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Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009     (1)

Title: BioPortal and related Ontology Repository Implementations and Development     (1A)

Session Chair: Dr. NatashaNoy (Stanford) - [ opening slides ]     (1B)

Panelists:     (1C)

Archives     (1J)

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  • Discussions and Q & A:     (1K6)
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  • 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.     (1K10)

Attendees     (1L)

Abstract     (1M)

Title: BioPortal and related Ontology Repository Implementations and Development     (1M1)
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 ]     (1M2)
Here are the abstracts of the briefings from our panelists that will seed our discussion:     (1M3)
  • "MMI Ontology Registry and Repository" - by Carlos Rueda, Paul Alexander & John Graybeal - [ slides ]     (1M4)
    • 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.     (1M4A)
  • " OOR Progress, Federation, and Other Thoughts" - by Mike Dean - [ slides ]     (1M5)
    • 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.     (1M5A)
  • "Utilizing NCBO Tools to Develop & Use an ECG Ontology" - by StephenGranite - [ slides ]     (1M6)
    • 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 (     (1M6A)
  • "The Ontology Repository for Assistive Technologies, ORATE" - by AlexGarcia - [ slides ]     (1M7)
    • Abstract: We are currently extending Bioportal and Prot��g�� 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.     (1M7A)
  • "OOR at Northeastern" - by Ken Baclawski - [ slides ]     (1M8)
    • 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.     (1M8A)
  • "Common Logic Ontology Repository" - by Michael Grüninger - [ slides ]     (1M9)
    • 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.     (1M9A)

Resources     (1O)

1. Opening by session Chair (NatashaNoy)     (1O9A)

2. Briefings from Panelists -- Carlos Rueda et al., StephenGranite, AlexGarcia, Katherine Goodier, Ken Baclawski, Michael Grüninger & Mike Dean     (1O9B)

3. Q & A and Open Discussion (All) -- please refer to process above     (1O9C)

4. Summary and Next Steps (NatashaNoy)     (1O9D)

Proceedings     (1P)

Please refer to the archives above     (1P1)

IM Chat Transcript captured during the session    (1P2)

(The chat transcript below has been lightly edited to help improve on clarity of the conversation.)     (1P2A)

Peter P. Yim: Welcome to: Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009     (1P2B)

Title: BioPortal and related Ontology Repository Implementations and Development     (1P2C)

Session Chair: Dr. Natasha Noy (Stanford)     (1P2D)

Panelists:     (1P2E)

  • Mr. StephenGranite (Johns Hopkins) - "Utilizing NCBO Tools to Develop & Use an ECG Ontology"     (1P2H)
  • Dr. AlexGarcia (Bremen) - "The Ontology Repository for Assistive Technologies, ORATE"     (1P2I)

anonymous morphed into Randy Kerber     (1P2N)

anonymous1 morphed into Rex Brooks     (1P2O)

anonymous morphed into Stuart Turner     (1P2P)

anonymous morphed into MichaelDorf     (1P2Q)

anonymous1 morphed into MyCoyne     (1P2R)

anonymous morphed into Kurt Conrad     (1P2S)

anonymous morphed into Arturo Sanchez     (1P2T)

anonymous morphed into StephenGranite     (1P2U)

anonymous1 morphed into AlexGarcia     (1P2V)

anonymous morphed into Pavithra Kenjige     (1P2W)

Paul Alexander: The BioPortal GUI deployment document I was referring to is located     (1P2X)

Ravi Sharma: Mike Dean, What is the OMV, ontology metadata view? based on what?     (1P2Z)

AlexGarcia: OMV = ontology metadata vocabulary     (1P2AA)

John Graybeal: Ontology Metadata Vocabulary, a vocabulary which provides a particular set of metadata     (1P2AB)

relevant to ontologies.     (1P2AC)

Peter P. Yim: @ Ravi Sharma - see PeterHaase's OMV presentation     (1P2AD)

Ravi Sharma: John,Peter and Alex Thanks. Mike What is the end objective, at least like vocab. term, owl     (1P2AF)

or RDF links and integration towards executable ontologies?     (1P2AG)

Ravi Sharma: already asked question on voiceline. thanks.     (1P2AH)

AlexGarcia: not sure, the OMV just describes some basic features of an ontology. for instance was a     (1P2AI)

methodology followed? there are some basic very basic versioning descriptive features as well...     (1P2AJ)

Ravi Sharma: Alex- Can this be used for Concept Matching?     (1P2AK)

AlexGarcia: yes it can     (1P2AL)

Ravi Sharma: Stephen - Can you go beyond synthetic ECG (Novel) that have physical occurence in actual     (1P2AM)

patient databses that then can be matched to preexisting trends before severe events such as     (1P2AN)

fibrillations occur?     (1P2AO)

Ravi Sharma: Stephen - how will you find reliability of synthetic waveforms, by any occurences of such     (1P2AP)

forms in exisiting databases or during trace of events relating to cardi vascular abnormalities -     (1P2AQ)

various grades     (1P2AR)

StephenGranite: @ Ravi Sharma - that is part of the plan of the CVRG itself. The ECGs visualized are     (1P2AS)

actual subject ECGs, derived from primary de-identified ECG data files. We have referenced and placed     (1P2AT)

the Minnesota Code Classification System concepts in the ECG Ontology, so that annotations to the     (1P2AU)

waveforms by cardiologists can utilize a standardized annotation method. These annotations are     (1P2AV)

persisted at the current time in a relational database for prototype purposes, but we have an object     (1P2AW)

model with future plans for XML database persistence. Within the CVRG, we have several data services     (1P2AX)

that span relational and XML databases. Information on those can be found in the CVRG wiki     (1P2AY)

AlexGarcia: users are able to compare, visually, up to 3 ontologies     (1P2AAA)

John Graybeal: why is a SOAP interface important to the OOR registry?     (1P2AAB)

AlexGarcia: the idea is simple, via P4 users query several repositories at the same time. they are then     (1P2AAC)

presented with some basic info for those ontologies part of the resulting set. users then select those     (1P2AAD)

they would like to look in more detail and then they can visually inspect them.     (1P2AAE)

AlexGarcia: ok, thanks everybody but I will be running out of battery any time soon....     (1P2AAF)

Peter P. Yim: Ref. Ken's plan to use the OOR for their students ... question for NCBO folks, any idea when     (1P2AAG)

will we start running into scalability issues?     (1P2AAH)

John Graybeal: has there been any discussion of how to integrate all the student feedback for OOR's     (1P2AAI)

registry with the activities of the BioPortal (and other) registry teams?     (1P2AAJ)

Carlos Rueda: @NatashaNoy & BioPortal team: are there/will there be any schema for facilititaing the     (1P2AAK)

client-server communication using the REST services? (something similar to SOAP, but for REST)     (1P2AAL)

Arturo Sanchez: Question for Ken: to what NSF program did you submit the DataNet proposal and if you can     (1P2AAM)

elaborate on it and why did they find it to be not a good match ...     (1P2AAN)

Arturo Sanchez: OOPS ... sorry ... offline?     (1P2AAO)

Ken Baclawski: Arturo: Either send me email or attend the session next week.     (1P2AAP)

Arturo Sanchez: @Ken: Thank you. I'll follow up with an email.     (1P2AAQ)

Ravi Sharma: Ken - Why are we not connecting repository metadata to domain specific ontologies     (1P2AAR)

semantically? at least through the Vocabularies and or Terms?     (1P2AAS)

anonymous morphed into Tom Russ     (1P2AAT)

Ravi Sharma: Ken - I guess I would like to get clarity on "Annotates" legend in slide 4 - does that mean     (1P2AAU)

a marker or collection?     (1P2AAV)

Rex Brooks: For Natasha: Is there any plan to provide a SOAP-based interface that would allow the     (1P2AAW)

BioPortal to be included in a structured SOA Service aggregation?     (1P2AAX)

Peter P. Yim: Question for the panel (or the participants) ... Is anyone already doing, or have anyone     (1P2AAY)

thought of doing, generic front ends to allow xml schemas and DTDs, maybe even database schemas to be     (1P2AAZ)

translated and accepted into the OOR? ... this, preumably, will expand the OOR's utility tremendously     (1P2AAAA)

(especially when a mapping service is available)     (1P2AAAB)

John Graybeal: @ Peter P. Yim -- A lot of projects are working on the kind of conversions you describe, some     (1P2AAAC)

with impressive success I think. Unfortunately don't have links in hand, but I think it is clearly going     (1P2AAAD)

this direction.     (1P2AAAE)

John Graybeal: Unfortunately I will have to excuse myself in a few minutes. Thanks all for the     (1P2AAAF)

discussion/presentations. (I will listen later for the answer to my question about "integrating feedback     (1P2AAAG)

and modifications back to BioPortal/other developments".)     (1P2AAAH)

Ravi Sharma: Rex- do you mean orchestration or SOAF?     (1P2AAAI)

Rex Brooks: Actually I mean structured choreographies that would allow the future resources I expect to     (1P2AAAJ)

be included in the BioPortal to be available in Emergencies where an ontology of symptoms plotted     (1P2AAAK)

against diagnoses and outcomes could be consulted in an emergency.     (1P2AAAL)

Ravi Sharma: Rex- very interessting, will you be creating orchestration among services based on semantic     (1P2AAAM)

or ontology based rules?     (1P2AAAN)

Rex Brooks: For my purposes, I can use REST for one-off needs, but for pre-arranging aggregations of     (1P2AAAO)

services, I suspect SOAP may be easier to allow policy-based aggregations.     (1P2AAAP)

Rex Brooks: Not orchestrations, which have no flexibility because the services are controlled/hard-wired     (1P2AAAQ)

into rigid workflows.     (1P2AAAR)

Mike Dean: I recall that WSDL can express both SOAP and REST. Are there better standards now for a     (1P2AAAS)

formal specification of services that can support both?     (1P2AAAT)

Bobbin Teegarden: Any such thing as REST nesting?     (1P2AAAU)

Rex Brooks: But yes, definitely ontology-based rules. We are working on this in Emergency Data Exchange     (1P2AAAV)

Language Reference Information Model.     (1P2AAAW)

Ravi Sharma: Rex - I am interested in understading how SOA relates to ontologies, not only as a tool but     (1P2AAAX)

as solution architecture?     (1P2AAAY)

Rex Brooks: These would be somewhat flexible, heuristics based decision trees.     (1P2AAAZ)

Rex Brooks: That's what we've been having weekly knock-down drag-outs over for more than 3 years in the     (1P2AAAAA)

OASIS SOA Reference Architecture Subcommittee*. We're almost ready for the second 60-Day Public Review.     (1P2AAAAB)

[ *OASIS SOA Reference Architecture SC is part of the SOA Reference Model Technical Committee ]     (1P2AAAAC)

Rex Brooks: We have to get the reference architecture in place in order to get to sound solution     (1P2AAAAD)

architectures.     (1P2AAAAE)

Rex Brooks: But we are aligning with OMG SoaML and The Open Group SOA Ontology.     (1P2AAAAF)

Ravi Sharma: Rex - I will go to OASIS SOA and study it, as activie participant in Elissa's efforts on OMG ODM I am     (1P2AAAAG)

still grappling on SOAML integration with OWL and UML.     (1P2AAAAH)

Paul Alexander: I think this raises good questions, will OOR be handling separate releases, bug     (1P2AAAAI)

tracking, feature requests, etc?     (1P2AAAAJ)

Rex Brooks: Yup, we're all working on integrating XML, RDF, OWL and UML. Not easy.     (1P2AAAAK)

Ravi Sharma: Rex- along with this the translation or inter conversion (interoperation) standards such as     (1P2AAAAL)

XMI version upgrades become key? do you agree?     (1P2AAAAM)

Rex Brooks: Yes, Ravi. We were talking about that this morning.     (1P2AAAAN)

Peter P. Yim: Natasha suggested - (for OOR sandbox) report technical/support issues to the [oor-dev] listserv:     (1P2AAAAO) ... and (for BioPortal) to:     (1P2AAAAP)

Peter P. Yim: eventually, when we have large number of users, we will have a [oor-users] listserv, I bet     (1P2AAAAQ)

Peter P. Yim: I will create this [oor-users] listserv before mid-Sep (that is when classes start for     (1P2AAAAR)

Ken's student     (1P2AAAAS)

Ravi Sharma: Rex - please keep me on your email lists on interoperable standards and emerging SOA ones.     (1P2AAAAT)

Paul Alexander: I would really like to see something like Google Code or Gforge available for OOR     (1P2AAAAU)

Paul Alexander: Especially if OOR releases will be separate from BioPortal releases. We'll have our own     (1P2AAAAV)

issues to deal with.     (1P2AAAAW)

Rex Brooks: In the OASIS EDXL-RIM SC we're building the model behind the scenes and as the technical     (1P2AAAAX)

foundation for the specifications we will be producing, combining the use of Protege and Enterprise     (1P2AAAAY)

Ravi Sharma: Appreciate and value your approach Rex.     (1P2AAAAAA)

Rex Brooks: Will be in touch.     (1P2AAAAAB)

Rex Brooks: Your opinions are valued.     (1P2AAAAAC)

Ravi Sharma: Rex- with these efforts i would think that we will get best of promise of SOA and Model     (1P2AAAAAE)

Driven architectures both!     (1P2AAAAAF)

Rex Brooks: That's one of my main goals.     (1P2AAAAAG)

Rex Brooks: Is that related to that thing called vacation?     (1P2AAAAAI)

Ravi Sharma: Rex- Great, very worthwhile goal. hope the participants also see it as important, of course     (1P2AAAAAJ)

partly demonstrated in the work today, but Services were more of enablers on OOR and i am thinking that     (1P2AAAAAK)

Solutions use both SOA and Ontology as integrated capabilities to make each other happen in a meaningful     (1P2AAAAAL)

Rex Brooks: IN EDXL-RIM yes, in SOA-RM-RA not so much.     (1P2AAAAAN)

Rex Brooks: Getting past class diagrams is pulling teeth.     (1P2AAAAAO)

Ravi Sharma: Rex- I agree, with attraction of MOF how do we go beyond BPM type UML2 i.e. user friendly     (1P2AAAAAP)

constructs and ontological frameworks that integrate?     (1P2AAAAAQ)

Rex Brooks: hmmn, good question. I don't have a ready answer. I'm still trying to get more formal UML 2     (1P2AAAAAR)

accepted in the standards process. Even though its not new, it tends to intimidate people.     (1P2AAAAAS)

Rex Brooks: Thanks indeed everyone!     (1P2AAAAAU)

Paul Alexander: Thank you all, look forward to next time.     (1P2AAAAAV)

Ravi Sharma: Rex- yes it does but conceptually i think it should be friendly in notation like BPMN2 and     (1P2AAAAAW)

then we can remove some of the inhibitions, I am also not up dated on all profiles in UML!     (1P2AAAAAX)

Peter P. Yim: inspired by Paul's remark just now ... we should start addressing the "Gatekeeping" issues     (1P2AAAAAY)

... which we have ignored in the OOR-sandbox, so far ... but as we are near to deployment the OOR-     (1P2AAAAAZ)

production instance, that would be one thing that needs to be in place ... discussion today? .. or next     (1P2AAAAAAA)

Peter P. Yim: great session ... thank you Natasha, thanks to all panelists and to everyone for your     (1P2AAAAAAC)

participation and contribution!     (1P2AAAAAAD)

Peter P. Yim: session adjourned 12:30pm PDT     (1P2AAAAAAE)

  • Further Question & Remarks - please post them to the [ oor-forum ] listserv     (1P2AAAAAAF)
    • if you are already subscribed, post to <oor-forum [at]>     (1P2AAAAAAF1)
    • (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]> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.     (1P2AAAAAAF2)

Audio Recording of this Session     (1Q)

For the record ...     (1Q6)

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