OMOP Specimen-domain codes (example subset)

omop-specimen-codes OMOP domain: Specimen 1 include

Codes that route a FHIR Specimen.type to the OMOP `specimen` table. Authoritative expansion: vocab.concept WHERE domain_id = 'Specimen' AND standard_concept = 'S'. SNOMED is the source-of-truth vocabulary for specimen material kinds (blood, urine, swab, tissue, etc.).

compose.include

include · SNOMED CT

vocab: SNOMEDloaded ✓ 7 codes

http://snomed.info/sct

Code	Display
119297000	Blood specimen
119364003	Serum specimen
119361006	Plasma specimen
122575003	Urine specimen
119376003	Tissue specimen
258500001	Nasopharyngeal swab
119334006	Sputum specimen

Authoritative expansion (run against the loaded Athena vocab)

SELECT vocabulary_id, concept_code, concept_name FROM vocab.concept WHERE domain_id = 'Specimen' AND standard_concept = 'S'

Raw JSON

{
  "resourceType": "ValueSet",
  "id": "omop-specimen-codes",
  "url": "https://fhir2omop.health-samurai.io/ValueSet/omop-specimen-codes",
  "version": "0.1.0",
  "name": "OmopSpecimenCodes",
  "title": "OMOP Specimen-domain codes (example subset)",
  "status": "draft",
  "experimental": true,
  "description": "Codes that route a FHIR Specimen.type to the OMOP `specimen` table. Authoritative expansion: vocab.concept WHERE domain_id = 'Specimen' AND standard_concept = 'S'. SNOMED is the source-of-truth vocabulary for specimen material kinds (blood, urine, swab, tissue, etc.).",
  "extension": [
    {
      "url": "https://fhir2omop.health-samurai.io/StructureDefinition/omop-domain",
      "valueString": "Specimen"
    },
    {
      "url": "https://fhir2omop.health-samurai.io/StructureDefinition/omop-expansion-sql",
      "valueString": "SELECT vocabulary_id, concept_code, concept_name FROM vocab.concept WHERE domain_id = 'Specimen' AND standard_concept = 'S'"
    }
  ],
  "compose": {
    "include": [
      {
        "system": "http://snomed.info/sct",
        "concept": [
          {
            "code": "119297000",
            "display": "Blood specimen"
          },
          {
            "code": "119364003",
            "display": "Serum specimen"
          },
          {
            "code": "119361006",
            "display": "Plasma specimen"
          },
          {
            "code": "122575003",
            "display": "Urine specimen"
          },
          {
            "code": "119376003",
            "display": "Tissue specimen"
          },
          {
            "code": "258500001",
            "display": "Nasopharyngeal swab"
          },
          {
            "code": "119334006",
            "display": "Sputum specimen"
          }
        ]
      }
    ]
  },
  "domain": "Specimen",
  "expansionSql": "SELECT vocabulary_id, concept_code, concept_name FROM vocab.concept WHERE domain_id = 'Specimen' AND standard_concept = 'S'"
}