Ontolog Forum

Health Sciences - Thu 2016-03-10

Session Co-Chairs: Leo Obrst and Ram D. Sriram


  • Healthcare and biomedical domains: a very large ecosystem of vocabularies and ontologies
  • Goal: To provide insight into the nature of semantic interoperability issues and approaches in the Healthcare ecosystem
  • Mission: Present issues of semantic interoperability and integration in domain of healthcare: Example: Semantic Electronic Health Record (EHR) and Systems
    • Discuss approaches in semantic interoperability and integration in healthcare: precoordination, postcoordination, mapping, anchoring, foundational ontologies and architectures, hybrid approaches
    • Discuss approaches for achieving semantic interoperability of vocabularies and ontologies in healthcare
    • Discuss gaps in current approaches in semantic interoperability in healthcare
    • Discuss current/future challenges and prospects in semantic interoperability in healthcare
    • Propose best methods for achieving semantic interoperability


Conference Call Details

  • Date: Thursday, 10-Mar-2016
  • Start Time: 9:30am PST / 12:30pm EST / 6:30pm CEST / 5:30pm BST / 1630 UTC
  • Expected Call Duration: ~2 hours
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[12:30] LeoObrst:

[12:37] Donna Fritzsche: *6 can be used to mute your phones!

[12:38] Donna Fritzsche: -- slides are here

[12:40] Mark Underwood: Session twitter hashtag #ontologysummit

[12:55] Mark Underwood: I teased @LexisNexis and @Law360 on Twitter

[13:11] Donna Fritzsche: thank-you Kincho - question- were there any tools to help users form Sparql queries (more user friendly than raw Sparql?)

[13:11] FrankOlken: Kincho, Why the choice of Virtuoso for the triple store?

[13:12] FrankOlken: Kincho, what infrastructure for the rules aspect?

[13:16] Kincho Law: Donna: We developed some elementary tabular form for user to enter query (which can then be translated into SparQL.

[13:19] Gary Berg-Cross: The Practical Impact of Ontologies on Biomedical InformaticsJ. J. Cimino, X. Zhu1,

[13:19] Kincho Law: FrankOlken: Virtuoso is open source, I believe. From what we could find at the time, Virtuoso was one triple store that supports OWL and RDF

[13:22] Donna Fritzsche: Thanks Kincho

[13:22] Kincho Law: FrankOlken: We used Semantic Web Rule Language (SWRL) which basically combines OWL and RuleML. We use Pellet reasoner and Jess (Jena library) for reasoning and inferencing.

[13:34] Donna Fritzsche:

[13:36] AndreaWesterinen: Kincho, did you think about moving to Stardog as a rule engine since it works with SWRL and includes a more advanced Pellet reasoner. Also, you can write your SWRL with SPARQL?

[13:37] AndreaWesterinen: (Sorry for the mismatched punctuation. I am multitasking. :-)

[13:38] Kincho Law: Thank you, Andrea.

[13:39] Gary Berg-Cross: @Olivier In many domains there are competing vocabularies and even competing ontologies that are hard to bridge. You provided a view of several vocabularies but it is unclear if they are hard to integrate. Is the OMOP effort on a common data model and effort to bridge models and their vocabularies?

[13:43] AndreaWesterinen: Kincho, Let me know if you need any info on using Stardog. We have been developing with it for quite some time now.

[13:43] Olivier Bodenreider: @GBC I did not have enough time to talk about UMLS. UMLS integrates terminologies. OMOP integrates information models (but prescribes the use of specific terminologies). 2 different levels.

[13:43] AndreaWesterinen: And, we do some ontology integration with it and SWRL. Somewhat similar to your approach but a different domain.

[13:48] Gary Berg-Cross: @Olivier Thanks for the clarification. We have similar issues in the GeoScience realm but no ULMS (or OMOP, I guess).

[13:49] Donna Fritzsche: Eric - Can you comment on use of k-d trees to address the type of problems you are discussing.

[13:49] Gary Berg-Cross: Hi Eric. Long time no see. Can you provide a reference for the statement "algorithm dev grew by 43,000x"?

[13:54] Eric Little: Donna - we do this kind of stuff for "nearest neighbor search" as an example. We also do work on inexact graph matching and graph isomorphism problems - where you don't know the shape of the graph or the "target". You may need to compute these things based on similarities or finding things in the neighborhood of what you want. We see algorithms as subsetting the graphs, then we can use semantics on those smaller graphs. In the other direction, you can imagine that the ontologies provide those math graphs with added nodes, improving matching and giving more context.

[13:56] Donna Fritzsche: Thank-you, it could get very interesting indeed.

[14:01] Eric Little: Hi Gary - There is a small interesting book I use in my classes at NYU called RACE AGAINST THE MACHINE ( - this statistic is taken from that source. There was also in 2010 a Report to the President and Congress where this was also cited - see this website:

[14:04] Gary Berg-Cross: @Parsa Do you have a SKOS "profile" by which you import different vocabularies into a standard SKOS form? Or was that not needed?

[14:05] Mark Underwood: @Parsa can u discuss the provenance and security models? Are they connected ontologies, separate? Use breadcrumbs? Like Prov-O?

[14:05] Donna Fritzsche: OMOP resource:

[14:05] Donna Fritzsche: Observational Medical Outcomes Partnership

[14:08] Gary Berg-Cross: @Parsa I'd be interested in knowing what semantic relations you found needed and useful for your work. The text on the slides is a bit small to read.

[14:08] Eric Little: Allotrope Information can be found here:

[14:11] Gary Berg-Cross: @Parsa where can I read more about this Blueprint idea for flexible annotations?

[14:13] FrankOlken: It would really help if speakers put page numbers on their slides.

[14:15] Donna Fritzsche: Hi Parsa, can you refer us to papers on the machine learning techniques used?

[14:18] Ram D. Sriram: @Frank: Adobe PDF generally displays the page number at the top left corner. If the slides are animated this may cause problems.

[14:21] Ram D. Sriram: @Brian: Olivier may have answered some of your concerns. We will follow up with VA on a follow-up to this panel.

[14:23] LeoObrst: We will have a couple speakers talking at the April 7 session about VA efforts.

[14:29] Donna Fritzsche: thank-you everyone!

[14:29] LeoObrst: Thanks all!

[14:30] FrankOlken: Bye


Audio Recording