Health Ontology Mapper
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CTSA Health Ontology Mapper

(The Health Ontology Mapper (OntoMapper) is an open source general purpose instance mapper for academic research, public hospitals and non-profits.)

Principal Investigators: Russ Cucina (UCSF) and Nick Anderson (UW)

Project Director: Rob Wynden (, 415-476-3728)

Ontology Mapper Original Design: Rob Wynden (UCSF), Davera Gabriel (UCD), Marco Casale (Rochester) and Maggie Massary (UPenn)

Mapping Workbench Design: Rob Wynden (UCSF)

(the original grant application technical proposal can be viewed here:

License: Open Source BSD License ... (For an optional commercial license contact:  Ellen Kats at UCSF Tech Transfer.)   If you would like to purchase a Support License for Ontology Mapper please contact Peter Emerson at Recombinant Data Corp at

To reference this project please use:  Wynden R, Weiner MG, Sim I, Gabriel D, Casale M, Carini S, Hastings S, Ervin D, Tu S, Gennari J, Anderson N, Mobed K, Lakshminarayanan P, Massary M, Cucina R. Ontology mapping and data discovery for the translational investigator. Presented at the 2010 AMIA Summit on Clinical Research Informatics meeting, March 12-13 2010, San Francisco, CA.  You can read it HERE

HOM call weekly status: 11AM Pacific every Tuesday at: 800 794 6702  Passcode: 5071491#
ConferencePlus (passcode 5071491#)
(please note that the UETL subteam has joined this same con-call as well...)

Files Section:

Publications: (our primary publication so far is shown in green above)

Weekly Minutes:

Schedule: (we just track dependencies on the gantt here... just ignore the dates)

Bug tracking is listed as a subproject of HOM here:

The UETL Sub-project is located at:

Ontology Mapper's data dictionary and HL7 CTS XML spec are published on access please contact Hillari Allen at

Revision Control is available on Subversion. Please contact Aaron Mandel for access to Subversion.
Subversion can be viewed from any web browser at:
Subversion clients can be obtained here:
Coding guidelines are posted here:

The PUBLIC website for the CTSA Ontology Mapper SHRINE integration is located here: http://www.i2b2cictr.orghowever the caGRID based site has not been made public yet (not because it's secret or anything but we haven't had the time yet) by OSU.

The Ontology Mapper project has been very active from its inception. We are now entering our Beta Release and our focus is now on creating an official build system and support pipeline.

This project is currently making our tools interoperable with both SHRINE and the OpenMDR TRIAD system at OSU.  The OpenMDR Wiki is available at:

Our short term goals (these are now partially completed):

  1. Using our use cases generate a large amount of test data (manufactured data which can be shared without HIPAA - affectionately called "the monster") - DONE MOSTLY
  2. Perform black box end-to-end testing using a small data set that has already been prepared (this data set is called "dinky") - DONE MOSTLY
    Note: the proof-of-concept has already been completed ... this is a QA infrastructure test - QA INFRASTRUCTURE IS DONE MOSTLY
  3. Create a large suite of automated tests which can verify that the Ontology Mapper works properly using the data generated in #1 - DONE MOSTLY
  4. Get Ontology Mapper running at several new sites and verify that the regression test suite runs properly there (we'll have UCSF, Rochester, UCD and UPenn before close of Alpha) - W.I.P. - This is a very active topic right now... we are installing at several sites at the moment.
  5. Document the system and publish a Road Map (How can this be done without coordination with Harvard?)
  6. Complete our initial map sets.  RxNorm is DONE .. now we just need to finish LabNorm (Rob has just completed the design for LabNorm - we can start that as soon as R is running)
  7. Announce our Version 1.0 Beta program and post the system for general availability (W.I.P. - RecomData is building the web site for this right now)
  8. Begin working with U.W. on the i2b2 grant for our Version 2.0 development
    • The i2b2 Cell Wrapper
      • The UETL component is almost done now - Vijay Rayanker (MOSTLY DONE) - See UETL wiki (link is above)
      • The HOM Mapping workbench is going to be integrated with SHRIMP (Rob is hiring a Ruby programmer right now)
    • Support for alternate transformation languages (SQL, Java and Perl are done, Xquery?, Horn and R) - John Gennari and Prakash and possibly Joe Adler (we need R NOW)
    • Creation of the Mapping Workbench (a user friendly interface for creating new instance maps) - John Gennari, John DeShazo and Prakash Lakshminarayanon (see Cell Wrapper)
    • White box test of SOAP interface built in 7a above (David Oppenheimer)
    • Plug our one set of regression tests into the regression test framework for (all of the cells). i2b2 will be creating a formal build system which will include this????
  9. Support the new users that adopt the Version 1.0 Beta and work that feedback into a General Release of Ontology Mapper 1.0 (W.I.P. - we are creating a support system with Recom now)
  10. Work with U.W. to complete the release of Ontology Mapper 2.0 (described in #7)
  11. Publish our final results and move on with life (We have already published our first paper ... see above... but with so much activity we already need 2 more papers...)

    Please note: although our HL7 CTS II transport spec (Ontology Mapper's transport spec was previously absorbed into the HL7 CTSII Technical Committee Functional Spec) for sharing instance maps is going very well (thanks to Davera) it is assumed that private industry will implement this part as that is the case with prior releases of HL7. So we don't need to worry about that too much at this point.

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