UMLS and the VDW           Dustin Key           Gene Hart  Group Health Research Institute       HMORN May 2012
UMLS• “If Frodo were carrying an ontology, it would be  UMLS.”   Meaningful Use and Beyond, A Guide for IT Staff in Health...
UMLS Points of Interest                       The UMLS “is organized by concept. One of itsSource     Number of   primary ...
UMLS Points of InterestUMLS preserves intra-source relationships and attributes. In many cases, theontology can be express...
Some Challenges Discovered• “Obsolete” codes  dropped.• Learning curve.• Local site codes not  included.• Licensing issues...
UMLS Benefits To Date                                   UMLS-enabled Procedure, Diagnosis,  1   i2b2/SHRINE Left-hand Side...
UMLS Benefits To Date 2   NDC Code Set Construction via RxNormRxNorm from UMLS pairs NDCs to Generic ingredients. This pow...
UMLS Benefits To Date 3 Concept Coding, and Note Retrieval        Coding                                          Retrieva...
UMLS Benefits To Date4 Diagnosis Code Set Development:  Charlson Categories on the CRN Portal                             ...
Looking Ahead: Suggested               Pursuits• Try UMLS concept coding the entire VDW.  – Positions us to apply any onto...
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UMLS as a Resource for Virtual Data Warehouse Infrastructure KEY

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UMLS as a Resource for Virtual Data Warehouse Infrastructure KEY

  1. 1. UMLS and the VDW Dustin Key Gene Hart Group Health Research Institute HMORN May 2012
  2. 2. UMLS• “If Frodo were carrying an ontology, it would be UMLS.” Meaningful Use and Beyond, A Guide for IT Staff in Health Care by Fred Trotter and David Uhlman• Unified Medical Language System is maintained by the National Library of Medicine, and was developed in 1986.• 100 Terminologies and 1 million concepts contained• http://www.nlm.nih.gov/research/umls/
  3. 3. UMLS Points of Interest The UMLS “is organized by concept. One of itsSource Number of primary purposes is to connect different names for Concepts the same concept from many differentICD09CM 20,997 vocabularies.”ICD10CM 98,178 UMLS Concept Unique Identifier (cui) UMLS DescriptionCPT 9,526Meta CPT 1,036 C0155870 “Influenza with pneumonia”HCPCS 5,651CDT 587RxNorm 204,081NCI 90,135DSM-IV 452 ICD09CM: 487.0 ICD10CM: J11.00LOINC 140,633 SnowmedCT: 195921001236CCS 1106 This is a good source for building code lists withSnowmed 324,494 associated and standardized descriptions.CT
  4. 4. UMLS Points of InterestUMLS preserves intra-source relationships and attributes. In many cases, theontology can be expressed in terms of a hierarchy. Here are three kinds ofrelationships from RxNorm, mapping to the concept of „Simvastatin.‟ NDC codeis an example of an attribute that can be paired to a concept. UMLS_CUI=C2242235 UMLS_CUI=C2242231 UMLS_CUI=C0074554 Screenshot from NCBO Bioportal
  5. 5. Some Challenges Discovered• “Obsolete” codes dropped.• Learning curve.• Local site codes not included.• Licensing issues potentially difficult discussion. Mount Ngauruhoe, New Zealand, aka, Mount Doom from Lord of the Rings. Photo by Peter Wright Hall.
  6. 6. UMLS Benefits To Date UMLS-enabled Procedure, Diagnosis, 1 i2b2/SHRINE Left-hand Side and Pharmacy Ontology. This same menu could be used for VDW queries.Screenshot ofI2B2
  7. 7. UMLS Benefits To Date 2 NDC Code Set Construction via RxNormRxNorm from UMLS pairs NDCs to Generic ingredients. This powers an NDCsearch-macro which can build very comprehensive code sets, that can then beshared or easily reconstructed within the HMORN.
  8. 8. UMLS Benefits To Date 3 Concept Coding, and Note Retrieval Coding Retrieval This is evidence of a %getnotes(cui=C0006826) neoplasm. %getnotes looks for NLP Concept Coding subclasses of Dictionary Neoplasm. Note 1 Note 2 C0006826 This is the UMLS ……..breast …Eyelid Nevus code for „neoplasm‟ Etc. carcinomaWe used the UMLS NCI ontology as the dictionary to concept code a year‟s worthof pathology notes. Then we created a note retrieval macro. The macro uses theNCI ontology‟s hierarchy, also available in the UMLS, to pull any notes with thespecified concept code, or any subclasses of that code.
  9. 9. UMLS Benefits To Date4 Diagnosis Code Set Development: Charlson Categories on the CRN Portal Select dx_code, description where path like „%Heart failure%‟ Similar to NDC Code Set development.
  10. 10. Looking Ahead: Suggested Pursuits• Try UMLS concept coding the entire VDW. – Positions us to apply any ontology as we want.• Try creating a file that has dropped obsolete codes. – Also, come up with some make-shift scheme to incorporate these into important hierarchies. Maybe work local codes into this scheme too.• Somehow make a standardized UMLS extract available to the HMORN. Start with the licensing areas we feel comfortable with (RxNorm, HCPCS, ICD09CM) and expand.

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