18.9 Resource SubstanceDefinition - Content

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
SubstanceDefinition	N		DomainResource	The detailed description of a substance, typically at a level beyond what is used for prescribing Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
identifier	Σ	0..*	Identifier	Identifier by which this substance is known
version	Σ	0..1	string	A business level edition or revision identifier
status	?!Σ	0..1	CodeableConcept	Status of substance within the catalogue e.g. active, retired Binding: PublicationStatus (Preferred)
classification	Σ	0..*	CodeableConcept	A categorization, high level e.g. polymer or nucleic acid, or food, chemical, biological, or lower e.g. polymer linear or branch chain, or type of impurity
domain	Σ	0..1	CodeableConcept	The applicable usage of the substance, as an example human or veterinary Binding: Medicinal Product Domain (Example)
grade	Σ	0..*	CodeableConcept	The quality standard, established benchmark, to which substance complies (e.g. USP/NF, BP) Binding: Substance Grade (Example)
description	Σ	0..1	markdown	Textual description of the substance
note	Σ	0..*	Annotation	Textual comment about the substance's catalogue or registry record
manufacturer	Σ	0..*	Reference(Organization)	The entity that creates, makes, produces or fabricates the substance
supplier	Σ	0..*	Reference(Organization)	An entity that is the source for the substance. It may be different from the manufacturer
moiety	Σ	0..*	BackboneElement	Moiety, for structural modifications
role	Σ	0..1	CodeableConcept	Role that the moiety is playing
identifier	Σ	0..*	Identifier	Identifier by which this moiety substance is known
name	Σ	0..1	string	Textual name for this moiety substance
stereochemistry	Σ	0..1	CodeableConcept	Stereochemistry type Binding: Stereochemistry (Example)
opticalActivity	Σ	0..1	CodeableConcept	Optical activity type Binding: Optical Activity (Example)
molecularFormula	Σ	0..1	string	Molecular formula for this moiety (e.g. with the Hill system)
amount[x]	Σ	0..1		Quantitative value for this moiety
amountQuantity			Quantity
amountString			string
measurementType	Σ	0..1	CodeableConcept	The measurement type of the quantitative value Binding: Substance Amount Type (Example)
characterization	Σ	0..*	BackboneElement	General specifications for this substance
technique	Σ	0..1	CodeableConcept	The method used to find the characterization e.g. HPLC Binding: Structure Technique (Example)
form	Σ	0..1	CodeableConcept	Describes the nature of the chemical entity and explains, for instance, whether this is a base or a salt form Binding: Substance Form (Example)
description	Σ	0..1	markdown	The description or justification in support of the interpretation of the data file
file	Σ	0..*	Attachment	The data produced by the analytical instrument or a pictorial representation of that data. Examples: a JCAMP, JDX, or ADX file, or a chromatogram or spectrum analysis
property	Σ	0..*	BackboneElement	General specifications for this substance
type	Σ	1..1	CodeableConcept	A code expressing the type of property Binding: Product Characteristic (Example)
value[x]	Σ	0..1		A value for the property
valueCodeableConcept			CodeableConcept
valueQuantity			Quantity
valueRange			Range
valueDate			date
valueBoolean			boolean
valueAttachment			Attachment
molecularWeight	Σ	0..*	BackboneElement	The average mass of a molecule of a compound
method	Σ	0..1	CodeableConcept	The method by which the weight was determined Binding: Weight Method (Example)
type	Σ	0..1	CodeableConcept	Type of molecular weight e.g. exact, average, weight average Binding: Weight Type (Example)
amount	Σ	1..1	Quantity	Used to capture quantitative values for a variety of elements
structure	Σ	0..1	BackboneElement	Structural information
stereochemistry	Σ	0..1	CodeableConcept	Stereochemistry type Binding: Stereochemistry (Example)
opticalActivity	Σ	0..1	CodeableConcept	Optical activity type Binding: Optical Activity (Example)
molecularFormula	Σ	0..1	string	An expression which states the number and type of atoms present in a molecule of a substance
molecularFormulaByMoiety	Σ	0..1	string	Specified per moiety according to the Hill system
molecularWeight	Σ	0..1	see molecularWeight	The molecular weight or weight range
technique	Σ	0..*	CodeableConcept	The method used to find the structure e.g. X-ray, NMR Binding: Structure Technique (Example)
sourceDocument	Σ	0..*	Reference(DocumentReference)	Source of information for the structure
representation	Σ	0..*	BackboneElement	A depiction of the structure of the substance
type	Σ	0..1	CodeableConcept	The kind of structural representation (e.g. full, partial) Binding: Substance Representation Type (Example)
representation	Σ	0..1	string	The structural representation as a text string in a standard format
format	Σ	0..1	CodeableConcept	The format of the representation e.g. InChI, SMILES, MOLFILE (note: not the physical file format) Binding: Substance Representation Format (Example)
document	Σ	0..1	Reference(DocumentReference)	An attachment with the structural representation e.g. a structure graphic or AnIML file
code	Σ	0..*	BackboneElement	Codes associated with the substance
code	Σ	0..1	CodeableConcept	The specific code
status	Σ	0..1	CodeableConcept	Status of the code assignment, for example 'provisional', 'approved' Binding: PublicationStatus (Preferred)
statusDate	Σ	0..1	dateTime	The date at which the code status was changed
note	Σ	0..*	Annotation	Any comment can be provided in this field
source	Σ	0..*	Reference(DocumentReference)	Supporting literature
name	Σ	0..*	BackboneElement	Names applicable to this substance
name	Σ	1..1	string	The actual name
type	Σ	0..1	CodeableConcept	Name type e.g. 'systematic', 'scientific, 'brand' Binding: Substance Name Type (Example)
status	Σ	0..1	CodeableConcept	The status of the name e.g. 'current', 'proposed' Binding: PublicationStatus (Preferred)
preferred	Σ	0..1	boolean	If this is the preferred name for this substance
language	Σ	0..*	CodeableConcept	Human language that the name is written in Binding: All Languages (Required) Additional Bindings Purpose Common Languages Starter
domain	Σ	0..*	CodeableConcept	The use context of this name e.g. as an active ingredient or as a food colour additive Binding: Substance Name Domain (Example)
jurisdiction	Σ	0..*	CodeableConcept	The jurisdiction where this name applies Binding: Jurisdiction ValueSet (Example)
synonym	Σ	0..*	see name	A synonym of this particular name, by which the substance is also known
translation	Σ	0..*	see name	A translation for this name into another human language
official	Σ	0..*	BackboneElement	Details of the official nature of this name
authority	Σ	0..1	CodeableConcept	Which authority uses this official name Binding: Substance Name Authority (Preferred)
status	Σ	0..1	CodeableConcept	The status of the official name, for example 'draft', 'active' Binding: PublicationStatus (Preferred)
date	Σ	0..1	dateTime	Date of official name change
source	Σ	0..*	Reference(DocumentReference)	Supporting literature
relationship	Σ	0..*	BackboneElement	A link between this substance and another
substanceDefinition[x]	Σ	0..1		A pointer to another substance, as a resource or a representational code
substanceDefinitionReference			Reference(SubstanceDefinition)
substanceDefinitionCodeableConcept			CodeableConcept
type	Σ	1..1	CodeableConcept	For example "salt to parent", "active moiety" Binding: Substance Relationship Type (Example)
isDefining	Σ	0..1	boolean	For example where an enzyme strongly bonds with a particular substance, this is a defining relationship for that enzyme, out of several possible relationships
amount[x]	Σ	0..1		A numeric factor for the relationship, e.g. that a substance salt has some percentage of active substance in relation to some other
amountQuantity			Quantity
amountRatio			Ratio
amountString			string
amountRange			Range
ratioHighLimitAmount	Σ	0..1	Ratio	For use when the numeric has an uncertain range
comparator	Σ	0..1	CodeableConcept	An operator for the amount, for example "average", "approximately", "less than" Binding: Substance Amount Type (Example)
measurementType	Σ	0..1	CodeableConcept	The kind of measurement the amount represents (e.g. IC50, Kd, Ki, mole ratio) Binding: Substance Measurement Type (Example)
interaction	Σ	0..1	CodeableConcept	For target relationships, the kind of interaction (e.g. binding, inhibition, agonism) Binding: Substance Interaction Type (Example)
organism	Σ	0..1	CodeableConcept	For anti-infective target relationships, the specific organism targeted Binding: Substance Target Organism (Example)
organismType	Σ	0..1	CodeableConcept	For anti-infective target relationships, the high-level type of organism targeted Binding: Substance Target Organism Type (Example)
source	Σ	0..*	Reference(DocumentReference)	Supporting literature
sourceMaterial	Σ	0..1	BackboneElement	Material or taxonomic/anatomical source
type	Σ	0..1	CodeableConcept	Classification of the origin of the raw material. e.g. cat hair is an Animal source type Binding: Source Material Type (Example)
genus	Σ	0..1	CodeableConcept	The genus of an organism e.g. the Latin epithet of the plant/animal scientific name Binding: Source Material Genus (Example)
species	Σ	0..1	CodeableConcept	The species of an organism e.g. the Latin epithet of the species of the plant/animal Binding: Source Material Species (Example)
part	Σ	0..1	CodeableConcept	An anatomical origin of the source material within an organism Binding: Source Material Part (Example)
countryOfOrigin	Σ	0..*	CodeableConcept	The country or countries where the material is harvested Binding: Country ValueSet (Required)
nucleicAcid		0..1	BackboneElement	Data items specific to nucleic acids
sequenceType	Σ	0..1	CodeableConcept	The type of the sequence (e.g. DNA, RNA) Binding: Substance Sequence Type (Example)
numberOfSubunits	Σ	0..1	integer	The number of subunits — strands of nucleic acid that are tightly associated typically through Watson-Crick base pairing
areaOfHybridisation	Σ	0..1	string	The area of hybridisation, for double-stranded RNA or DNA. Expressed as the subunit number followed by the residue number, in increasing order
oligoNucleotideType	Σ	0..1	CodeableConcept	Type or class of the oligonucleotide Binding: Oligonucleotide Type (Example)
subunit	Σ	0..*	BackboneElement	A subunit constituting the nucleic acid
subunit	Σ	0..1	integer	Index of the subunit in decreasing length order
sequence	Σ	0..1	string	The nucleotide sequence in 5’→3’ notation using standard single-letter codes
length	Σ	0..1	integer	The length of the sequence
sequenceAttachment	Σ	0..1	Attachment	The sequence as an attached file
fivePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 5’ terminus. Since the sequence is represented 5’→3’, this is the first nucleotide in the sequence Binding: Nucleotide Terminus (Example)
threePrime	Σ	0..1	CodeableConcept	The nucleotide present at the 3’ terminus. Since the sequence is represented 5’→3’, this is the last nucleotide in the sequence Binding: Nucleotide Terminus (Example)
linkage	Σ	0..*	BackboneElement	The linkages between sugar residues in the nucleotide sequence
connectivity	Σ	0..1	string	The chemistry of the linkage
substance	Σ	0..1	CodeableReference(SubstanceDefinition)	The linkage substance, as a code or a reference to its SubstanceDefinition
residueSite	Σ	0..1	string	The residue positions at which this linkage applies, in 5’→3’ direction
sugar	Σ	0..*	BackboneElement	A sugar component of the nucleotide sequence
substance	Σ	0..1	CodeableReference(SubstanceDefinition)	The sugar substance, as a code or a reference to its SubstanceDefinition
residueSite	Σ	0..1	string	The residue positions at which this sugar applies, in 5’→3’ direction
gene	Σ	0..*	BackboneElement	The gene that codes for this substance
sequenceOrigin	Σ	0..1	CodeableConcept	The species or lineage from which the gene sequence originated Binding: Gene Sequence Origin (Example)
gene	Σ	0..1	CodeableReference(SubstanceDefinition)	The gene itself, as a code or a reference to a SubstanceDefinition
source	Σ	0..*	Reference(DocumentReference)	Supporting literature for the gene information
geneElement	Σ	0..*	BackboneElement	Gene elements that comprise a nucleic acid construct (used for gene therapy)
type	Σ	0..1	CodeableConcept	The functional role of the element (e.g. promoter, enhancer, coding sequence) Binding: Gene Element Type (Example)
element	Σ	0..1	CodeableReference(SubstanceDefinition)	The element itself, as a code or a reference to a SubstanceDefinition
source	Σ	0..*	Reference(DocumentReference)	Supporting literature for the gene element information
polymer		0..1	BackboneElement	Data items specific to polymers
class	Σ	0..1	CodeableConcept	Overall type of the polymer Binding: Polymer Class (Example)
geometry	Σ	0..1	CodeableConcept	Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic Binding: Polymer Geometry (Example)
copolymerConnectivity	Σ	0..*	CodeableConcept	Describes the copolymer sequence type (polymer connectivity) Binding: Copolymer Connectivity (Example)
modification	Σ	0..1	string	A modification applied to the polymer
monomerSet	Σ	0..*	BackboneElement	A set of monomers used to build the polymer
ratioType	Σ	0..1	CodeableConcept	Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio Binding: Polymer Monomer Ratio Type (Example)
startingMaterial	Σ	0..*	BackboneElement	The starting materials - monomer(s) used in the synthesis of the polymer
code	Σ	0..1	CodeableReference(SubstanceDefinition)	The substance acting as starting material, as a code or a reference to a SubstanceDefinition Binding: Substance Code (Example)
category	Σ	0..1	CodeableConcept	Substance high level category, e.g. chemical substance Binding: Polymer Starting Material Category (Example)
isDefining	Σ	0..1	boolean	Whether this starting material is part of what defines the polymer's unique identity
amount	Σ	0..1	Quantity	A percentage
repeat	Σ	0..*	BackboneElement	Specifies and quantifies the repeated units and their configuration
averageMolecularFormula	Σ	0..1	string	A representation of an (average) molecular formula from a polymer
repeatUnitAmountType	Σ	0..1	CodeableConcept	How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average) Binding: Polymer Monomer Ratio Type (Example)
repeatUnit	Σ	0..*	BackboneElement	An SRU - Structural Repeat Unit
unit	Σ	0..1	string	Identification of the structural repeat unit (SRU)
orientation	Σ	0..1	CodeableConcept	The orientation of the polymerisation, e.g. head-tail, head-head, random Binding: Polymerisation Orientation (Example)
amount	Σ	0..1	integer	Number of repeats of this unit
degreeOfPolymerisation	Σ	0..*	BackboneElement	Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
type	Σ	0..1	CodeableConcept	The type of degree of polymerisation, e.g. SRU/Polymer ratio Binding: Degree of Polymerisation Type (Example)
average	Σ	0..1	integer	An average amount of polymerisation
low	Σ	0..1	integer	A low expected limit of the amount
high	Σ	0..1	integer	A high expected limit of the amount
structuralRepresentation	Σ	0..*	see representation	A graphical structure for this SRU
protein		0..1	BackboneElement	Data items specific to proteins
sequenceType	Σ	0..1	CodeableConcept	Whether the sequence is complete or partial Binding: Substance Sequence Type (Example)
numberOfSubunits	Σ	0..1	integer	Number of subunits — linear sequences of amino acids linked through peptide bonds
disulfideLinkage	Σ	0..*	string	Disulphide bond(s) between cysteine residues on the same subunit or across two different subunits. Positions are listed in increasing order of subunit number and intra-subunit position, followed by the amino-acid abbreviations. The positions should contain Cysteine residues
subunit	Σ	0..*	BackboneElement	Each subunit constituting the protein. A subunit is a linear sequence of amino acids linked through peptide bonds. Used when the finished protein is a complex of multiple sequences (not for domains within a single sequence). Subunits are listed in order of decreasing length; ties resolved by decreasing molecular weight; identical sequences are repeated
subunit	Σ	0..1	integer	Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts
sequence	Σ	0..1	string	The amino-acid sequence, listed N- to C-terminal using standard single-letter amino-acid codes. Uppercase denotes L-amino acids, lowercase denotes D-amino acids. Transcribed proteins are described using the translated sequence; for synthetic peptides containing amino acids without a single-letter code, X is used. Modified amino acids are identified by their position in the sequence
length	Σ	0..1	integer	Length of linear sequences of amino acids contained in the subunit
sequenceAttachment	Σ	0..1	Attachment	The amino-acid sequence as an attached file
nTerminalModification	Σ	0..1	CodeableReference(SubstanceDefinition)	The modification fragment at the N-terminal of the protein
cTerminalModification	Σ	0..1	CodeableReference(SubstanceDefinition)	The modification fragment at the C-terminal of the protein
gene	Σ	0..*	see gene	The gene that codes for this substance
Documentation for this format

See the Extensions for this resource

<SubstanceDefinition xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Identifier by which this substance is known --></identifier>
 <version value="[string]"/><!-- 0..1 A business level edition or revision identifier -->
 <status><!-- 0..1 CodeableConcept Status of substance within the catalogue e.g. active, retired --></status>
 <classification><!-- 0..* CodeableConcept A categorization, high level e.g. polymer or nucleic acid, or food, chemical, biological, or lower e.g. polymer linear or branch chain, or type of impurity --></classification>
 <domain><!-- 0..1 CodeableConcept The applicable usage of the substance, as an example human or veterinary --></domain>
 <grade><!-- 0..* CodeableConcept The quality standard, established benchmark, to which substance complies (e.g. USP/NF, BP) --></grade>
 <description value="[markdown]"/><!-- 0..1 Textual description of the substance -->
 <note><!-- 0..* Annotation Textual comment about the substance's catalogue or registry record --></note>
 <manufacturer><!-- 0..* Reference(Organization) The entity that creates, makes, produces or fabricates the substance --></manufacturer>
 <supplier><!-- 0..* Reference(Organization) An entity that is the source for the substance. It may be different from the manufacturer --></supplier>
 <moiety>  <!-- 0..* Moiety, for structural modifications -->
  <role><!-- 0..1 CodeableConcept Role that the moiety is playing --></role>
  <identifier><!-- 0..* Identifier Identifier by which this moiety substance is known --></identifier>
  <name value="[string]"/><!-- 0..1 Textual name for this moiety substance -->
  <stereochemistry><!-- 0..1 CodeableConcept Stereochemistry type --></stereochemistry>
  <opticalActivity><!-- 0..1 CodeableConcept Optical activity type --></opticalActivity>
  <molecularFormula value="[string]"/><!-- 0..1 Molecular formula for this moiety (e.g. with the Hill system) -->
  <amount[x]><!-- 0..1 Quantity|string Quantitative value for this moiety --></amount[x]>
  <measurementType><!-- 0..1 CodeableConcept The measurement type of the quantitative value --></measurementType>
 </moiety>
 <characterization>  <!-- 0..* General specifications for this substance -->
  <technique><!-- 0..1 CodeableConcept The method used to find the characterization e.g. HPLC --></technique>
  <form><!-- 0..1 CodeableConcept Describes the nature of the chemical entity and explains, for instance, whether this is a base or a salt form --></form>
  <description value="[markdown]"/><!-- 0..1 The description or justification in support of the interpretation of the data file -->
  <file><!-- 0..* Attachment The data produced by the analytical instrument or a pictorial representation of that data. Examples: a JCAMP, JDX, or ADX file, or a chromatogram or spectrum analysis --></file>
 </characterization>
 <property>  <!-- 0..* General specifications for this substance -->
  <type><!-- 1..1 CodeableConcept A code expressing the type of property --></type>
  <value[x]><!-- 0..1 CodeableConcept|Quantity|Range|date|boolean|Attachment A value for the property --></value[x]>
 </property>
 <molecularWeight>  <!-- 0..* The average mass of a molecule of a compound -->
  <method><!-- 0..1 CodeableConcept The method by which the weight was determined --></method>
  <type><!-- 0..1 CodeableConcept Type of molecular weight e.g. exact, average, weight average --></type>
  <amount><!-- 1..1 Quantity Used to capture quantitative values for a variety of elements --></amount>
 </molecularWeight>
 <structure>  <!-- 0..1 Structural information -->
  <stereochemistry><!-- 0..1 CodeableConcept Stereochemistry type --></stereochemistry>
  <opticalActivity><!-- 0..1 CodeableConcept Optical activity type --></opticalActivity>
  <molecularFormula value="[string]"/><!-- 0..1 An expression which states the number and type of atoms present in a molecule of a substance -->
  <molecularFormulaByMoiety value="[string]"/><!-- 0..1 Specified per moiety according to the Hill system -->
  <molecularWeight><!-- 0..1 Content as for SubstanceDefinition.molecularWeight The molecular weight or weight range --></molecularWeight>
  <technique><!-- 0..* CodeableConcept The method used to find the structure e.g. X-ray, NMR --></technique>
  <sourceDocument><!-- 0..* Reference(DocumentReference) Source of information for the structure --></sourceDocument>
  <representation>  <!-- 0..* A depiction of the structure of the substance -->
   <type><!-- 0..1 CodeableConcept The kind of structural representation (e.g. full, partial) --></type>
   <representation value="[string]"/><!-- 0..1 The structural representation as a text string in a standard format -->
   <format><!-- 0..1 CodeableConcept The format of the representation e.g. InChI, SMILES, MOLFILE (note: not the physical file format) --></format>
   <document><!-- 0..1 Reference(DocumentReference) An attachment with the structural representation e.g. a structure graphic or AnIML file --></document>
  </representation>
 </structure>
 <code>  <!-- 0..* Codes associated with the substance -->
  <code><!-- 0..1 CodeableConcept The specific code --></code>
  <status><!-- 0..1 CodeableConcept Status of the code assignment, for example 'provisional', 'approved' --></status>
  <statusDate value="[dateTime]"/><!-- 0..1 The date at which the code status was changed -->
  <note><!-- 0..* Annotation Any comment can be provided in this field --></note>
  <source><!-- 0..* Reference(DocumentReference) Supporting literature --></source>
 </code>
 <name>  <!-- 0..* Names applicable to this substance -->
  <name value="[string]"/><!-- 1..1 The actual name -->
  <type><!-- 0..1 CodeableConcept Name type e.g. 'systematic',  'scientific, 'brand' --></type>
  <status><!-- 0..1 CodeableConcept The status of the name e.g. 'current', 'proposed' --></status>
  <preferred value="[boolean]"/><!-- 0..1 If this is the preferred name for this substance -->
  <language><!-- 0..* CodeableConcept Human language that the name is written in --></language>
  <domain><!-- 0..* CodeableConcept The use context of this name e.g. as an active ingredient or as a food colour additive --></domain>
  <jurisdiction><!-- 0..* CodeableConcept The jurisdiction where this name applies  --></jurisdiction>
  <synonym><!-- 0..* Content as for SubstanceDefinition.name A synonym of this particular name, by which the substance is also known --></synonym>
  <translation><!-- 0..* Content as for SubstanceDefinition.name A translation for this name into another human language --></translation>
  <official>  <!-- 0..* Details of the official nature of this name -->
   <authority><!-- 0..1 CodeableConcept Which authority uses this official name --></authority>
   <status><!-- 0..1 CodeableConcept The status of the official name, for example 'draft', 'active' --></status>
   <date value="[dateTime]"/><!-- 0..1 Date of official name change -->
  </official>
  <source><!-- 0..* Reference(DocumentReference) Supporting literature --></source>
 </name>
 <relationship>  <!-- 0..* A link between this substance and another -->
  <substanceDefinition[x]><!-- 0..1 Reference(SubstanceDefinition)|
    CodeableConcept A pointer to another substance, as a resource or a representational code --></substanceDefinition[x]>
  <type><!-- 1..1 CodeableConcept For example "salt to parent", "active moiety" --></type>
  <isDefining value="[boolean]"/><!-- 0..1 For example where an enzyme strongly bonds with a particular substance, this is a defining relationship for that enzyme, out of several possible relationships -->
  <amount[x]><!-- 0..1 Quantity|Ratio|string|Range A numeric factor for the relationship, e.g. that a substance salt has some percentage of active substance in relation to some other --></amount[x]>
  <ratioHighLimitAmount><!-- 0..1 Ratio For use when the numeric has an uncertain range --></ratioHighLimitAmount>
  <comparator><!-- 0..1 CodeableConcept An operator for the amount, for example "average", "approximately", "less than" --></comparator>
  <measurementType><!-- 0..1 CodeableConcept The kind of measurement the amount represents (e.g. IC50, Kd, Ki, mole ratio) --></measurementType>
  <interaction><!-- 0..1 CodeableConcept For target relationships, the kind of interaction (e.g. binding, inhibition, agonism) --></interaction>
  <organism><!-- 0..1 CodeableConcept For anti-infective target relationships, the specific organism targeted --></organism>
  <organismType><!-- 0..1 CodeableConcept For anti-infective target relationships, the high-level type of organism targeted --></organismType>
  <source><!-- 0..* Reference(DocumentReference) Supporting literature --></source>
 </relationship>
 <sourceMaterial>  <!-- 0..1 Material or taxonomic/anatomical source -->
  <type><!-- 0..1 CodeableConcept Classification of the origin of the raw material. e.g. cat hair is an Animal source type --></type>
  <genus><!-- 0..1 CodeableConcept The genus of an organism e.g. the Latin epithet of the plant/animal scientific name --></genus>
  <species><!-- 0..1 CodeableConcept The species of an organism e.g. the Latin epithet of the species of the plant/animal --></species>
  <part><!-- 0..1 CodeableConcept An anatomical origin of the source material within an organism --></part>
  <countryOfOrigin><!-- 0..* CodeableConcept The country or countries where the material is harvested --></countryOfOrigin>
 </sourceMaterial>
 <nucleicAcid>  <!-- 0..1 Data items specific to nucleic acids -->
  <sequenceType><!-- 0..1 CodeableConcept The type of the sequence (e.g. DNA, RNA) --></sequenceType>
  <numberOfSubunits value="[integer]"/><!-- 0..1 The number of subunits — strands of nucleic acid that are tightly associated typically through Watson-Crick base pairing -->
  <areaOfHybridisation value="[string]"/><!-- 0..1 The area of hybridisation, for double-stranded RNA or DNA. Expressed as the subunit number followed by the residue number, in increasing order -->
  <oligoNucleotideType><!-- 0..1 CodeableConcept Type or class of the oligonucleotide --></oligoNucleotideType>
  <subunit>  <!-- 0..* A subunit constituting the nucleic acid -->
   <subunit value="[integer]"/><!-- 0..1 Index of the subunit in decreasing length order -->
   <sequence value="[string]"/><!-- 0..1 The nucleotide sequence in 5’→3’ notation using standard single-letter codes -->
   <length value="[integer]"/><!-- 0..1 The length of the sequence -->
   <sequenceAttachment><!-- 0..1 Attachment The sequence as an attached file --></sequenceAttachment>
   <fivePrime><!-- 0..1 CodeableConcept The nucleotide present at the 5’ terminus. Since the sequence is represented 5’→3’, this is the first nucleotide in the sequence --></fivePrime>
   <threePrime><!-- 0..1 CodeableConcept The nucleotide present at the 3’ terminus. Since the sequence is represented 5’→3’, this is the last nucleotide in the sequence --></threePrime>
   <linkage>  <!-- 0..* The linkages between sugar residues in the nucleotide sequence -->
    <connectivity value="[string]"/><!-- 0..1 The chemistry of the linkage -->
    <substance><!-- 0..1 CodeableReference(SubstanceDefinition) The linkage substance, as a code or a reference to its SubstanceDefinition --></substance>
    <residueSite value="[string]"/><!-- 0..1 The residue positions at which this linkage applies, in 5’→3’ direction -->
   </linkage>
   <sugar>  <!-- 0..* A sugar component of the nucleotide sequence -->
    <substance><!-- 0..1 CodeableReference(SubstanceDefinition) The sugar substance, as a code or a reference to its SubstanceDefinition --></substance>
    <residueSite value="[string]"/><!-- 0..1 The residue positions at which this sugar applies, in 5’→3’ direction -->
   </sugar>
  </subunit>
  <gene>  <!-- 0..* The gene that codes for this substance -->
   <sequenceOrigin><!-- 0..1 CodeableConcept The species or lineage from which the gene sequence originated --></sequenceOrigin>
   <gene><!-- 0..1 CodeableReference(SubstanceDefinition) The gene itself, as a code or a reference to a SubstanceDefinition --></gene>
   <source><!-- 0..* Reference(DocumentReference) Supporting literature for the gene information --></source>
  </gene>
  <geneElement>  <!-- 0..* Gene elements that comprise a nucleic acid construct (used for gene therapy) -->
   <type><!-- 0..1 CodeableConcept The functional role of the element (e.g. promoter, enhancer, coding sequence) --></type>
   <element><!-- 0..1 CodeableReference(SubstanceDefinition) The element itself, as a code or a reference to a SubstanceDefinition --></element>
   <source><!-- 0..* Reference(DocumentReference) Supporting literature for the gene element information --></source>
  </geneElement>
 </nucleicAcid>
 <polymer>  <!-- 0..1 Data items specific to polymers -->
  <class><!-- 0..1 CodeableConcept Overall type of the polymer --></class>
  <geometry><!-- 0..1 CodeableConcept Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic --></geometry>
  <copolymerConnectivity><!-- 0..* CodeableConcept Describes the copolymer sequence type (polymer connectivity) --></copolymerConnectivity>
  <modification value="[string]"/><!-- 0..1 A modification applied to the polymer -->
  <monomerSet>  <!-- 0..* A set of monomers used to build the polymer -->
   <ratioType><!-- 0..1 CodeableConcept Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio --></ratioType>
   <startingMaterial>  <!-- 0..* The starting materials - monomer(s) used in the synthesis of the polymer -->
    <code><!-- 0..1 CodeableReference(SubstanceDefinition) The substance acting as starting material, as a code or a reference to a SubstanceDefinition --></code>
    <category><!-- 0..1 CodeableConcept Substance high level category, e.g. chemical substance --></category>
    <isDefining value="[boolean]"/><!-- 0..1 Whether this starting material is part of what defines the polymer's unique identity -->
    <amount><!-- 0..1 Quantity A percentage --></amount>
   </startingMaterial>
  </monomerSet>
  <repeat>  <!-- 0..* Specifies and quantifies the repeated units and their configuration -->
   <averageMolecularFormula value="[string]"/><!-- 0..1 A representation of an (average) molecular formula from a polymer -->
   <repeatUnitAmountType><!-- 0..1 CodeableConcept How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average) --></repeatUnitAmountType>
   <repeatUnit>  <!-- 0..* An SRU - Structural Repeat Unit -->
    <unit value="[string]"/><!-- 0..1 Identification of the structural repeat unit (SRU) -->
    <orientation><!-- 0..1 CodeableConcept The orientation of the polymerisation, e.g. head-tail, head-head, random --></orientation>
    <amount value="[integer]"/><!-- 0..1 Number of repeats of this unit -->
    <degreeOfPolymerisation>  <!-- 0..* Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described -->
     <type><!-- 0..1 CodeableConcept The type of degree of polymerisation, e.g. SRU/Polymer ratio --></type>
     <average value="[integer]"/><!-- 0..1 An average amount of polymerisation -->
     <low value="[integer]"/><!-- 0..1 A low expected limit of the amount -->
     <high value="[integer]"/><!-- 0..1 A high expected limit of the amount -->
    </degreeOfPolymerisation>
    <structuralRepresentation><!-- 0..* Content as for SubstanceDefinition.structure.representation A graphical structure for this SRU --></structuralRepresentation>
   </repeatUnit>
  </repeat>
 </polymer>
 <protein>  <!-- 0..1 Data items specific to proteins -->
  <sequenceType><!-- 0..1 CodeableConcept Whether the sequence is complete or partial --></sequenceType>
  <numberOfSubunits value="[integer]"/><!-- 0..1 Number of subunits — linear sequences of amino acids linked through peptide bonds -->
  <disulfideLinkage value="[string]"/><!-- 0..* Disulphide bond(s) between cysteine residues on the same subunit or across two different subunits. Positions are listed in increasing order of subunit number and intra-subunit position, followed by the amino-acid abbreviations. The positions should contain Cysteine residues -->
  <subunit>  <!-- 0..* Each subunit constituting the protein. A subunit is a linear sequence of amino acids linked through peptide bonds. Used when the finished protein is a complex of multiple sequences (not for domains within a single sequence). Subunits are listed in order of decreasing length; ties resolved by decreasing molecular weight; identical sequences are repeated -->
   <subunit value="[integer]"/><!-- 0..1 Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts -->
   <sequence value="[string]"/><!-- 0..1 The amino-acid sequence, listed N- to C-terminal using standard single-letter amino-acid codes. Uppercase denotes L-amino acids, lowercase denotes D-amino acids. Transcribed proteins are described using the translated sequence; for synthetic peptides containing amino acids without a single-letter code, X is used. Modified amino acids are identified by their position in the sequence -->
   <length value="[integer]"/><!-- 0..1 Length of linear sequences of amino acids contained in the subunit -->
   <sequenceAttachment><!-- 0..1 Attachment The amino-acid sequence as an attached file --></sequenceAttachment>
   <nTerminalModification><!-- 0..1 CodeableReference(SubstanceDefinition) The modification fragment at the N-terminal of the protein --></nTerminalModification>
   <cTerminalModification><!-- 0..1 CodeableReference(SubstanceDefinition) The modification fragment at the C-terminal of the protein --></cTerminalModification>
  </subunit>
  <gene><!-- 0..* Content as for SubstanceDefinition.nucleicAcid.gene The gene that codes for this substance --></gene>
 </protein>
</SubstanceDefinition>

{
  "resourceType" : "SubstanceDefinition",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Identifier by which this substance is known
  "version" : "<string>", // A business level edition or revision identifier
  "status" : { CodeableConcept }, // Status of substance within the catalogue e.g. active, retired
  "classification" : [{ CodeableConcept }], // A categorization, high level e.g. polymer or nucleic acid, or food, chemical, biological, or lower e.g. polymer linear or branch chain, or type of impurity
  "domain" : { CodeableConcept }, // The applicable usage of the substance, as an example human or veterinary
  "grade" : [{ CodeableConcept }], // The quality standard, established benchmark, to which substance complies (e.g. USP/NF, BP)
  "description" : "<markdown>", // Textual description of the substance
  "note" : [{ Annotation }], // Textual comment about the substance's catalogue or registry record
  "manufacturer" : [{ Reference(Organization) }], // The entity that creates, makes, produces or fabricates the substance
  "supplier" : [{ Reference(Organization) }], // An entity that is the source for the substance. It may be different from the manufacturer
  "moiety" : [{ // Moiety, for structural modifications
    "role" : { CodeableConcept }, // Role that the moiety is playing
    "identifier" : [{ Identifier }], // Identifier by which this moiety substance is known
    "name" : "<string>", // Textual name for this moiety substance
    "stereochemistry" : { CodeableConcept }, // Stereochemistry type
    "opticalActivity" : { CodeableConcept }, // Optical activity type
    "molecularFormula" : "<string>", // Molecular formula for this moiety (e.g. with the Hill system)
    // amount[x]: Quantitative value for this moiety. One of these 2:
    "amountQuantity" : { Quantity },
    "amountString" : "<string>",
    "measurementType" : { CodeableConcept } // The measurement type of the quantitative value
  }],
  "characterization" : [{ // General specifications for this substance
    "technique" : { CodeableConcept }, // The method used to find the characterization e.g. HPLC
    "form" : { CodeableConcept }, // Describes the nature of the chemical entity and explains, for instance, whether this is a base or a salt form
    "description" : "<markdown>", // The description or justification in support of the interpretation of the data file
    "file" : [{ Attachment }] // The data produced by the analytical instrument or a pictorial representation of that data. Examples: a JCAMP, JDX, or ADX file, or a chromatogram or spectrum analysis
  }],
  "property" : [{ // General specifications for this substance
    "type" : { CodeableConcept }, // R!  A code expressing the type of property
    // value[x]: A value for the property. One of these 6:
    "valueCodeableConcept" : { CodeableConcept },
    "valueQuantity" : { Quantity },
    "valueRange" : { Range },
    "valueDate" : "<date>",
    "valueBoolean" : <boolean>,
    "valueAttachment" : { Attachment }
  }],
  "molecularWeight" : [{ // The average mass of a molecule of a compound
    "method" : { CodeableConcept }, // The method by which the weight was determined
    "type" : { CodeableConcept }, // Type of molecular weight e.g. exact, average, weight average
    "amount" : { Quantity } // R!  Used to capture quantitative values for a variety of elements
  }],
  "structure" : { // Structural information
    "stereochemistry" : { CodeableConcept }, // Stereochemistry type
    "opticalActivity" : { CodeableConcept }, // Optical activity type
    "molecularFormula" : "<string>", // An expression which states the number and type of atoms present in a molecule of a substance
    "molecularFormulaByMoiety" : "<string>", // Specified per moiety according to the Hill system
    "molecularWeight" : { Content as for SubstanceDefinition.molecularWeight }, // The molecular weight or weight range
    "technique" : [{ CodeableConcept }], // The method used to find the structure e.g. X-ray, NMR
    "sourceDocument" : [{ Reference(DocumentReference) }], // Source of information for the structure
    "representation" : [{ // A depiction of the structure of the substance
      "type" : { CodeableConcept }, // The kind of structural representation (e.g. full, partial)
      "representation" : "<string>", // The structural representation as a text string in a standard format
      "format" : { CodeableConcept }, // The format of the representation e.g. InChI, SMILES, MOLFILE (note: not the physical file format)
      "document" : { Reference(DocumentReference) } // An attachment with the structural representation e.g. a structure graphic or AnIML file
    }]
  },
  "code" : [{ // Codes associated with the substance
    "code" : { CodeableConcept }, // The specific code
    "status" : { CodeableConcept }, // Status of the code assignment, for example 'provisional', 'approved'
    "statusDate" : "<dateTime>", // The date at which the code status was changed
    "note" : [{ Annotation }], // Any comment can be provided in this field
    "source" : [{ Reference(DocumentReference) }] // Supporting literature
  }],
  "name" : [{ // Names applicable to this substance
    "name" : "<string>", // R!  The actual name
    "type" : { CodeableConcept }, // Name type e.g. 'systematic',  'scientific, 'brand'
    "status" : { CodeableConcept }, // The status of the name e.g. 'current', 'proposed'
    "preferred" : <boolean>, // If this is the preferred name for this substance
    "language" : [{ CodeableConcept }], // Human language that the name is written in
    "domain" : [{ CodeableConcept }], // The use context of this name e.g. as an active ingredient or as a food colour additive
    "jurisdiction" : [{ CodeableConcept }], // The jurisdiction where this name applies 
    "synonym" : [{ Content as for SubstanceDefinition.name }], // A synonym of this particular name, by which the substance is also known
    "translation" : [{ Content as for SubstanceDefinition.name }], // A translation for this name into another human language
    "official" : [{ // Details of the official nature of this name
      "authority" : { CodeableConcept }, // Which authority uses this official name
      "status" : { CodeableConcept }, // The status of the official name, for example 'draft', 'active'
      "date" : "<dateTime>" // Date of official name change
    }],
    "source" : [{ Reference(DocumentReference) }] // Supporting literature
  }],
  "relationship" : [{ // A link between this substance and another
    // substanceDefinition[x]: A pointer to another substance, as a resource or a representational code. One of these 2:
    "substanceDefinitionReference" : { Reference(SubstanceDefinition) },
    "substanceDefinitionCodeableConcept" : { CodeableConcept },
    "type" : { CodeableConcept }, // R!  For example "salt to parent", "active moiety"
    "isDefining" : <boolean>, // For example where an enzyme strongly bonds with a particular substance, this is a defining relationship for that enzyme, out of several possible relationships
    // amount[x]: 
      A numeric factor for the relationship, e.g. that a substance salt has some percentage of active substance in relation to some other. One of these 4:
    "amountQuantity" : { Quantity },
    "amountRatio" : { Ratio },
    "amountString" : "<string>",
    "amountRange" : { Range },
    "ratioHighLimitAmount" : { Ratio }, // For use when the numeric has an uncertain range
    "comparator" : { CodeableConcept }, // An operator for the amount, for example "average", "approximately", "less than"
    "measurementType" : { CodeableConcept }, // The kind of measurement the amount represents (e.g. IC50, Kd, Ki, mole ratio)
    "interaction" : { CodeableConcept }, // For target relationships, the kind of interaction (e.g. binding, inhibition, agonism)
    "organism" : { CodeableConcept }, // For anti-infective target relationships, the specific organism targeted
    "organismType" : { CodeableConcept }, // For anti-infective target relationships, the high-level type of organism targeted
    "source" : [{ Reference(DocumentReference) }] // Supporting literature
  }],
  "sourceMaterial" : { // Material or taxonomic/anatomical source
    "type" : { CodeableConcept }, // Classification of the origin of the raw material. e.g. cat hair is an Animal source type
    "genus" : { CodeableConcept }, // The genus of an organism e.g. the Latin epithet of the plant/animal scientific name
    "species" : { CodeableConcept }, // The species of an organism e.g. the Latin epithet of the species of the plant/animal
    "part" : { CodeableConcept }, // An anatomical origin of the source material within an organism
    "countryOfOrigin" : [{ CodeableConcept }] // The country or countries where the material is harvested
  },
  "nucleicAcid" : { // Data items specific to nucleic acids
    "sequenceType" : { CodeableConcept }, // The type of the sequence (e.g. DNA, RNA)
    "numberOfSubunits" : <integer>, // The number of subunits — strands of nucleic acid that are tightly associated typically through Watson-Crick base pairing
    "areaOfHybridisation" : "<string>", // The area of hybridisation, for double-stranded RNA or DNA. Expressed as the subunit number followed by the residue number, in increasing order
    "oligoNucleotideType" : { CodeableConcept }, // Type or class of the oligonucleotide
    "subunit" : [{ // A subunit constituting the nucleic acid
      "subunit" : <integer>, // Index of the subunit in decreasing length order
      "sequence" : "<string>", // The nucleotide sequence in 5’→3’ notation using standard single-letter codes
      "length" : <integer>, // The length of the sequence
      "sequenceAttachment" : { Attachment }, // The sequence as an attached file
      "fivePrime" : { CodeableConcept }, // The nucleotide present at the 5’ terminus. Since the sequence is represented 5’→3’, this is the first nucleotide in the sequence
      "threePrime" : { CodeableConcept }, // The nucleotide present at the 3’ terminus. Since the sequence is represented 5’→3’, this is the last nucleotide in the sequence
      "linkage" : [{ // The linkages between sugar residues in the nucleotide sequence
        "connectivity" : "<string>", // The chemistry of the linkage
        "substance" : { CodeableReference(SubstanceDefinition) }, // The linkage substance, as a code or a reference to its SubstanceDefinition
        "residueSite" : "<string>" // The residue positions at which this linkage applies, in 5’→3’ direction
      }],
      "sugar" : [{ // A sugar component of the nucleotide sequence
        "substance" : { CodeableReference(SubstanceDefinition) }, // The sugar substance, as a code or a reference to its SubstanceDefinition
        "residueSite" : "<string>" // The residue positions at which this sugar applies, in 5’→3’ direction
      }]
    }],
    "gene" : [{ // The gene that codes for this substance
      "sequenceOrigin" : { CodeableConcept }, // The species or lineage from which the gene sequence originated
      "gene" : { CodeableReference(SubstanceDefinition) }, // The gene itself, as a code or a reference to a SubstanceDefinition
      "source" : [{ Reference(DocumentReference) }] // Supporting literature for the gene information
    }],
    "geneElement" : [{ // Gene elements that comprise a nucleic acid construct (used for gene therapy)
      "type" : { CodeableConcept }, // The functional role of the element (e.g. promoter, enhancer, coding sequence)
      "element" : { CodeableReference(SubstanceDefinition) }, // The element itself, as a code or a reference to a SubstanceDefinition
      "source" : [{ Reference(DocumentReference) }] // Supporting literature for the gene element information
    }]
  },
  "polymer" : { // Data items specific to polymers
    "class" : { CodeableConcept }, // Overall type of the polymer
    "geometry" : { CodeableConcept }, // Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
    "copolymerConnectivity" : [{ CodeableConcept }], // Describes the copolymer sequence type (polymer connectivity)
    "modification" : "<string>", // A modification applied to the polymer
    "monomerSet" : [{ // A set of monomers used to build the polymer
      "ratioType" : { CodeableConcept }, // Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
      "startingMaterial" : [{ // The starting materials - monomer(s) used in the synthesis of the polymer
        "code" : { CodeableReference(SubstanceDefinition) }, // The substance acting as starting material, as a code or a reference to a SubstanceDefinition
        "category" : { CodeableConcept }, // Substance high level category, e.g. chemical substance
        "isDefining" : <boolean>, // Whether this starting material is part of what defines the polymer's unique identity
        "amount" : { Quantity } // A percentage
      }]
    }],
    "repeat" : [{ // Specifies and quantifies the repeated units and their configuration
      "averageMolecularFormula" : "<string>", // A representation of an (average) molecular formula from a polymer
      "repeatUnitAmountType" : { CodeableConcept }, // How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
      "repeatUnit" : [{ // An SRU - Structural Repeat Unit
        "unit" : "<string>", // Identification of the structural repeat unit (SRU)
        "orientation" : { CodeableConcept }, // The orientation of the polymerisation, e.g. head-tail, head-head, random
        "amount" : <integer>, // Number of repeats of this unit
        "degreeOfPolymerisation" : [{ // Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
          "type" : { CodeableConcept }, // The type of degree of polymerisation, e.g. SRU/Polymer ratio
          "average" : <integer>, // An average amount of polymerisation
          "low" : <integer>, // A low expected limit of the amount
          "high" : <integer> // A high expected limit of the amount
        }],
        "structuralRepresentation" : [{ Content as for SubstanceDefinition.structure.representation }] // A graphical structure for this SRU
      }]
    }]
  },
  "protein" : { // Data items specific to proteins
    "sequenceType" : { CodeableConcept }, // Whether the sequence is complete or partial
    "numberOfSubunits" : <integer>, // Number of subunits — linear sequences of amino acids linked through peptide bonds
    "disulfideLinkage" : ["<string>"], // Disulphide bond(s) between cysteine residues on the same subunit or across two different subunits. Positions are listed in increasing order of subunit number and intra-subunit position, followed by the amino-acid abbreviations. The positions should contain Cysteine residues
    "subunit" : [{ // Each subunit constituting the protein. A subunit is a linear sequence of amino acids linked through peptide bonds. Used when the finished protein is a complex of multiple sequences (not for domains within a single sequence). Subunits are listed in order of decreasing length; ties resolved by decreasing molecular weight; identical sequences are repeated
      "subunit" : <integer>, // Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts
      "sequence" : "<string>", // The amino-acid sequence, listed N- to C-terminal using standard single-letter amino-acid codes. Uppercase denotes L-amino acids, lowercase denotes D-amino acids. Transcribed proteins are described using the translated sequence; for synthetic peptides containing amino acids without a single-letter code, X is used. Modified amino acids are identified by their position in the sequence
      "length" : <integer>, // Length of linear sequences of amino acids contained in the subunit
      "sequenceAttachment" : { Attachment }, // The amino-acid sequence as an attached file
      "nTerminalModification" : { CodeableReference(SubstanceDefinition) }, // The modification fragment at the N-terminal of the protein
      "cTerminalModification" : { CodeableReference(SubstanceDefinition) } // The modification fragment at the C-terminal of the protein
    }],
    "gene" : [{ Content as for SubstanceDefinition.nucleicAcid.gene }] // The gene that codes for this substance
  }
}

@prefix fhir: <http://hl7.org/fhir/> .


[ a fhir:SubstanceDefinition;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: fhir:id, fhir:meta, fhir:implicitRules, and fhir:language
  # from DomainResource: fhir:text, fhir:contained, fhir:extension, and fhir:modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Identifier by which this substance is known
  fhir:version [ string ] ; # 0..1 A business level edition or revision identifier
  fhir:status [ CodeableConcept ] ; # 0..1 Status of substance within the catalogue e.g. active, retired
  fhir:classification  ( [ CodeableConcept ] ... ) ; # 0..* A categorization, high level e.g. polymer or nucleic acid, or food, chemical, biological, or lower e.g. polymer linear or branch chain, or type of impurity
  fhir:domain [ CodeableConcept ] ; # 0..1 The applicable usage of the substance, as an example human or veterinary
  fhir:grade  ( [ CodeableConcept ] ... ) ; # 0..* The quality standard, established benchmark, to which substance complies (e.g. USP/NF, BP)
  fhir:description [ markdown ] ; # 0..1 Textual description of the substance
  fhir:note  ( [ Annotation ] ... ) ; # 0..* Textual comment about the substance's catalogue or registry record
  fhir:manufacturer  ( [ Reference(Organization) ] ... ) ; # 0..* The entity that creates, makes, produces or fabricates the substance
  fhir:supplier  ( [ Reference(Organization) ] ... ) ; # 0..* An entity that is the source for the substance. It may be different from the manufacturer
  fhir:moiety ( [ # 0..* Moiety, for structural modifications
    fhir:role [ CodeableConcept ] ; # 0..1 Role that the moiety is playing
    fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Identifier by which this moiety substance is known
    fhir:name [ string ] ; # 0..1 Textual name for this moiety substance
    fhir:stereochemistry [ CodeableConcept ] ; # 0..1 Stereochemistry type
    fhir:opticalActivity [ CodeableConcept ] ; # 0..1 Optical activity type
    fhir:molecularFormula [ string ] ; # 0..1 Molecular formula for this moiety (e.g. with the Hill system)
    # amount[x] : 0..1 Quantitative value for this moiety. One of these 2
      fhir:amount [  a fhir:Quantity ; Quantity ]
      fhir:amount [  a fhir:String ; string ]
    fhir:measurementType [ CodeableConcept ] ; # 0..1 The measurement type of the quantitative value
  ] ... ) ;
  fhir:characterization ( [ # 0..* General specifications for this substance
    fhir:technique [ CodeableConcept ] ; # 0..1 The method used to find the characterization e.g. HPLC
    fhir:form [ CodeableConcept ] ; # 0..1 Describes the nature of the chemical entity and explains, for instance, whether this is a base or a salt form
    fhir:description [ markdown ] ; # 0..1 The description or justification in support of the interpretation of the data file
    fhir:file  ( [ Attachment ] ... ) ; # 0..* The data produced by the analytical instrument or a pictorial representation of that data. Examples: a JCAMP, JDX, or ADX file, or a chromatogram or spectrum analysis
  ] ... ) ;
  fhir:property ( [ # 0..* General specifications for this substance
    fhir:type [ CodeableConcept ] ; # 1..1 A code expressing the type of property
    # value[x] : 0..1 A value for the property. One of these 6
      fhir:value [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:value [  a fhir:Quantity ; Quantity ]
      fhir:value [  a fhir:Range ; Range ]
      fhir:value [  a fhir:Date ; date ]
      fhir:value [  a fhir:Boolean ; boolean ]
      fhir:value [  a fhir:Attachment ; Attachment ]
  ] ... ) ;
  fhir:molecularWeight ( [ # 0..* The average mass of a molecule of a compound
    fhir:method [ CodeableConcept ] ; # 0..1 The method by which the weight was determined
    fhir:type [ CodeableConcept ] ; # 0..1 Type of molecular weight e.g. exact, average, weight average
    fhir:amount [ Quantity ] ; # 1..1 Used to capture quantitative values for a variety of elements
  ] ... ) ;
  fhir:structure [ # 0..1 Structural information
    fhir:stereochemistry [ CodeableConcept ] ; # 0..1 Stereochemistry type
    fhir:opticalActivity [ CodeableConcept ] ; # 0..1 Optical activity type
    fhir:molecularFormula [ string ] ; # 0..1 An expression which states the number and type of atoms present in a molecule of a substance
    fhir:molecularFormulaByMoiety [ string ] ; # 0..1 Specified per moiety according to the Hill system
    fhir:molecularWeight [ See SubstanceDefinition.molecularWeight ] ; # 0..1 The molecular weight or weight range
    fhir:technique  ( [ CodeableConcept ] ... ) ; # 0..* The method used to find the structure e.g. X-ray, NMR
    fhir:sourceDocument  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Source of information for the structure
    fhir:representation ( [ # 0..* A depiction of the structure of the substance
      fhir:type [ CodeableConcept ] ; # 0..1 The kind of structural representation (e.g. full, partial)
      fhir:representation [ string ] ; # 0..1 The structural representation as a text string in a standard format
      fhir:format [ CodeableConcept ] ; # 0..1 The format of the representation e.g. InChI, SMILES, MOLFILE (note: not the physical file format)
      fhir:document [ Reference(DocumentReference) ] ; # 0..1 An attachment with the structural representation e.g. a structure graphic or AnIML file
    ] ... ) ;
  ] ;
  fhir:code ( [ # 0..* Codes associated with the substance
    fhir:code [ CodeableConcept ] ; # 0..1 The specific code
    fhir:status [ CodeableConcept ] ; # 0..1 Status of the code assignment, for example 'provisional', 'approved'
    fhir:statusDate [ dateTime ] ; # 0..1 The date at which the code status was changed
    fhir:note  ( [ Annotation ] ... ) ; # 0..* Any comment can be provided in this field
    fhir:source  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Supporting literature
  ] ... ) ;
  fhir:name ( [ # 0..* Names applicable to this substance
    fhir:name [ string ] ; # 1..1 The actual name
    fhir:type [ CodeableConcept ] ; # 0..1 Name type e.g. 'systematic',  'scientific, 'brand'
    fhir:status [ CodeableConcept ] ; # 0..1 The status of the name e.g. 'current', 'proposed'
    fhir:preferred [ boolean ] ; # 0..1 If this is the preferred name for this substance
    fhir:language  ( [ CodeableConcept ] ... ) ; # 0..* Human language that the name is written in
    fhir:domain  ( [ CodeableConcept ] ... ) ; # 0..* The use context of this name e.g. as an active ingredient or as a food colour additive
    fhir:jurisdiction  ( [ CodeableConcept ] ... ) ; # 0..* The jurisdiction where this name applies
    fhir:synonym  ( [ See SubstanceDefinition.name ] ... ) ; # 0..* A synonym of this particular name, by which the substance is also known
    fhir:translation  ( [ See SubstanceDefinition.name ] ... ) ; # 0..* A translation for this name into another human language
    fhir:official ( [ # 0..* Details of the official nature of this name
      fhir:authority [ CodeableConcept ] ; # 0..1 Which authority uses this official name
      fhir:status [ CodeableConcept ] ; # 0..1 The status of the official name, for example 'draft', 'active'
      fhir:date [ dateTime ] ; # 0..1 Date of official name change
    ] ... ) ;
    fhir:source  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Supporting literature
  ] ... ) ;
  fhir:relationship ( [ # 0..* A link between this substance and another
    # substanceDefinition[x] : 0..1 A pointer to another substance, as a resource or a representational code. One of these 2
      fhir:substanceDefinition [  a fhir:Reference ; Reference(SubstanceDefinition) ]
      fhir:substanceDefinition [  a fhir:CodeableConcept ; CodeableConcept ]
    fhir:type [ CodeableConcept ] ; # 1..1 For example "salt to parent", "active moiety"
    fhir:isDefining [ boolean ] ; # 0..1 For example where an enzyme strongly bonds with a particular substance, this is a defining relationship for that enzyme, out of several possible relationships
    # amount[x] : 0..1 A numeric factor for the relationship, e.g. that a substance salt has some percentage of active substance in relation to some other. One of these 4
      fhir:amount [  a fhir:Quantity ; Quantity ]
      fhir:amount [  a fhir:Ratio ; Ratio ]
      fhir:amount [  a fhir:String ; string ]
      fhir:amount [  a fhir:Range ; Range ]
    fhir:ratioHighLimitAmount [ Ratio ] ; # 0..1 For use when the numeric has an uncertain range
    fhir:comparator [ CodeableConcept ] ; # 0..1 An operator for the amount, for example "average", "approximately", "less than"
    fhir:measurementType [ CodeableConcept ] ; # 0..1 The kind of measurement the amount represents (e.g. IC50, Kd, Ki, mole ratio)
    fhir:interaction [ CodeableConcept ] ; # 0..1 For target relationships, the kind of interaction (e.g. binding, inhibition, agonism)
    fhir:organism [ CodeableConcept ] ; # 0..1 For anti-infective target relationships, the specific organism targeted
    fhir:organismType [ CodeableConcept ] ; # 0..1 For anti-infective target relationships, the high-level type of organism targeted
    fhir:source  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Supporting literature
  ] ... ) ;
  fhir:sourceMaterial [ # 0..1 Material or taxonomic/anatomical source
    fhir:type [ CodeableConcept ] ; # 0..1 Classification of the origin of the raw material. e.g. cat hair is an Animal source type
    fhir:genus [ CodeableConcept ] ; # 0..1 The genus of an organism e.g. the Latin epithet of the plant/animal scientific name
    fhir:species [ CodeableConcept ] ; # 0..1 The species of an organism e.g. the Latin epithet of the species of the plant/animal
    fhir:part [ CodeableConcept ] ; # 0..1 An anatomical origin of the source material within an organism
    fhir:countryOfOrigin  ( [ CodeableConcept ] ... ) ; # 0..* The country or countries where the material is harvested
  ] ;
  fhir:nucleicAcid [ # 0..1 Data items specific to nucleic acids
    fhir:sequenceType [ CodeableConcept ] ; # 0..1 The type of the sequence (e.g. DNA, RNA)
    fhir:numberOfSubunits [ integer ] ; # 0..1 The number of subunits — strands of nucleic acid that are tightly associated typically through Watson-Crick base pairing
    fhir:areaOfHybridisation [ string ] ; # 0..1 The area of hybridisation, for double-stranded RNA or DNA. Expressed as the subunit number followed by the residue number, in increasing order
    fhir:oligoNucleotideType [ CodeableConcept ] ; # 0..1 Type or class of the oligonucleotide
    fhir:subunit ( [ # 0..* A subunit constituting the nucleic acid
      fhir:subunit [ integer ] ; # 0..1 Index of the subunit in decreasing length order
      fhir:sequence [ string ] ; # 0..1 The nucleotide sequence in 5’→3’ notation using standard single-letter codes
      fhir:length [ integer ] ; # 0..1 The length of the sequence
      fhir:sequenceAttachment [ Attachment ] ; # 0..1 The sequence as an attached file
      fhir:fivePrime [ CodeableConcept ] ; # 0..1 The nucleotide present at the 5’ terminus. Since the sequence is represented 5’→3’, this is the first nucleotide in the sequence
      fhir:threePrime [ CodeableConcept ] ; # 0..1 The nucleotide present at the 3’ terminus. Since the sequence is represented 5’→3’, this is the last nucleotide in the sequence
      fhir:linkage ( [ # 0..* The linkages between sugar residues in the nucleotide sequence
        fhir:connectivity [ string ] ; # 0..1 The chemistry of the linkage
        fhir:substance [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The linkage substance, as a code or a reference to its SubstanceDefinition
        fhir:residueSite [ string ] ; # 0..1 The residue positions at which this linkage applies, in 5’→3’ direction
      ] ... ) ;
      fhir:sugar ( [ # 0..* A sugar component of the nucleotide sequence
        fhir:substance [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The sugar substance, as a code or a reference to its SubstanceDefinition
        fhir:residueSite [ string ] ; # 0..1 The residue positions at which this sugar applies, in 5’→3’ direction
      ] ... ) ;
    ] ... ) ;
    fhir:gene ( [ # 0..* The gene that codes for this substance
      fhir:sequenceOrigin [ CodeableConcept ] ; # 0..1 The species or lineage from which the gene sequence originated
      fhir:gene [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The gene itself, as a code or a reference to a SubstanceDefinition
      fhir:source  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Supporting literature for the gene information
    ] ... ) ;
    fhir:geneElement ( [ # 0..* Gene elements that comprise a nucleic acid construct (used for gene therapy)
      fhir:type [ CodeableConcept ] ; # 0..1 The functional role of the element (e.g. promoter, enhancer, coding sequence)
      fhir:element [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The element itself, as a code or a reference to a SubstanceDefinition
      fhir:source  ( [ Reference(DocumentReference) ] ... ) ; # 0..* Supporting literature for the gene element information
    ] ... ) ;
  ] ;
  fhir:polymer [ # 0..1 Data items specific to polymers
    fhir:class [ CodeableConcept ] ; # 0..1 Overall type of the polymer
    fhir:geometry [ CodeableConcept ] ; # 0..1 Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
    fhir:copolymerConnectivity  ( [ CodeableConcept ] ... ) ; # 0..* Describes the copolymer sequence type (polymer connectivity)
    fhir:modification [ string ] ; # 0..1 A modification applied to the polymer
    fhir:monomerSet ( [ # 0..* A set of monomers used to build the polymer
      fhir:ratioType [ CodeableConcept ] ; # 0..1 Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
      fhir:startingMaterial ( [ # 0..* The starting materials - monomer(s) used in the synthesis of the polymer
        fhir:code [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The substance acting as starting material, as a code or a reference to a SubstanceDefinition
        fhir:category [ CodeableConcept ] ; # 0..1 Substance high level category, e.g. chemical substance
        fhir:isDefining [ boolean ] ; # 0..1 Whether this starting material is part of what defines the polymer's unique identity
        fhir:amount [ Quantity ] ; # 0..1 A percentage
      ] ... ) ;
    ] ... ) ;
    fhir:repeat ( [ # 0..* Specifies and quantifies the repeated units and their configuration
      fhir:averageMolecularFormula [ string ] ; # 0..1 A representation of an (average) molecular formula from a polymer
      fhir:repeatUnitAmountType [ CodeableConcept ] ; # 0..1 How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
      fhir:repeatUnit ( [ # 0..* An SRU - Structural Repeat Unit
        fhir:unit [ string ] ; # 0..1 Identification of the structural repeat unit (SRU)
        fhir:orientation [ CodeableConcept ] ; # 0..1 The orientation of the polymerisation, e.g. head-tail, head-head, random
        fhir:amount [ integer ] ; # 0..1 Number of repeats of this unit
        fhir:degreeOfPolymerisation ( [ # 0..* Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
          fhir:type [ CodeableConcept ] ; # 0..1 The type of degree of polymerisation, e.g. SRU/Polymer ratio
          fhir:average [ integer ] ; # 0..1 An average amount of polymerisation
          fhir:low [ integer ] ; # 0..1 A low expected limit of the amount
          fhir:high [ integer ] ; # 0..1 A high expected limit of the amount
        ] ... ) ;
        fhir:structuralRepresentation  ( [ See SubstanceDefinition.structure.representation ] ... ) ; # 0..* A graphical structure for this SRU
      ] ... ) ;
    ] ... ) ;
  ] ;
  fhir:protein [ # 0..1 Data items specific to proteins
    fhir:sequenceType [ CodeableConcept ] ; # 0..1 Whether the sequence is complete or partial
    fhir:numberOfSubunits [ integer ] ; # 0..1 Number of subunits — linear sequences of amino acids linked through peptide bonds
    fhir:disulfideLinkage  ( [ string ] ... ) ; # 0..* Disulphide bond(s) between cysteine residues on the same subunit or across two different subunits. Positions are listed in increasing order of subunit number and intra-subunit position, followed by the amino-acid abbreviations. The positions should contain Cysteine residues
    fhir:subunit ( [ # 0..* Each subunit constituting the protein. A subunit is a linear sequence of amino acids linked through peptide bonds. Used when the finished protein is a complex of multiple sequences (not for domains within a single sequence). Subunits are listed in order of decreasing length; ties resolved by decreasing molecular weight; identical sequences are repeated
      fhir:subunit [ integer ] ; # 0..1 Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts
      fhir:sequence [ string ] ; # 0..1 The amino-acid sequence, listed N- to C-terminal using standard single-letter amino-acid codes. Uppercase denotes L-amino acids, lowercase denotes D-amino acids. Transcribed proteins are described using the translated sequence; for synthetic peptides containing amino acids without a single-letter code, X is used. Modified amino acids are identified by their position in the sequence
      fhir:length [ integer ] ; # 0..1 Length of linear sequences of amino acids contained in the subunit
      fhir:sequenceAttachment [ Attachment ] ; # 0..1 The amino-acid sequence as an attached file
      fhir:nTerminalModification [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The modification fragment at the N-terminal of the protein
      fhir:cTerminalModification [ CodeableReference(SubstanceDefinition) ] ; # 0..1 The modification fragment at the C-terminal of the protein
    ] ... ) ;
    fhir:gene  ( [ See SubstanceDefinition.nucleicAcid.gene ] ... ) ; # 0..* The gene that codes for this substance
  ] ;
]

Changes from R5 to R6

Changes from R4B to R6

Changes from R4 to R6

This resource did not exist in Release R4

See the Full Difference for further information

This analysis is available for R4 as XML or JSON and for R4B as XML or JSON.