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Substancedefinition.shex

Biomedical Research and Regulation Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: No defined compartments

Raw ShEx

ShEx statement for substancedefinition

PREFIX fhir: <http://hl7.org/fhir/> 
PREFIX fhirvs: <http://hl7.org/fhir/ValueSet/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

IMPORT <date.shex>
IMPORT <Ratio.shex>
IMPORT <string.shex>
IMPORT <boolean.shex>
IMPORT <markdown.shex>
IMPORT <Quantity.shex>
IMPORT <dateTime.shex>
IMPORT <Citation.shex>
IMPORT <Reference.shex>
IMPORT <Identifier.shex>
IMPORT <Annotation.shex>
IMPORT <Attachment.shex>
IMPORT <Organization.shex>
IMPORT <DomainResource.shex>
IMPORT <CodeableConcept.shex>
IMPORT <BackboneElement.shex>
IMPORT <SubstancePolymer.shex>
IMPORT <SubstanceProtein.shex>
IMPORT <DocumentReference.shex>
IMPORT <SubstanceNucleicAcid.shex>
IMPORT <SubstanceReferenceInformation.shex>


start=@<SubstanceDefinition> AND {fhir:nodeRole [fhir:treeRoot]}

# The detailed description of a substance, typically at a level beyond what is used for prescribing
<SubstanceDefinition> EXTENDS @<DomainResource> CLOSED {   

    a [fhir:SubstanceDefinition]?;
    fhir:nodeRole [fhir:treeRoot]?;

    fhir:identifier @<OneOrMore_Identifier>?;  # Identifier by which this substance 
                                            # is known 
    fhir:version @<string>?;                # A business level version 
                                            # identifier of the substance 
    fhir:status @<CodeableConcept>?;        # Status of substance within the 
                                            # catalogue e.g. active, retired 
    fhir:classification @<OneOrMore_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 
    fhir:domain @<CodeableConcept>?;        # If the substance applies to human 
                                            # or veterinary use 
    fhir:grade @<OneOrMore_CodeableConcept>?;  # The quality standard, established 
                                            # benchmark, to which substance 
                                            # complies (e.g. USP/NF, BP) 
    fhir:description @<markdown>?;          # Textual description of the 
                                            # substance 
    fhir:informationSource @<OneOrMore_Reference_Citation>?;  # Supporting literature
    fhir:note @<OneOrMore_Annotation>?;     # Textual comment about the 
                                            # substance's catalogue or registry 
                                            # record 
    fhir:manufacturer @<OneOrMore_Reference_Organization>?;  # The entity that creates, makes, 
                                            # produces or fabricates the 
                                            # substance 
    fhir:supplier @<OneOrMore_Reference_Organization>?;  # An entity that is the source for 
                                            # the substance. It may be different 
                                            # from the manufacturer 
    fhir:moiety @<OneOrMore_SubstanceDefinition.moiety>?;  # Moiety, for structural 
                                            # modifications 
    fhir:characterization @<OneOrMore_SubstanceDefinition.characterization>?;  # General specifications for this 
                                            # substance 
    fhir:property @<OneOrMore_SubstanceDefinition.property>?;  # General specifications for this 
                                            # substance 
    fhir:referenceInformation @<Reference> AND {fhir:link 
    			@<SubstanceReferenceInformation> ? }?;  # General information detailing this 
                                            # substance 
    fhir:molecularWeight @<OneOrMore_SubstanceDefinition.molecularWeight>?;  # The average mass of a molecule of 
                                            # a compound 
    fhir:structure @<SubstanceDefinition.structure>?;  # Structural information
    fhir:code @<OneOrMore_SubstanceDefinition.code>?;  # Codes associated with the substance
    fhir:name @<OneOrMore_SubstanceDefinition.name>?;  # Names applicable to this substance
    fhir:relationship @<OneOrMore_SubstanceDefinition.relationship>?;  # A link between this substance and 
                                            # another 
    fhir:nucleicAcid @<Reference> AND {fhir:link 
    			@<SubstanceNucleicAcid> ? }?;  # Data items specific to nucleic 
                                            # acids 
    fhir:polymer @<Reference> AND {fhir:link 
    			@<SubstancePolymer> ? }?;  # Data items specific to polymers
    fhir:protein @<Reference> AND {fhir:link 
    			@<SubstanceProtein> ? }?;  # Data items specific to proteins
    fhir:sourceMaterial @<SubstanceDefinition.sourceMaterial>?;  # Material or taxonomic/anatomical 
                                            # source 
}  

# General specifications for this substance
<SubstanceDefinition.characterization> EXTENDS @<BackboneElement> CLOSED {   
    fhir:technique @<CodeableConcept>?;     # The method used to find the 
                                            # characterization e.g. HPLC 
    fhir:form @<CodeableConcept>?;          # Describes the nature of the 
                                            # chemical entity and explains, for 
                                            # instance, whether this is a base 
                                            # or a salt form 
    fhir:description @<markdown>?;          # The description or justification 
                                            # in support of the interpretation 
                                            # of the data file 
    fhir:file @<OneOrMore_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 
}  

# A translation for this name into another human language
<SubstanceDefinition.name.translationnull> CLOSED {   
}  

# The average mass of a molecule of a compound
<SubstanceDefinition.molecularWeight> EXTENDS @<BackboneElement> CLOSED {   
    fhir:method @<CodeableConcept>?;        # The method by which the weight was 
                                            # determined 
    fhir:type @<CodeableConcept>?;          # Type of molecular weight e.g. 
                                            # exact, average, weight average 
    fhir:amount @<Quantity>;                # Used to capture quantitative 
                                            # values for a variety of elements 
}  

# Structural information
<SubstanceDefinition.structure> EXTENDS @<BackboneElement> CLOSED {   
    fhir:stereochemistry @<CodeableConcept>?;  # Stereochemistry type
    fhir:opticalActivity @<CodeableConcept>?;  # Optical activity type
    fhir:molecularFormula @<string>?;       # An expression which states the 
                                            # number and type of atoms present 
                                            # in a molecule of a substance 
    fhir:molecularFormulaByMoiety @<string>?;  # Specified per moiety according to 
                                            # the Hill system 
    fhir:molecularWeight @<SubstanceDefinition.molecularWeight>?;  # The molecular weight or weight 
                                            # range 
    fhir:technique @<OneOrMore_CodeableConcept>?;  # The method used to find the 
                                            # structure e.g. X-ray, NMR 
    fhir:sourceDocument @<OneOrMore_Reference_DocumentReference>?;  # Source of information for the 
                                            # structure 
    fhir:representation @<OneOrMore_SubstanceDefinition.structure.representation>?;  # A depiction of the structure of 
                                            # the substance 
}  

# General specifications for this substance
<SubstanceDefinition.property> EXTENDS @<BackboneElement> CLOSED {   
    fhir:type @<CodeableConcept>;           # A code expressing the type of 
                                            # property 
    fhir:value @<CodeableConcept>  OR 
    			@<Quantity>  OR 
    			@<date>  OR 
    			@<boolean>  OR 
    			@<Attachment>  ?;  # A value for the property
}  

# Codes associated with the substance
<SubstanceDefinition.code> EXTENDS @<BackboneElement> CLOSED {   
    fhir:code @<CodeableConcept>?;          # The specific code
    fhir:status @<CodeableConcept>?;        # Status of the code assignment, for 
                                            # example 'provisional', 'approved' 
    fhir:statusDate @<dateTime>?;           # The date at which the code status 
                                            # was changed 
    fhir:note @<OneOrMore_Annotation>?;     # Any comment can be provided in 
                                            # this field 
    fhir:source @<OneOrMore_Reference_DocumentReference>?;  # Supporting literature
}  

# A synonym of this particular name, by which the substance is also known
<SubstanceDefinition.name.synonymnull> CLOSED {   
}  

# A depiction of the structure of the substance
<SubstanceDefinition.structure.representation> EXTENDS @<BackboneElement> CLOSED {   
    fhir:type @<CodeableConcept>?;          # The kind of structural 
                                            # representation (e.g. full, 
                                            # partial) 
    fhir:representation @<string>?;         # The structural representation as a 
                                            # text string in a standard format 
    fhir:format @<CodeableConcept>?;        # The format of the representation 
                                            # e.g. InChI, SMILES, MOLFILE (note: 
                                            # not the physical file format) 
    fhir:document @<Reference> AND {fhir:link 
    			@<DocumentReference> ? }?;  # An attachment with the structural 
                                            # representation e.g. a structure 
                                            # graphic or AnIML file 
}  

# A link between this substance and another
<SubstanceDefinition.relationship> EXTENDS @<BackboneElement> CLOSED {   
    fhir:substanceDefinition (@<Reference>  AND {fhir:link @<SubstanceDefinition> })  OR 
    			@<CodeableConcept>  ?;  # A pointer to another substance, as 
                                            # a resource or a representational 
                                            # code 
    fhir:type @<CodeableConcept>;           # For example "salt to parent", 
                                            # "active moiety" 
    fhir: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 
    fhir:amount @<Quantity>  OR 
    			@<Ratio>  OR 
    			@<string>  ?;  # A numeric factor for the 
                                            # relationship, e.g. that a 
                                            # substance salt has some percentage 
                                            # of active substance in relation to 
                                            # some other 
    fhir:ratioHighLimitAmount @<Ratio>?;    # For use when the numeric has an 
                                            # uncertain range 
    fhir:comparator @<CodeableConcept>?;    # An operator for the amount, for 
                                            # example "average", 
                                            # "approximately", "less than" 
    fhir:source @<OneOrMore_Reference_DocumentReference>?;  # Supporting literature
}  

# Names applicable to this substance
<SubstanceDefinition.name> EXTENDS @<BackboneElement> CLOSED {   
    fhir:name @<string>;                    # The actual name
    fhir:type @<CodeableConcept>?;          # Name type e.g. 'systematic',  
                                            # 'scientific, 'brand' 
    fhir:status @<CodeableConcept>?;        # The status of the name e.g. 
                                            # 'current', 'proposed' 
    fhir:preferred @<boolean>?;             # If this is the preferred name for 
                                            # this substance 
    fhir:language @<OneOrMore_CodeableConcept>?;  # Human language that the name is 
                                            # written in 
    fhir:domain @<OneOrMore_CodeableConcept>?;  # The use context of this name e.g. 
                                            # as an active ingredient or as a 
                                            # food colour additive 
    fhir:jurisdiction @<OneOrMore_CodeableConcept>?;  # The jurisdiction where this name 
                                            # applies 
    fhir:synonym @<OneOrMore_SubstanceDefinition.name>?;  # A synonym of this particular name, 
                                            # by which the substance is also 
                                            # known 
    fhir:translation @<OneOrMore_SubstanceDefinition.name>?;  # A translation for this name into 
                                            # another human language 
    fhir:official @<OneOrMore_SubstanceDefinition.name.official>?;  # Details of the official nature of 
                                            # this name 
    fhir:source @<OneOrMore_Reference_DocumentReference>?;  # Supporting literature
}  

# Moiety, for structural modifications
<SubstanceDefinition.moiety> EXTENDS @<BackboneElement> CLOSED {   
    fhir:role @<CodeableConcept>?;          # Role that the moiety is playing
    fhir:identifier @<Identifier>?;         # Identifier by which this moiety 
                                            # substance is known 
    fhir:name @<string>?;                   # Textual name for this moiety 
                                            # substance 
    fhir:stereochemistry @<CodeableConcept>?;  # Stereochemistry type
    fhir:opticalActivity @<CodeableConcept>?;  # Optical activity type
    fhir:molecularFormula @<string>?;       # Molecular formula for this moiety 
                                            # (e.g. with the Hill system) 
    fhir:amount @<Quantity>  OR 
    			@<string>  ?;  # Quantitative value for this moiety
    fhir:measurementType @<CodeableConcept>?;  # The measurement type of the 
                                            # quantitative value 
}  

# Details of the official nature of this name
<SubstanceDefinition.name.official> EXTENDS @<BackboneElement> CLOSED {   
    fhir:authority @<CodeableConcept>?;     # Which authority uses this official 
                                            # name 
    fhir:status @<CodeableConcept>?;        # The status of the official name, 
                                            # for example 'draft', 'active' 
    fhir:date @<dateTime>?;                 # Date of official name change
}  

# Material or taxonomic/anatomical source
<SubstanceDefinition.sourceMaterial> EXTENDS @<BackboneElement> CLOSED {   
    fhir:type @<CodeableConcept>?;          # Classification of the origin of 
                                            # the raw material. e.g. cat hair is 
                                            # an Animal source type 
    fhir:genus @<CodeableConcept>?;         # The genus of an organism e.g. the 
                                            # Latin epithet of the plant/animal 
                                            # scientific name 
    fhir:species @<CodeableConcept>?;       # The species of an organism e.g. 
                                            # the Latin epithet of the species 
                                            # of the plant/animal 
    fhir:part @<CodeableConcept>?;          # An anatomical origin of the source 
                                            # material within an organism 
    fhir:countryOfOrigin @<OneOrMore_CodeableConcept>?;  # The country or countries where the 
                                            # material is harvested 
}  

#---------------------- Cardinality Types (OneOrMore) -------------------

<OneOrMore_Identifier> CLOSED {
    rdf:first @<Identifier>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Identifier> 
}

<OneOrMore_CodeableConcept> CLOSED {
    rdf:first @<CodeableConcept>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> 
}

<OneOrMore_Reference_Citation> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<Citation> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Citation> 
}

<OneOrMore_Annotation> CLOSED {
    rdf:first @<Annotation>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Annotation> 
}

<OneOrMore_Reference_Organization> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<Organization> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Organization> 
}

<OneOrMore_SubstanceDefinition.moiety> CLOSED {
    rdf:first @<SubstanceDefinition.moiety>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.moiety> 
}

<OneOrMore_SubstanceDefinition.characterization> CLOSED {
    rdf:first @<SubstanceDefinition.characterization>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.characterization> 
}

<OneOrMore_SubstanceDefinition.property> CLOSED {
    rdf:first @<SubstanceDefinition.property>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.property> 
}

<OneOrMore_SubstanceDefinition.molecularWeight> CLOSED {
    rdf:first @<SubstanceDefinition.molecularWeight>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.molecularWeight> 
}

<OneOrMore_SubstanceDefinition.code> CLOSED {
    rdf:first @<SubstanceDefinition.code>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.code> 
}

<OneOrMore_SubstanceDefinition.name> CLOSED {
    rdf:first @<SubstanceDefinition.name>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.name> 
}

<OneOrMore_SubstanceDefinition.relationship> CLOSED {
    rdf:first @<SubstanceDefinition.relationship>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.relationship> 
}

<OneOrMore_Attachment> CLOSED {
    rdf:first @<Attachment>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Attachment> 
}

<OneOrMore_Reference_DocumentReference> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<DocumentReference> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_DocumentReference> 
}

<OneOrMore_SubstanceDefinition.structure.representation> CLOSED {
    rdf:first @<SubstanceDefinition.structure.representation>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.structure.representation> 
}

<OneOrMore_SubstanceDefinition.name.official> CLOSED {
    rdf:first @<SubstanceDefinition.name.official>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SubstanceDefinition.name.official> 
}


Usage note: every effort has been made to ensure that the ShEx files are correct and useful, but they are not a normative part of the specification.