ConferenceCall 2009 07 30

= 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. CarlosRueda, Mr. PaulAlexander & 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

 * Abstract
 * Our panel's prepared slides can be accessed by clicking on each of the title links below:
 * Slides: . [ 0-chair ] . [ 1-Rueda/Alexander/Graybeal ] . [ 2-Dean ] . [ 3-Granite ] . [ 4-Garcia ] . [ 5-Baclawski ]
 * [ Audio Recording of the session ] (mp3)
 * [ Transcript of the online chat session ] during the panel discussion
 * Resources

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
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Attendees

 * Registered attendees:
 * NatashaNoy
 * CarlosRueda
 * PaulAlexander
 * JohnGraybeal
 * AlexGarcia
 * StephenGranite
 * KenBaclawski
 * MichaelGruninger
 * MikeDean
 * MarkMusen
 * PeterYim
 * LeoObrst
 * BartGajderowicz
 * BrandNiemann
 * RoyRoebuck
 * MichaelDorf
 * SteveRay
 * ArturoSanchez
 * PavithraKenjige
 * RaviSharma
 * MalaMehrotra
 * My Coyne (Bioinformatics Consultant for NDAR/NIH)
 * StuartTurner
 * TomRuss
 * BobbinTeegarden
 * RexBrooks
 * ElgarPichler
 * JerrySmith
 * GaryBergCross
 * DougHolmes
 * Randy Kerber (Sandpiper Software)
 * KurtConrad
 * PatCassidy
 * ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail  so that we can reserve enough resources to support everyone's participation. ...
 * ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * ToddSchneider
 * KatherineGoodier

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: NatashaNoy - [ opening slides ]


 * Here are the abstracts of the briefings from our panelists that will seed our discussion:


 * "MMI Ontology Registry and Repository" - by CarlosRueda, PaulAlexander & JohnGraybeal - [ 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 MikeDean - [ 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 Prot¨¦g¨¦ 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 KenBaclawski - [ 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 MichaelGruninger - [ 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:

 * NCBO BioPortal project sites
 * OpenOntologyRepository - homepage for the OOR initiative - http://OpenOntologyRepository.org
 * our first sandbox instance of OOR - http://oor-01.cim3.net/ (currently still on the BioPortal v2.0 revision level)
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development
 * UML-EA diagrams on the recently released BioPortal (v1016 of Jul-2009) system - http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_ver1016_UML-EA_Model--NCBO_ToddSchneider_20090729a/BioPortal_v1016_Jul2009_HTML/
 * from the two recent Ontolog-OOR panel sessions:
 * ConferenceCall_2009_07_16
 * ConferenceCall_2009_07_30
 * Join us at the [ oor-forum ] listserv. See message archive at - http://ontolog.cim3.net/forum/oor-forum/
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 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-dev ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

Agenda
1. Opening by session Chair (NatashaNoy)

2. Briefings from Panelists -- CarlosRueda et al., StephenGranite, AlexGarcia, KatherineGoodier, KenBaclawski, MichaelGruninger & MikeDean

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.)

PeterYim: Welcome to: Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009

Title: BioPortal and related Ontology Repository Implementations and Development

Session Chair: Dr. NatashaNoy (Stanford)

Panelists:


 * Dr. CarlosRueda, Mr. PaulAlexander & Mr. JohnGraybeal (MBARI) - "MMI Ontology Registry and Repository"
 * Mr. MikeDean (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"
 * Professor KenBaclawski (Northeastern) - "OOR at Northeastern"
 * Professor MichaelGruninger (Toronto) - "Common Logic Ontology Repository" (in absentia)

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

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

anonymous morphed into Randy Kerber

anonymous1 morphed into RexBrooks

anonymous morphed into StuartTurner

anonymous morphed into MichaelDorf

anonymous1 morphed into [[MyCoyne]]

anonymous morphed into KurtConrad

anonymous morphed into ArturoSanchez

anonymous morphed into StephenGranite

anonymous1 morphed into AlexGarcia

anonymous morphed into PavithraKenjige

PaulAlexander: The BioPortal GUI deployment document I was referring to is located here: http://www.bioontology.org/wiki/images/3/32/Bioportal_GUI_Deployment.doc

RaviSharma: MikeDean, What is the OMV, ontology metadata view? based on what?

AlexGarcia: OMV = ontology metadata vocabulary

JohnGraybeal: Ontology Metadata Vocabulary, a vocabulary which provides a particular set of metadata relevant to ontologies.

PeterYim: @ RaviSharma - see PeterHaase's OMV presentation at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2008_04_10#nid1D5E

RaviSharma: 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?

RaviSharma: 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...

RaviSharma: Alex- Can this be used for Concept Matching?

AlexGarcia: yes it can

RaviSharma: 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?

RaviSharma: 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: @ RaviSharma - 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

JohnGraybeal: 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....

PeterYim: 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?

JohnGraybeal: 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?

CarlosRueda: @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)

ArturoSanchez: 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 ...

ArturoSanchez: OOPS ... sorry ... offline?

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

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

RaviSharma: Ken - Why are we not connecting repository metadata to domain specific ontologies semantically? at least through the Vocabularies and or Terms?

anonymous morphed into TomRuss

RaviSharma: Ken - I guess I would like to get clarity on "Annotates" legend in slide 4 - does that mean a marker or collection?

RexBrooks: 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?

PeterYim: 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)

JohnGraybeal: @ PeterYim -- 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.

JohnGraybeal: 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".)

RaviSharma: Rex- do you mean orchestration or SOAF?

RexBrooks: 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.

RaviSharma: Rex- very interessting, will you be creating orchestration among services based on semantic or ontology based rules?

RexBrooks: 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.

RexBrooks: Not orchestrations, which have no flexibility because the services are controlled/hard-wired into rigid workflows.

MikeDean: 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?

BobbinTeegarden: Any such thing as REST nesting?

RexBrooks: But yes, definitely ontology-based rules. We are working on this in Emergency Data Exchange Language Reference Information Model.

RaviSharma: Rex - I am interested in understading how SOA relates to ontologies, not only as a tool but as solution architecture?

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

RexBrooks: 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 ]

RexBrooks: We have to get the reference architecture in place in order to get to sound solution architectures.

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

RaviSharma: 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.

PaulAlexander: I think this raises good questions, will OOR be handling separate releases, bug tracking, feature requests, etc?

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

RaviSharma: Rex- along with this the translation or inter conversion (interoperation) standards such as XMI version upgrades become key? do you agree?

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

PeterYim: 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

PeterYim: eventually, when we have large number of users, we will have a [oor-users] listserv, I bet

PeterYim: I will create this [oor-users] listserv before mid-Sep (that is when classes start for Ken's student

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

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

PaulAlexander: Especially if OOR releases will be separate from BioPortal releases. We'll have our own issues to deal with.

RexBrooks: 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.

RaviSharma: Appreciate and value your approach Rex.

RexBrooks: Will be in touch.

RexBrooks: Your opinions are valued.

RexBrooks: highly.

RaviSharma: Rex- with these efforts i would think that we will get best of promise of SOA and Model Driven architectures both!

RexBrooks: That's one of my main goals.

RexBrooks: Extra cycles?

RexBrooks: Is that related to that thing called vacation?

RaviSharma: 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.

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

RexBrooks: Getting past class diagrams is pulling teeth.

RaviSharma: 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?

RexBrooks: 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.

RaviSharma: Thanks everyone

RexBrooks: Thanks indeed everyone!

PaulAlexander: Thank you all, look forward to next time.

RaviSharma: 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!

PeterYim: 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?

PeterYim: great session ... thank you Natasha, thanks to all panelists and to everyone for your participation and contribution!

PeterYim: session adjourned 12:30pm PDT


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Audio Recording of this Session

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 * Conference Date and Time:	30-Jul-2009 10:38am~12:26pm PDT
 * Duration of Recording:	1 Hour 48 Minutes
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