SubstanceSourceMaterial — Biological origin of a substance

Describes the living organism a derived substance comes from: kingdom (plant, animal, microbe, mineral), taxonomic species, part used (bark, root, blood, fermentation), geographic harvest area.

Purpose of the resource

A substantial part of the pharmacopoeia still comes from natural extracts — taxol (bark of Taxus brevifolia), morphine (Papaver somniferum), vincristine (Catharanthus roseus), historical animal insulin, porcine heparin, egg-grown vaccines, horse / goat antibodies, botulinum antitoxin. For such a substance to be registrable, its biological origin must be traced precisely.

SubstanceSourceMaterial structures that traceability with the taxonomic rank (kingdom, phylum, class, order, family, genus, species), the part used, the state (fresh, dry, lyophilised), the developmental stage (germination, flowering, ripening), and the geographic harvest area (essential for traditional pharmacopoeia).

Key fields

JSON example

Taxol origin: historical extraction from fresh bark of Taxus brevifolia harvested in the Pacific Northwest (USA).

{
  "resourceType": "SubstanceSourceMaterial",
  "id": "example-taxol",
  "sourceMaterialClass": {
    "coding": [{
      "system": "http://terminology.hl7.org/CodeSystem/source-material-class",
      "code": "plant",
      "display": "Plant"
    }]
  },
  "sourceMaterialType": {
    "coding": [{
      "system": "http://terminology.hl7.org/CodeSystem/source-material-type",
      "code": "whole-organism",
      "display": "Whole organism"
    }]
  },
  "sourceMaterialState": {
    "coding": [{
      "system": "http://terminology.hl7.org/CodeSystem/source-material-state",
      "code": "fresh",
      "display": "Fresh"
    }]
  },
  "organismId": {
    "system": "http://www.ncbi.nlm.nih.gov/taxonomy",
    "value": "4023"
  },
  "organismName": "Taxus brevifolia",
  "organism": {
    "family": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/taxonomic-family",
        "code": "Taxaceae"
      }]
    },
    "genus": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/taxonomic-genus",
        "code": "Taxus"
      }]
    },
    "species": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/taxonomic-species",
        "code": "Taxus brevifolia"
      }]
    },
    "intraspecificType": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/intraspecific-type",
        "code": "Variant",
        "display": "Variant"
      }]
    }
  },
  "partDescription": [{
    "part": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/anatomy-plant",
        "code": "bark"
      }]
    },
    "partLocation": {
      "coding": [{
        "system": "http://terminology.hl7.org/CodeSystem/source-material-location",
        "code": "Pacific Northwest, USA"
      }]
    }
  }]
}

Typical use cases

• Herbal medicines: teas, tinctures, standardised extracts.
• Animal-derived medicines: heparin, historical bovine/porcine insulin, antivenom, gelatin.
• Vaccines: embryonated egg culture, fermentation, cell culture.
• Probiotics: strains defined by species + line.
• Traditional medicine: codification of Chinese (TCM), Ayurvedic phytotherapies.

Common pitfalls

• Vernacular name: "poppy" is not codable. Always use the Latin binomial (Papaver somniferum) + an NCBI Taxonomy identifier.
• Vague geographic origin: "Asia" is not enough. For CITES traceability and counterfeit prevention, specify country or recognised geographic region.
• Unspecified part: "echinacea" is ambiguous: root, aerial part or whole plant? Chemical composition differs by part.
• Developmental stage omitted: alkaloid concentration in a plant varies sharply between flowering and ripening.
• Confusion with SubstanceDefinition: SubstanceSourceMaterial describes the origin, SubstanceDefinition the extracted chemical substance. Distinct but linked (a Taxus brevifolia source yields a defined Taxol).

Related resources

• SubstanceDefinition — references this block via sourceMaterial.
• SubstanceNucleicAcid, SubstancePolymer, SubstanceProtein, SubstanceReferenceInformation.
• MedicinalProductDefinition — finished product.
• Ingredient — naturally derived ingredient.

See also: SubstanceDefinition and Ingredient.