ppy/chat-transcript_20090730c.txt


anonymous morphed into Randy Kerber

anonymous1 morphed into RexBrooks

anonymous morphed into StuartTurner

anonymous morphed into Michael Dorf

anonymous1 morphed into MyCoyne

PeterYim: Welcome to: Joint Ontolog-OOR Panel Discussion Session - Thu 30-July-2009    (1Y4T)

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

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

Panelists:    (1ZOT)

    * Dr. CarlosRueda, Mr. PaulAlexander & Mr. JohnGraybeal (MBARI) - "MMI Ontology Registry and Repository" - [ slides ]    (1ZOU)
    * Mr. MikeDean (BBN) - " OOR Progress, Federation, and Other Thoughts" - [ [ slides] ]    (1ZOZ)
    * Mr. StephenGranite (Johns Hopkins) - "Utilizing NCBO Tools to Develop & Use an ECG Ontology" - [ slides ]    (1ZOV)
    * Dr. AlexGarcia (Bremen) - "The Ontology Repository for Assistive Technologies, ORATE" - [ slides ]    (1ZOW)
    * Professor KenBaclawski (Northeastern) - "OOR at Northeastern" - [ slides ]    (1ZU7)
    * Professor MichaelGruninger (Toronto) - "Common Logic Ontology Repository" - [ slides ] (in absentia)    (1ZOX)

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 KurtConrad

anonymous morphed into ArturoSanchez

anonymous morphed into Stephen Granite

Stephen Granite requests a private chat with you

Stephen Granite morphed into Stephen Granite (Johns Hopkins)

anonymous1 morphed into alexgarcia

anonymous morphed into PavithraKenjige

RaviSharma: Can not hear.

alexgarcia: neither do I, but my connection is very bad...

MyCoyne: I have to telephone in (+1-218-844-8060 ), concurrently with the web presentation

PeterYim: Paul ... if you are with Carlos, can you signal him to speak up, please

alexgarcia: who is next?

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

PeterYim: @MyCoyne - is that a question? .. if so, yes

PeterYim: @AlexGarcia - see latest session page (http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_30 ) for speaker order

MyCoyne: @PeterYim:  No, it's not a question.  I thought I give Ravi help that he has to call in, in addition to the the web to view the slides.

PeterYim: @MyCoyne - thanks

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

alexgarcia: ontology metadata vocabulary

alexgarcia: OMV

John Graybeal: 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: Jhon,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 q 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: 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

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

Stephen Granite (Johns Hopkins): @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: yes it can

Stephen Granite (Johns Hopkins): *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....

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?

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?

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?

Carlos Rueda (MBARI): @Natasha&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)

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

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)

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 Bio-Portal to be included in a structured SOA Service aggregation?

RaviSharma: Rex- do you mean orchestration or SOAF?

John Graybeal: @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.

RexBrooks: Actually I mean structured choreographies that would allow the future resources I expect to be included in the Bio-Portal to be available in Emergencies where an ontology of symptoms plotted against diagnoses and outcomes could be consulted in an emergency.

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?

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".)

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.

Bobbin Teegarden: 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 R=SOA Reference Architecture Subcommittee. We're almost ready for the second 60-Day Public Review.

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

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

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

RexBrooks: aligning--oops!

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

RaviSharma: Rex - I will go to R+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.

RexBrooks: Actaul that "R" was a typo just OASIS SOA Reference Architecture SC, it is part of the SOA Reference Model Technical Committee.

Paul Alexander: 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?

PeterYim: Natasha suggested - report technical/support issues to: (for OOR sandbox) oor-dev@ontolog.cim3.net  ... and (for BioPortal) tO; support@bioontology.org

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

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

RaviSharma: 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.

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.

RexBrooks: Your email, Ravi?

RexBrooks: Mine is rexb@starbourne.com

RaviSharma: ravisharma@comcast.net

RexBrooks: Captured it!

RaviSharma: Appreciate and value your approach Rex.

RexBrooks: Will be in touch.

RexBrooks: Your opinions are valued.

RexBrooks: highly.

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

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.

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?

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!

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

PeterYim: session adjourned 12:30pm PDT