# Presentation: 541287

## An Efficient Approach To Map LOINC Concepts To Notifiable Conditions 

**Wei Li, MD****1****, Jerome I. Tokars, MD, MPH****1****,**
**Nikolay Lipskiy, DrPH****1****, Sundak Ganesan, MD****2**
***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 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 

- 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

**LOINC to Notifiable Conditions Mapping**

## 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

- 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](http://www.cdc.gov/epo/dphsi/phs/infdis2007.htm)_

**Mapping Methods**

## 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

## 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

- Component
- Method Type
- Class
- Date Last Changed
- Map To
- Short Name
- Related Names 2

**Mapping Methods (continued)**

## RELMA v3.19

## Results:  Comparison of Mapping Tables

|  | 2004 Table | 2007 Table |
| --- | --- | --- |
| Number of Notifiable Conditions | 92 | 146 |
| Total Number of LOINC Codes | 3,194 | 5,352 |
| Number of LOINC codes added | NA | 2,455 |
| Number of LOINC codes deleted  | NA | 257 |

## Comparison of Mapping Methods

| 
Mapping Method | No. of LOINC Codes Identified | Person-Hours of Effort |
| --- | --- | --- |
| RELMA | 5,352 | 200 |
| Manual Process | 5,352 | 1,050 |
| Automated Text Search (SAS) | 4,901 | 40 |

## 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 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) |
| 8 | Class* | An arbitrary cllasfication of the terms for grouping related observation together. (LOINC specified 41 classes for the Laboratory Term Classes) |
| 9 | Date Last Changed* | Date last changed, in the format YYYYMMDD |
| 10 | Changed Type* | 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 other than name |

*** Copied from LOINC database**

## Product: LOINC to Condition Table Data Dictionary

| Field # | Field Name | Description  |
| --- | --- | --- |
| 11 | Map To* | 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, Map To contains the LOINC code of the new term that should be used. |
| 12 | Short Name* | This field is a concatenation of the fully specified LOINC name. It was introduced in version 2.07 |
| 13 | Related Names 2* | It contains synonyms for each of the parts of fully specified LOINC name (component, property, time, system, scale, method).  |
| 14 | Condition Name | The nnotifiiable disease condition name specified by CDC's EPO (Epidemiology Program Office) and the CSTE (Council of State and Territorial Epidemiologists) |
| 15 | NNDSS Code | The unique NNDSS Code is a string in the format of nnnnn produced by EPO and CSTE |
| 16 | NNDSS Status | 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 nationally. |
| 17 | Reporting Criteria | 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 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 

**Wei Li: for5@cdc.gov **