APHL 48” x 72” (4’ x 6’) Poster Template
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FEEDBACK
If you have comments about how this template worked for you or questions on using
PowerPoint for your design, email ben.moyer@aphl.org.
The Specimen Cross Mapping Table –
A Tool for Harmonizing the Specimen Vocabulary Domain
Riki Merrick, MPH1
Eric Haas, DVM, MS2
INTRODUCTION
HL7 V2 messages, starting with Version 2.5, can include a specimen
segment (SPM) that contains several field to describe specimen source
information, which carries more information than in the older message
versions. The APHL informatics team, while working on the Public Health
Interoperability Project (PHLIP), identified several deficits and issues
when mapping the public health laboratory’s specimen terms to standard
vocabulary during the initial design and implementation of an HL7 v2.6
electronic order message between state public health laboratories and
the CDC Salmonella laboratory, as HL7 messages starting with Version
2.5 can include a specimen segment
It was found that most laboratories supported one or at most 2 fields to
describe specimen, and thus frequently combined specimen type and
body source site into a single pre-coordinated term. Furthermore, many
of these local specimen terms did not have a related concept in the
existing HL7 terminologies, HL7 table 0070 and its successor HL7 table
0487. These specimen vocabularies turned out to be limited and
ambiguous. For example, the common respiratory sample,
“Nasopharyngeal Swab” is absent , and terms like “GEN - Genital” could
be interpreted as the body site or as a genital swab specimen or tissue
specimen.
Therefore, the APHL informatics team decided to use the SNOMED (SCT)
medical terminology for our mapping of specimen related terms, following
the example set by National Animal Health Network (NAHLN), which
defined SNOMED hierarchies for each of the SPM fields (Figure 1). It was
also decided to use the multiple specimen descriptor fields in the SPM
segment to allows for a richer and more accurate description of specimen
concepts. This lead to the basis for the Specimen Cross Mapping Table
(Specimen-CMT) to harmonize the various local specimen terms to core
set of standard vocabulary for use in HL7 messaging.
In order to accommodate the different local terms among various
laboratories, a PHLIP-preferred term was created that represented a
specific concept and allowed the mapping across the multiple fields in
the SPM segment. In other words, one PHLIP-preferred term could map
to 6 different SNOMED concepts - in essence, post coordinating local
specimen terms where needed.
A clear definition for each PHLIP-preferred term where added after as a
result of input from the Laboratory Messaging Community of Practice
(LMCoP), APHL informatics’ goal is for the Specimen-CMT to become a
national resource for curated specimen related vocabulary, the
establishment of a community review and long-term content oversight
structure. Current efforts are underway to achieve these goals.
METHODS
The APHL informatics team collected varied local terms from partner labs
as well as public health departments . These descriptions form the basis
of the concepts considered for inclusion in the Specimen-CMT.
In order to accommodate the differences among local specimen terms, a
PHLIP-preferred term, along with a definition describing the standard
concept, was created. Based on the definition, each PHLIP-preferred term
was mapped first for specimen type to the SNOMED specimen hierarchy
and, if needed to properly identify the concept, additional SPM fields.
A constrained set of SCT specimen terms were created with three goals in
mind: 1) Harmonization of standard specimen terms among APHL’s
informatics many partners. 2) Mapping the SCT terms to the HL7 terms.
3) Identifying and filling any gaps in the SCT specimen terminology.
Although many local concepts can be expressed with a single specimen
SCT concept, other local and HL7 concepts need additional data
elements such as specimen source site to fully describe them. An
Examples of terms in the Specimen-CMT are shown in Figure 2 below.
After presentation of this Specimen-CMT to the ELR2PH 2.5.1 guide
authors and the LMCoP, more terms spanning human, animal and
environmental samples were collected for inclusion. Inspired by the
success of the Reportable Condition Mapping Table (RCMT) review
format, the Specimen-CMT is presented to the Public Health Lab
community through LMCoP webinars and phConnect in order to work
through several outstanding issues. We have invited attendees with
subject matter expertise in environmental and animal testing,
pathology and SNOMED to help facilitate discussion, refine, and
standardize the specimen vocabulary across the community.
The Specimen-CMT is being leveraged by APHL Informatics’ ELR
technical assistance team to help many Public Health Laboratories
map there local specimen term to standard SNOMED vocabulary. By
using the Specimen-CMT, the standard specimen terminology among
the various public health laboratories has become more harmonized.
Additionally, through the process of using the Specimen-CMT, it
became more comprehensive because new additions were made to it
and the cross-mapping of HL7 table 0070 and 00487 terms to
SNOMED via the PHLIP-preferred terms nearly completed.
Through this process many new specimen type concepts have been
identified and will be submitted to SNOMED CT by the APHL informatics
team for consideration. By developing and implementing of the
Specimen-CMT, several key issues with ELR2PH251 vocabulary
constraints were uncovered and forwarded to the National ELRtaskforce for discussion and resolution. Through the process of
development and use of the Specimen-CMT the standard specimen
terminology is being applied consistently across the public health
domain.
Figure 2:
HL7 SPM Fields with the Identified Vocabularies from
HL7 and SNOMED Hierarchies
Specimen CMT Examples
HL7 Name
SPM.4
Specimen Type
SPM.5
Specimen Type
Modifier
SPM.6 Specimen Additives
SPM.7
SPM.8
SPM.9
Specimen
Collection Method
Specimen Source
Site
Specimen Source
Site Modifier
Value set defined by ELR2PH251
HL7 table 0487
SNOMED CT Specimen Hierarchy
SNOMED CT Qualifier Hierarchy
possibly SNOMED CT morphologic
abnormalities Hierarchy
HL7 table 0371
HL7 Table 0488
SNOMED CT Specimen Collection
Hierarchy
SNOMED CT Body Site Hierarchy
SNOMED CT Modifier and Qualifier
Hierarchy
PHLIP
Preferred
Name
Acknowledgements / Sources
PHLIP@ APHL.ORG
http://www.phconnect.org/group/laboratorymessagingcommunityofpractice/forum/topics/specimen-crossmap
Consulting, (Contractor to APHL), San Francisco, CA
2The St John’s Group (Contractor to APHL, Atlanta, GA)
Definition
HL7 SPM.4
HL7 SPM.5
Specimen type Specimen type
(SNOMED)
modifier or
qualifier
(SNOMED)
Stool or Feces, also known as excrement, is a waste
product from an animal's digestive tract expelled
Stool specimen
Stool
through the anus or cloaca during a process called
(specimen)
defecation.
http://en.wikipedia.org/wiki/Feces
NASOPHARYNGEAL SWAB COLLECTION:
Nasopharynge
Nasopharyngeal
1. Insert dry swab through one nostril straight back
al swab
swab (specimen)
(not upwards …
Specimen from
The 3 major forms of liver abscess, classified by
Abscess_Liver
abscess
etiology, ..
(specimen)
For diffuse and relatively uniform lung involvement
Bronchoalveola with the disease process, the right middle lobe and Bronchoalveolar
r
lingula of the left upper lobe are typically chosen lavage fluid
Lavage_Middle as convenient sites that are easily accessed for
sample
Lobe_Right
wedge positioning of the distal bronchoscope in
(specimen)
segmental bronchi….
For More Information
1iConnect
The LMCoP is partnering with CDC programs working on education
through the creation of a specimen collection manual. The long term
deliverable is a proposed set of preferred specimen concepts for use
as a the recommended vocabulary on a national scale that will be
made publically available for inclusion in LIMS and EHR system
products.
RESULTS
Figure1:
Field
To encourage standardization of specimen term coding outside of the
Public Health domain, participation in the LMCoP was expanded
through the vocabulary group of the Lab Results Interface (LRI) WG of
the Standards and Interoperability (S&I) Framework to include
commercial and hospital labs as well as LIMS vendors.
Current work continues in the LMCoP to create guidance around proper
specimen submission based on the lab domain in question – for
example a specimen collected one way may be suitable for testing in
the chemistry lab, but may not be suitable for microbiological tests like
culturing.
CONCLUSION
The LMCoP will continue to work on the Specimen-CMT until the long
term goal of a national preferred specimen vocabulary is achieved and
then turn to other messaging issues involving specimens, including
how to express whether the sample is a clinical specimen vs. a
derivative like an isolate or DNA, and how to message environmental
samples.
So join us!
HL7 SPM.6
Specimen
Additives
(SNOMED)
HL7 SPM.7
Specimen
Collection
Method
(SNOMED)
Hl7 SPM.8
Source
site/Body site
(SNOMED)
HL7 SPM.9
Specimen type
modifier or
qualifier
(SNOMED)
-
-
-
-
-
-
-
-
-
-
-
Liver structure
(body
structure)
-
-
-
Bronchoalveolar
lavage
(procedure)
HL7 Table
0070
HL7 Table
0487
Stool =
Fecal
Stool =
Fecal
Structure of
middle lobe of
right (qualifier)
lung (body
structure)
PHLIP is supported by Cooperative Agreement #CCU303019 from the Centers for
Disease Control and Prevention (CDC).
LTIAPH is supported by Cooperative Agreement #1U50HK000105 from Centers
for Disease Control and Prevention (CDC).
The findings and conclusions in this poster are those of the authors and do not
necessarily represent the official position of CDC or the Agency for Toxic
Substances and Disease Registry
© Copyright 2012, Association of Public Health Laboratories. All Rights Reserved.