...

Health Ontology Mapper (HOM)

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

Principal Investigators: Rob Wynden (UCSF), Russ Cucina (UCSF) and Nick Anderson (UW)Project Director: Rob Wynden (rob.wynden@ucsf.edu, 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

Lead Terminologist: Ketty Mobed (UCSF)

HOM Interpreter Programming Lead: Prakash Lakshminarayanan (UCSF)

UETL Programming Lead: Vijay Rayanker (UCSF)

(the original grant application technical proposal can be viewed here: httphttps://wikicommunity.recomdatai2b2.comorg/wiki/download/attachments/38669082195462/Ontomapper+Grant+v.7+4.14.08+FINAL.pdf)

License: Open Source BSD License http://www.linfo.org/bsdlicense.html HOM BSD ... (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 pemerson@recomdata.com.

Image Removed Files Section: http://wiki.recomdata.com/pages/viewpageattachments.action?pageId=3866908

Image Added Weekly Meeting Minutes

Image Added Files Section

Image Added Publications Page Image Removed Publications: http://wiki.recomdata.com/pages/viewpageattachments.action?pageId=6097393 (our primary publication so far is shown in green above)

Image Removed Weekly Minutes: http://wiki.recomdata.com/display/OntoMapper/Minutes

Image Removed Schedule: http://wiki.recomdata.com/pages/viewpageattachments.action?pageId=6750509 (we just track dependencies on the gantt here... just ignore the dates)

the AMIA 2010 paper that got best paper award highlighted and linked on this page above...)

...

The PUBLIC website for the CTSA Health Ontology Mapper SHRINE integration is located here: http://www.i2b2cictr.org however 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 and our work continues at a brisk pace.

We are now entering our Beta Release and our focus is now on creating an official build system and support pipeline.working on version 2: This project is currently making our tools interoperable with both SHRINE and the NCBO BioPortal with the OpenMDR TRIAD system at OSU.  The OpenMDR Wiki is available at: http://cagrid.org/display/MDR/Home

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

...

• 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 i2b2.org (all of the cells). i2b2 will be creating a formal build system which will include this????

...

We have an active project under way to allow the command line operation of UETL and HOM from batch job processing environments and there is an exploratory project that would allow NLP extraction of biomedical concepts from incoming full text data fields.

...

Navigate space

...