Documentations of Advanced Heath Care Directives Where Are They TAI_SEALE
UMLS as a Resource for Virtual Data Warehouse Infrastructure KEY
1. UMLS and the VDW
Dustin Key
Gene Hart
Group Health Research Institute
HMORN May 2012
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. UMLS Points of Interest
The UMLS “is organized by concept. One of its
Source Number of primary purposes is to connect different names for
Concepts the same concept from many different
ICD09CM 20,997 vocabularies.”
ICD10CM 98,178
UMLS Concept Unique Identifier (cui) UMLS Description
CPT 9,526
Meta CPT 1,036 C0155870 “Influenza with pneumonia”
HCPCS 5,651
CDT 587
RxNorm 204,081
NCI 90,135
DSM-IV 452 ICD09CM: 487.0 ICD10CM: J11.00
LOINC 140,633 SnowmedCT: 195921001
236
CCS 1106
This is a good source for building code lists with
Snowmed 324,494 associated and standardized descriptions.
CT
4. UMLS Points of Interest
UMLS 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.
UMLS_CUI=C2242235
UMLS_CUI=C2242231
UMLS_CUI=C0074554
Screenshot from NCBO Bioportal
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. 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 of
I2B2
7. UMLS Benefits To Date
2 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.
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.
carcinoma
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.
9. 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.
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.