UMLS and the VDW

Dustin KeyGene Hart

Group Health Research InstituteHMORN May 2012

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/

UMLS Points of InterestSource Number of

Concepts

ICD09CM 20,997

ICD10CM 98,178

CPT 9,526

Meta CPT 1,036

HCPCS 5,651

CDT 587

RxNorm 204,081

NCI 90,135

DSM-IV 452

LOINC 236

140,633

CCS 1106

SnowmedCT

324,494

“Influenza with pneumonia”

ICD09CM: 487.0 ICD10CM: J11.00

C0155870

SnowmedCT: 195921001

The UMLS “is organized by concept. One of its primary purposes is to connect different names for the same concept from many different vocabularies.”

UMLS Concept Unique Identifier (cui) UMLS Description

This is a good source for building code lists with associated and standardized descriptions.

UMLS Points of InterestUMLS preserves intra-source relationships and attributes. In many cases, the ontology can be expressed in terms of a hierarchy. Here are three kinds of relationships from RxNorm, mapping to the concept of ‘Simvastatin.’ NDC code is an example of an attribute that can be paired to a concept.

Screenshot from NCBO Bioportal

UMLS_CUI=C0074554

UMLS_CUI=C2242235

UMLS_CUI=C2242231

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.

UMLS Benefits To Datei2b2/SHRINE Left-hand Side

UMLS-enabled Procedure, Diagnosis, and Pharmacy Ontology. This same menu could be used for VDW queries.

1

Screenshot of I2B2

UMLS Benefits To Date2 NDC Code Set Construction via RxNorm

RxNorm from UMLS pairs NDCs to Generic ingredients. This powers an NDC search-macro which can build very comprehensive code sets, that can then be shared or easily reconstructed within the HMORN.

UMLS Benefits To Date3 Concept Coding, and Note Retrieval

This is evidence of a neoplasm.

C0006826

NLP Concept Coding Dictionary

We used the UMLS NCI ontology as the dictionary to concept code a year’s worth of pathology notes. Then we created a note retrieval macro. The macro uses the NCI ontology’s hierarchy, also available in the UMLS, to pull any notes with the specified concept code, or any subclasses of that code.

Coding Retrieval

……..breast carcinoma

%getnotes(cui=C0006826)

…Eyelid Nevus

%getnotes looks for subclasses of Neoplasm.

Note 1 Note 2

Etc.This is the UMLS code for ‘neoplasm’

UMLS Benefits To Date

4 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.

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.