An Efficient Approach To Map LOINC Concepts To Notifiable by b07i7k

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									  An Efficient Approach
To Map LOINC Concepts To
   Notifiable Conditions
         Wei Li, MD1, Jerome I. Tokars, MD, MPH1,
       Nikolay Lipskiy, DrPH1, Sundak Ganesan, MD2


                 1. Division of emergency Response and Preparedness
                 National Center for Public Health Informatics (NCPHI)
                   Centers for Disease Control and Prevention (CDC)
                            2. SAIC Consultant to NCPHI, CDC




Disclaimer: The findings and conclusions in this presentation are
those of the author(s) and do not necessarily represent the views of
the Centers for Disease Control and Prevention/the Agency for Toxic
Substances and Disease Registry.
 Notifiable Diseases/Conditions
• Surveillance for notifiable conditions traditionally
  includes manual reporting using written case
  definitions
• The availability of laboratory data in electronic format
  makes automated reporting feasible
• Mapping of notifiable conditions to standard
  vocabularies are required
• A table mapping notifiable diseases to LOINC
  (laboratory) and SNOMED (organism) codes was first
  made by Dianne Dwyer in later 1990s and last
  updated in 2004
             Purposes of Mapping
• A tool to filter the messages from public health and clinical labs
  to identify laboratory test results of public health importance
    – BioSense receives laboratory test results from 30 hospitals and from a
      large national laboratory—need to automatically identify results that
      MAY indicate a notifiable condition
    – 43 pathogens that cause notifable conditions are also Category A, B, or
      C Bioterrorism Agents (73%)
• Electronic laboratory report (ELR) and interoperability
    – A framework for the development and maintenance of a controlled
      vocabulary for reportable events of public health importance
    – Developing reusable component for intelligent surveillance
      information system architectures
• Towards development of notifiable disease controlled vocabulary
  for Unified Medical Language System (UMLS)
                     Objective
• To develop a method to map Logical
  Observation Identifier Names and Codes
  (LOINC) to notifiable conditions
  – Efficient
  – Easy to update
 Notifiable Diseases and Other Conditions of
           Public Health Importance

• Notifiable Diseases and Other Conditions of
  Public Health Importance (n=152)
  – Reportable either nationally (n=86) or to states
  – Active and inactive
  – Infectious diseases, injuries, toxins
  Event Code List: Notifiable Diseases and
Other Conditions of Public Health Importance

Event Code                               Condition name
10110                   Hepatitis A, acute*
10100                   Hepatitis B, acute*
10105                   Hepatitis B virus infection, chronic*
10106                   Hepatitis C virus infection, past or present*
10101                   Hepatitis C, acute*
10103                   Hepatitis E, acute
42020                   Head Injury
50000                   Kawasaki Disease
32010                   Lead poisoning

*Bolded indicating NND and should be reported to CDC on a regular basis
               Event Code List
• Event Code changes year to year
  – Retire and replace
     • Enterohemorrhagic Escherichia Coli (EHEC) O157:H7
       (10560,11562, 11564) were added in 1994 but retired in
       2006
     • Shiga toxin-producing Escherichia Coli (STEC) was added in
       2006
  – New code
     • Polyovirus infection, nonparalytic (10405) was added in
       2007.
    Logical Observation Identifiers
     Names and Codes (LOINC®)*
• A standard vocabulary identifies laboratory tests and
  clinical observations
• A common language for building electronic medical
  records
• Founded in 1994 and initial release in 1995 with 6,000
  lab tests
• The latest release (v2.21) covered 48,043 terms
• Allow users to merge clinical results from many sources
  into one database for patient care, clinical research, or
  management.


      * Regenstrief Institute
 LOINC to Notifiable Conditions
           Mapping
• LOINC to Condition Mapping Tables
  – Component of Public Health Information Network (PHIN)
  – Original version by Dr. Dwyer, updated by Dr. Sable
  – Last updated by PHIN in 2004
• LOINC
  – There are 46,812 terms in the LOINC version 2.19, which
    revealed 11,972 new terms added (34% increase) since
    2004
  – > 12,000 terms have been deprecated since then
  – LOINC has changed the properties of its database and
    expanded its fields to 61
                  Mapping Methods
• List of 152 Notifiable Diseases and Other Conditions of Public
  Health Importance
   – Excluded events without lab test or unknown organism
        • Silicosis, Spinal cord injury, and Head Injury, etc
        • Kawasaki Disease, Reye Syndrome, etc
• List to be mapped includes 146 conditions
   – All nationally notifiable infectious diseases
   – 46 Other infectious diseases
   – 7 Toxins
• Determine organisms related to each disease
• Find Systematized Nomenclature of Medicine (SNOMED) codes for
  organisms
• Map tests for organisms/toxins to LOINC codes by 3 methods



        http://www.cdc.gov/epo/dphsi/phs/infdis2007.htm
  Mapping Methods (continued)
• The Regenstrief LOINC Mapping Assistant (RELMA
  v3.19) was used to identify lab tests and LOINC
  codes associated with each organism/toxin

• A SAS (v9.1.3) program was developed to perform a
  text search of the LOINC database to find words
  that matched notifiable conditions or
  microorganisms

• Manual process
  Mapping Methods (continued)
• Manual process. Check the following LOINC
  database fields against the list of notifiable
  conditions
  –   Component
  –   Method Type
  –   Class
  –   Date Last Changed
  –   Map To
  –   Short Name
  –   Related Names 2
RELMA v3.19
  Results: Comparison of Mapping
              Tables
                       2004 Table   2007 Table
Number of Notifiable
                          92           146
Conditions
Total Number of
                         3,194        5,352
LOINC Codes
Number of LOINC
                          NA          2,455
codes added
Number of LOINC
                          NA           257
codes deleted
  Comparison of Mapping Methods

                  No. of LOINC      Person-Hours of
Mapping Method   Codes Identified        Effort

RELMA                 5,352              200

Manual Process        5,352             1,050

Automated Text
                      4,901               40
Search (SAS)
                  Text Search
• The text search parsing program found only
  4901 LOINC
• 451 LOINC entries not found by text search
  most had a non-specific test name, e.g.
  – Code 33700-6 (a spore identification test) is used to
    identify Anthrax
• Search field does not contain the word that used
  for searching, e.g. ―anthrax‖
LOINC to Condition Table Example: Anthrax mappings




  LOINC has several Scale types:
  • Quantitative scale (QN) : numerical results
  • Ordinal scale (ORD) : Positive, Negative, 1+, 2+, Not detected, etc.
  • Nominal scale (NOM) : The name of an organism
     Product: LOINC to Condition Table
               Data Dictionary
Field #   Field Name                                                Description
1         LOINC Num*           The unique LOINC Code is a string in the format of nnnnn-n

2         Component*           The name of the component or analyte measured (e.g. glucose, propranolol)
3         Property*            The property observed (e.g. substance concentration, mass, volume)

4         Time Aspect*         The timing of the measurement (e.g. is it over time or momentary)
5         System*              The type of sample (e.g. urine, serum)

6         Scale Type*          The scale of measurement (e.g. qualitative vs. quantitative) and where relevant
7         Method Type*         The method of the measurement (e.g. radioimmunoassay, immune blot)

                               An arbitrary cllasfication of the terms for grouping related observation together.
8         Class*                    (LOINC specified 41 classes for the Laboratory Term Classes)

9         Date Last Changed*   Date last changed, in the format YYYYMMDD
                               Change Type Code. DEL=Delete; ADD=add; NAM=change to Analyte/Component;
                                   MAJ=change to name field other than Analyte/Component; MIN=change to field
10        Changed Type*            other than name




               * Copied from LOINC database
     Product: LOINC to Condition Table
               Data Dictionary
Field #   Field Name                                                Description
                               Used when a field has been dropped from the active database )by entering "DEL" in
                               the Status field) because it has been replaced by an updated term. In those cases,
11        Map To*              Map To contains the LOINC code of the new term that should be used.
                               This field is a concatenation of the fully specified LOINC name. It was introduced in
12        Short Name*          version 2.07
                               It contains synonyms for each of the parts of fully specified LOINC name
13        Related Names 2*     (component, property, time, system, scale, method).
                               The nnotifiiable disease condition name specified by CDC's EPO (Epidemiology
14        Condition Name       Program Office) and the CSTE (Council of State and Territorial Epidemiologists)
                               The unique NNDSS Code is a string in the format of nnnnn produced by EPO and
15        NNDSS Code           CSTE
                               Specify the disease conditions that are/were either nationally notifiable in the US or
                               are/were notifiable at state level but not nationally. NND=conditions that are
                               nationally notifiable. State=conditions that are notifiable in one or more ststes but not
16        NNDSS Status         nationally.
                               In most cases the reporting criteria is a positive test that have "Positive". For some
                               LOINC tests, such as cultures and microscopy tests that identify organisms, it is an
17        Reporting Criteria   Organism List
18        Sort Order           The unique number that sorts the order of condition name.


               * Copied from LOINC database
                    Conclusions
• Compared with the 2004 LOINC to Condition Table, our 2007
  table added >2000 entries and deleted >200.

• The methods we used were labor intensive but currently
  necessary

• Efforts to improve the text search method by adding additional
  search terms such as ―spore‖ may enable more frequent
  automated updates.

• In the interim, the use of RELMA to identify lab tests provides
  an accurate and efficient semi-automated process to update
  the LOINC to Condition Mapping Table
              Future Plans
• Update LOINC to Notifiable Conditions Mapping
  Table to latest LOINC version 2.21
• Re-create/modify the text search program to
  increase accuracy
• Explore programs other than SAS to perform
  text searches
• Incorporate terms in the latest release of
  SNOMED
• Ultimately, use updated mapping table to
  improve laboratory-based surveillance
Wei Li: for5@cdc.gov

								
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