia: OMV = ontology metadata vocabulary

John Graybeal: Ontology Metadata Vocabulary, a vocabulary which provides a particular set of metadata

relevant to ontologies.

Peter P. Yim: @ Ravi Sharma - see PeterHaase's OMV presentation

at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2008_04_10#nid1D5E

Ravi Sharma: John,Peter and Alex Thanks. Mike What is the end objective, at least like vocab. term, owl

or RDF links and integration towards executable ontologies?

Ravi Sharma: already asked question on voiceline. thanks.

AlexGarcia: not sure, the OMV just describes some basic features of an ontology. for instance was a

methodology followed? there are some basic very basic versioning descriptive features as well...

Ravi Sharma: Alex- Can this be used for Concept Matching?

AlexGarcia: yes it can

Ravi Sharma: Stephen - Can you go beyond synthetic ECG (Novel) that have physical occurence in actual

patient databses that then can be matched to preexisting trends before severe events such as

fibrillations occur?

Ravi Sharma: Stephen - how will you find reliability of synthetic waveforms, by any occurences of such

forms in exisiting databases or during trace of events relating to cardi vascular abnormalities -

various grades

StephenGranite: @ Ravi Sharma - that is part of the plan of the CVRG itself. The ECGs visualized are

actual subject ECGs, derived from primary de-identified ECG data files. We have referenced and placed

the Minnesota Code Classification System concepts in the ECG Ontology, so that annotations to the

waveforms by cardiologists can utilize a standardized annotation method. These annotations are

persisted at the current time in a relational database for prototype purposes, but we have an object

model with future plans for XML database persistence. Within the CVRG, we have several data services

that span relational and XML databases. Information on those can be found in the CVRG wiki

(http://wiki.cvrgrid.org)

AlexGarcia: users are able to compare, visually, up to 3 ontologies

John Graybeal: why is a SOAP interface important to the OOR registry?

AlexGarcia: the idea is simple, via P4 users query several repositories at the same time. they are then

presented with some basic info for those ontologies part of the resulting set. users then select those

they would like to look in more detail and then they can visually inspect them.

AlexGarcia: ok, thanks everybody but I will be running out of battery any time soon....

Peter P. Yim: Ref. Ken's plan to use the OOR for their students ... question for NCBO folks, any idea when

will we start running into scalability issues?

John Graybeal: has there been any discussion of how to integrate all the student feedback for OOR's

registry with the activities of the BioPortal (and other) registry teams?

Carlos Rueda: @NatashaNoy & BioPortal team: are there/will there be any schema for facilititaing the

client-server communication using the REST services? (something similar to SOAP, but for REST)

Arturo Sanchez: Question for Ken: to what NSF program did you submit the DataNet proposal and if you can

elaborate on it and why did they find it to be not a good match ...

Arturo Sanchez: OOPS ... sorry ... offline?

Ken Baclawski: Arturo: Either send me email or attend the session next week.

Arturo Sanchez: @Ken: Thank you. I'll follow up with an email.

Ravi Sharma: Ken - Why are we not connecting repository metadata to domain specific ontologies

semantically? at least through the Vocabularies and or Terms?

anonymous morphed into Tom Russ

Ravi Sharma: Ken - I guess I would like to get clarity on "Annotates" legend in slide 4 - does that mean

a marker or collection?

Rex Brooks: For Natasha: Is there any plan to provide a SOAP-based interface that would allow the

BioPortal to be included in a structured SOA Service aggregation?

Peter P. Yim: Question for the panel (or the participants) ... Is anyone already doing, or have anyone

thought of doing, generic front ends to allow xml schemas and DTDs, maybe even database schemas to be

translated and accepted into the OOR? ... this, preumably, will expand the OOR's utility tremendously

(especially when a mapping service is available)

John Graybeal: @ Peter P. Yim -- A lot of projects are working on the kind of conversions you describe, some

with impressive success I think. Unfortunately don't have links in hand, but I think it is clearly going

this direction.

John Graybeal: Unfortunately I will have to excuse myself in a few minutes. Thanks all for the

discussion/presentations. (I will listen later for the answer to my question about "integrating feedback

and modifications back to BioPortal/other developments".)

Ravi Sharma: Rex- do you mean orchestration or SOAF?

Rex Brooks: Actually I mean structured choreographies that would allow the future resources I expect to

be included in the BioPortal to be available in Emergencies where an ontology of symptoms plotted

against diagnoses and outcomes could be consulted in an emergency.

Ravi Sharma: Rex- very interessting, will you be creating orchestration among services based on semantic

or ontology based rules?

Rex Brooks: For my purposes, I can use REST for one-off needs, but for pre-arranging aggregations of

services, I suspect SOAP may be easier to allow policy-based aggregations.

Rex Brooks: Not orchestrations, which have no flexibility because the services are controlled/hard-wired

into rigid workflows.

Mike Dean: I recall that WSDL can express both SOAP and REST. Are there better standards now for a

formal specification of services that can support both?

Bobbin Teegarden: Any such thing as REST nesting?

Rex Brooks: But yes, definitely ontology-based rules. We are working on this in Emergency Data Exchange

Language Reference Information Model.

Ravi Sharma: Rex - I am interested in understading how SOA relates to ontologies, not only as a tool but

as solution architecture?

Rex Brooks: These would be somewhat flexible, heuristics based decision trees.

Rex Brooks: That's what we've been having weekly knock-down drag-outs over for more than 3 years in the

OASIS SOA Reference Architecture Subcommittee*. We're almost ready for the second 60-Day Public Review.

[ *OASIS SOA Reference Architecture SC is part of the SOA Reference Model Technical Committee ]

Rex Brooks: We have to get the reference architecture in place in order to get to sound solution

architectures.

Rex Brooks: But we are aligning with OMG SoaML and The Open Group SOA Ontology.

Ravi Sharma: Rex - I will go to OASIS SOA and study it, as activie participant in Elissa's efforts on OMG ODM I am

still grappling on SOAML integration with OWL and UML.

Paul Alexander: I think this raises good questions, will OOR be handling separate releases, bug

tracking, feature requests, etc?

Rex Brooks: Yup, we're all working on integrating XML, RDF, OWL and UML. Not easy.

Ravi Sharma: Rex- along with this the translation or inter conversion (interoperation) standards such as

XMI version upgrades become key? do you agree?

Rex Brooks: Yes, Ravi. We were talking about that this morning.

Peter P. Yim: Natasha suggested - (for OOR sandbox) report technical/support issues to the [oor-dev] listserv:

oor-dev@ontolog.cim3.net ... and (for BioPortal) to: support@bioontology.org

Peter P. Yim: eventually, when we have large number of users, we will have a [oor-users] listserv, I bet

Peter P. Yim: I will create this [oor-users] listserv before mid-Sep (that is when classes start for

Ken's student

Ravi Sharma: Rex - please keep me on your email lists on interoperable standards and emerging SOA ones.

Paul Alexander: I would really like to see something like Google Code or Gforge available for OOR

Paul Alexander: Especially if OOR releases will be separate from BioPortal releases. We'll have our own

issues to deal with.

Rex Brooks: In the OASIS EDXL-RIM SC we're building the model behind the scenes and as the technical

foundation for the specifications we will be producing, combining the use of Protege and Enterprise

Architect.

Ravi Sharma: Appreciate and value your approach Rex.

Rex Brooks: Will be in touch.

Rex Brooks: Your opinions are valued.

Rex Brooks: highly.

Ravi Sharma: Rex- with these efforts i would think that we will get best of promise of SOA and Model

Driven architectures both!

Rex Brooks: That's one of my main goals.

Rex Brooks: Extra cycles?

Rex Brooks: Is that related to that thing called vacation?

Ravi Sharma: Rex- Great, very worthwhile goal. hope the participants also see it as important, of course

partly demonstrated in the work today, but Services were more of enablers on OOR and i am thinking that

Solutions use both SOA and Ontology as integrated capabilities to make each other happen in a meaningful

way.

Rex Brooks: IN EDXL-RIM yes, in SOA-RM-RA not so much.

Rex Brooks: Getting past class diagrams is pulling teeth.

Ravi Sharma: Rex- I agree, with attraction of MOF how do we go beyond BPM type UML2 i.e. user friendly

constructs and ontological frameworks that integrate?

Rex Brooks: hmmn, good question. I don't have a ready answer. I'm still trying to get more formal UML 2

accepted in the standards process. Even though its not new, it tends to intimidate people.

Ravi Sharma: Thanks everyone

Rex Brooks: Thanks indeed everyone!

Paul Alexander: Thank you all, look forward to next time.

Ravi Sharma: Rex- yes it does but conceptually i think it should be friendly in notation like BPMN2 and

then we can remove some of the inhibitions, I am also not up dated on all profiles in UML!

Peter P. Yim: inspired by Paul's remark just now ... we should start addressing the "Gatekeeping" issues

... which we have ignored in the OOR-sandbox, so far ... but as we are near to deployment the OOR-

production instance, that would be one thing that needs to be in place ... discussion today? .. or next

week?

Peter P. Yim: great session ... thank you Natasha, thanks to all panelists and to everyone for your

participation and contribution!

Peter P. Yim: session adjourned 12:30pm PDT

  • Further Question & Remarks - please post them to the [ oor-forum ] listserv
    • if you are already subscribed, post to <oor-forum [at] ontolog.cim3.net>
    • (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

Audio Recording of this Session

  • To download the 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: 30-Jul-2009 10:38am~12:26pm PDT
  • Duration of Recording: 1 Hour 48 Minutes
  • Recording File Size: 12.4 MB (in mp3 format)
  • suggestions:
    • its best that you listen to the session while having the respective presentations opened in front of you. You'll be prompted to advance slides by the speaker.
    • Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the archives of noteworthy past Ontolog events. (References on how to subscribe to our podcast can also be found there.)

For the record ...

How To Join (while the session is in progress)



Retrieved from "https://ontologforum.com/index.php?title=ConferenceCall_2009_07_30&oldid=1258"