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Recommendation: Were specimen source (type, source site and collection method) is conveyed in attributes other than the test name, these values should be coded using SNOMED CT.
Explanation: Laboratory test names typically include the specimen (e.g. the LOINC "System") upon which the observation was made, but some attributes about the specimen can be carried in other parts of the information or messaging model. Where such other specimen attributes are reported as coded values, they should use SNOMED CT concepts. |
EXAMPLE 1: Part of the Value set for Specimen Type. PHIN-VADS (CDC)
Value Set Code NHSNSpecimenTypeCode |
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Concept Code | Preferred Concept Name | Code System Name |
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258414004 | Adipose tissue sample | SNOMED-CT |
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309141004 | Adrenal gland specimen | SNOMED-CT |
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119373006 | Amniotic fluid specimen | SNOMED-CT |
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309479002 | Artery sample | SNOMED-CT |
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309493009 | Bile duct biopsy sample | SNOMED-CT |
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119341000 | Bile specimen | SNOMED-CT |
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309491006 | Biliary tract tissue sample | SNOMED-CT |
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119297000 | Blood specimen | SNOMED-CT |
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119359002 | Bone marrow specimen | SNOMED-CT |
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https://phinvads.cdc.gov/vads/ViewValueSet.action?id=6F61F377-E515-43D2-BFEB-4BF135244033# |
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EXAMPLE 2: Specimen type and specimen source site in NAHLN messaging
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An example of coded value for SPM.4 is shown below:
| Code Block | ||
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<SPM.4> |
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<CWE. |
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1>661000009100</CWE.1> |
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<CWE.2>Oropharyngeal swab</CWE.2> |
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<CWE. |
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3>SCT</CWE.3> |
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<CWE. |
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9>OP swabs</CWE.9> |
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</SPM.4> |
The Specimen Source Site (SPM.8) contains an identifier for the source of the specimen (i.e the anatomical location, organ or site from which the specimen originated). This field is needed when the SNOMED specimen hierarchy does not contain a precoordinated term that adequately describes the specimen. For example, in the case where tonsillar tissue is obtained from a pig by scraping, the source would be 'Tonsillar structure (palatine)' In general this field is only needed when additional information about the region from where the specimen was collected is needed. For environmental specimens this field may supply additional information on where the specimen originated. In cases where the specimen and specimen source are identical, this field need not be populated.
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An example of SPM.8, used in conjunction with SPM.4 is shown below:
| Code Block | ||
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<SPM.4> |
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<CWE. |
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1>128168004</CWE.1> |
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<CWE.2>Tissue specimen from liver</CWE.2> |
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<CWE. |
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3>SCT</CWE.3> |
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</SPM.4> |
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<SPM.8> |
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<CWE. |
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1>89255003</CWE.1> |
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<CWE.2>right lateral lobe of liver</CWE.2> |
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<CWE. |
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3>SCT</CWE.3> |
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</SPM.8> |
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