Release 5 Preview #3

15.10 Resource SubstancePolymer - Content

Biomedical Research and Regulation Work GroupMaturity Level: 0 Trial UseSecurity Category: Anonymous Compartments: Not linked to any defined compartments

Properties of a substance specific to it being a polymer.

This resource is still undergoing development and review by the appropriate Workgroups. At this time, is considered only as a draft resource not suitable for production implementation

This resource is referenced by SubstanceDefinition.

This resource does not implement any patterns.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstancePolymer ΣTUDomainResourceProperties of a substance specific to it being a polymer
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..1IdentifierA business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
... class Σ0..1CodeableConceptOverall type of the polymer
... geometry Σ0..1CodeableConceptPolymer geometry, e.g. linear, branched, cross-linked, network or dendritic
... modification Σ0..1stringTodo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
... monomerSet Σ0..*BackboneElementTodo
.... ratioType Σ0..1CodeableConceptCaptures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
.... startingMaterial Σ0..*BackboneElementThe starting materials - monomer(s) used in the synthesis of the polymer
..... code Σ0..1CodeableConceptThe type of substance for this starting material
..... category Σ0..1CodeableConceptSubstance high level category, e.g. chemical substance
..... isDefining Σ0..1booleanUsed to specify whether the attribute described is a defining element for the unique identification of the polymer
..... amount Σ0..1QuantityA percentage
... repeat Σ0..*BackboneElementSpecifies and quantifies the repeated units and their configuration
.... averageMolecularFormula Σ0..1stringA representation of an (average) molecular formula from a polymer
.... repeatUnitAmountType Σ0..1CodeableConceptHow the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
.... repeatUnit Σ0..*BackboneElementAn SRU - Structural Repeat Unit
..... unit Σ0..1stringStructural repeat units are essential elements for defining polymers
..... orientation Σ0..1CodeableConceptThe orientation of the polymerisation, e.g. head-tail, head-head, random
..... amount Σ0..1integerNumber of repeats of this unit
..... degreeOfPolymerisation Σ0..*BackboneElementApplies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
...... type Σ0..1CodeableConceptThe type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratio
...... average Σ0..1integerAn average amount of polymerisation
...... low Σ0..1integerA low expected limit of the amount
...... high Σ0..1integerA high expected limit of the amount
..... structuralRepresentation Σ0..*BackboneElementA graphical structure for this SRU
...... type Σ0..1CodeableConceptThe type of structure (e.g. Full, Partial, Representative)
...... representation Σ0..1stringThe structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
...... format Σ0..1CodeableConceptThe format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
...... attachment Σ0..1AttachmentAn attached file with the structural representation

doco Documentation for this format

UML Diagram (Legend)

SubstancePolymer (DomainResource)A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifieridentifier : Identifier [0..1]Overall type of the polymerclass : CodeableConcept [0..1]Polymer geometry, e.g. linear, branched, cross-linked, network or dendriticgeometry : CodeableConcept [0..1]Descrtibes the copolymer sequence type (polymer connectivity)copolymerConnectivity : CodeableConcept [0..*]Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholdermodification : string [0..1]MonomerSetCaptures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer RatioratioType : CodeableConcept [0..1]StartingMaterialThe type of substance for this starting materialcode : CodeableConcept [0..1]Substance high level category, e.g. chemical substancecategory : CodeableConcept [0..1]Used to specify whether the attribute described is a defining element for the unique identification of the polymerisDefining : boolean [0..1]A percentageamount : Quantity [0..1]RepeatA representation of an (average) molecular formula from a polymeraverageMolecularFormula : string [0..1]How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)repeatUnitAmountType : CodeableConcept [0..1]RepeatUnitStructural repeat units are essential elements for defining polymersunit : string [0..1]The orientation of the polymerisation, e.g. head-tail, head-head, randomorientation : CodeableConcept [0..1]Number of repeats of this unitamount : integer [0..1]DegreeOfPolymerisationThe type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratiotype : CodeableConcept [0..1]An average amount of polymerisationaverage : integer [0..1]A low expected limit of the amountlow : integer [0..1]A high expected limit of the amounthigh : integer [0..1]StructuralRepresentationThe type of structure (e.g. Full, Partial, Representative)type : CodeableConcept [0..1]The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIFrepresentation : string [0..1]The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIFformat : CodeableConcept [0..1]An attached file with the structural representationattachment : Attachment [0..1]The starting materials - monomer(s) used in the synthesis of the polymerstartingMaterial[0..*]TodomonomerSet[0..*]Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be describeddegreeOfPolymerisation[0..*]A graphical structure for this SRUstructuralRepresentation[0..*]An SRU - Structural Repeat UnitrepeatUnit[0..*]Specifies and quantifies the repeated units and their configurationrepeat[0..*]

XML Template

<SubstancePolymer xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..1 Identifier A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier --></identifier>
 <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 Descrtibes the copolymer sequence type (polymer connectivity) --></copolymerConnectivity>
 <modification value="[string]"/><!-- 0..1 Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder -->
 <monomerSet>  <!-- 0..* Todo -->
  <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 CodeableConcept The type of substance for this starting material --></code>
   <category><!-- 0..1 CodeableConcept Substance high level category, e.g. chemical substance --></category>
   <isDefining value="[boolean]"/><!-- 0..1 Used to specify whether the attribute described is a defining element for the unique identification of the polymer -->
   <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 Structural repeat units are essential elements for defining polymers -->
   <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 the degree of polymerisation shall be described, 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..* A graphical structure for this SRU -->
    <type><!-- 0..1 CodeableConcept The type of structure (e.g. Full, Partial, Representative) --></type>
    <representation value="[string]"/><!-- 0..1 The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF -->
    <format><!-- 0..1 CodeableConcept The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF --></format>
    <attachment><!-- 0..1 Attachment An attached file with the structural representation --></attachment>
   </structuralRepresentation>
  </repeatUnit>
 </repeat>
</SubstancePolymer>

JSON Template

{doco
  "resourceType" : "SubstancePolymer",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : { Identifier }, // A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
  "class" : { CodeableConcept }, // Overall type of the polymer
  "geometry" : { CodeableConcept }, // Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
  "copolymerConnectivity" : [{ CodeableConcept }], // Descrtibes the copolymer sequence type (polymer connectivity)
  "modification" : "<string>", // Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
  "monomerSet" : [{ // Todo
    "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" : { CodeableConcept }, // The type of substance for this starting material
      "category" : { CodeableConcept }, // Substance high level category, e.g. chemical substance
      "isDefining" : <boolean>, // Used to specify whether the attribute described is a defining element for the unique identification of the polymer
      "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>", // Structural repeat units are essential elements for defining polymers
      "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 the degree of polymerisation shall be described, 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" : [{ // A graphical structure for this SRU
        "type" : { CodeableConcept }, // The type of structure (e.g. Full, Partial, Representative)
        "representation" : "<string>", // The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        "format" : { CodeableConcept }, // The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        "attachment" : { Attachment } // An attached file with the structural representation
      }]
    }]
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:SubstancePolymer.identifier [ Identifier ]; # 0..1 A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
  fhir:SubstancePolymer.class [ CodeableConcept ]; # 0..1 Overall type of the polymer
  fhir:SubstancePolymer.geometry [ CodeableConcept ]; # 0..1 Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
  fhir:SubstancePolymer.copolymerConnectivity [ CodeableConcept ], ... ; # 0..* Descrtibes the copolymer sequence type (polymer connectivity)
  fhir:SubstancePolymer.modification [ string ]; # 0..1 Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
  fhir:SubstancePolymer.monomerSet [ # 0..* Todo
    fhir:SubstancePolymer.monomerSet.ratioType [ CodeableConcept ]; # 0..1 Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
    fhir:SubstancePolymer.monomerSet.startingMaterial [ # 0..* The starting materials - monomer(s) used in the synthesis of the polymer
      fhir:SubstancePolymer.monomerSet.startingMaterial.code [ CodeableConcept ]; # 0..1 The type of substance for this starting material
      fhir:SubstancePolymer.monomerSet.startingMaterial.category [ CodeableConcept ]; # 0..1 Substance high level category, e.g. chemical substance
      fhir:SubstancePolymer.monomerSet.startingMaterial.isDefining [ boolean ]; # 0..1 Used to specify whether the attribute described is a defining element for the unique identification of the polymer
      fhir:SubstancePolymer.monomerSet.startingMaterial.amount [ Quantity ]; # 0..1 A percentage
    ], ...;
  ], ...;
  fhir:SubstancePolymer.repeat [ # 0..* Specifies and quantifies the repeated units and their configuration
    fhir:SubstancePolymer.repeat.averageMolecularFormula [ string ]; # 0..1 A representation of an (average) molecular formula from a polymer
    fhir:SubstancePolymer.repeat.repeatUnitAmountType [ CodeableConcept ]; # 0..1 How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
    fhir:SubstancePolymer.repeat.repeatUnit [ # 0..* An SRU - Structural Repeat Unit
      fhir:SubstancePolymer.repeat.repeatUnit.unit [ string ]; # 0..1 Structural repeat units are essential elements for defining polymers
      fhir:SubstancePolymer.repeat.repeatUnit.orientation [ CodeableConcept ]; # 0..1 The orientation of the polymerisation, e.g. head-tail, head-head, random
      fhir:SubstancePolymer.repeat.repeatUnit.amount [ integer ]; # 0..1 Number of repeats of this unit
      fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation [ # 0..* Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.type [ CodeableConcept ]; # 0..1 The type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratio
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.average [ integer ]; # 0..1 An average amount of polymerisation
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.low [ integer ]; # 0..1 A low expected limit of the amount
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.high [ integer ]; # 0..1 A high expected limit of the amount
      ], ...;
      fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation [ # 0..* A graphical structure for this SRU
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.type [ CodeableConcept ]; # 0..1 The type of structure (e.g. Full, Partial, Representative)
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.representation [ string ]; # 0..1 The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.format [ CodeableConcept ]; # 0..1 The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.attachment [ Attachment ]; # 0..1 An attached file with the structural representation
      ], ...;
    ], ...;
  ], ...;
]

Changes since R3

SubstancePolymer
SubstancePolymer.identifier
  • Added Element
SubstancePolymer.modification
  • Max Cardinality changed from * to 1
SubstancePolymer.monomerSet.startingMaterial.code
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.category
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.amount
  • Type changed from SubstanceAmount to Quantity
SubstancePolymer.repeat.repeatUnit.unit
  • Added Element
SubstancePolymer.repeat.repeatUnit.orientation
  • Added Element
SubstancePolymer.repeat.repeatUnit.amount
  • Type changed from SubstanceAmount to integer
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.type
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.average
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.low
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.high
  • Added Element
SubstancePolymer.repeat.repeatUnit.structuralRepresentation.format
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.material
  • deleted
SubstancePolymer.monomerSet.startingMaterial.type
  • deleted
SubstancePolymer.repeat.numberOfUnits
  • deleted
SubstancePolymer.repeat.repeatUnit.orientationOfPolymerisation
  • deleted
SubstancePolymer.repeat.repeatUnit.repeatUnit
  • deleted
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.degree
  • deleted
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.amount
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstancePolymer ΣTUDomainResourceProperties of a substance specific to it being a polymer
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..1IdentifierA business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
... class Σ0..1CodeableConceptOverall type of the polymer
... geometry Σ0..1CodeableConceptPolymer geometry, e.g. linear, branched, cross-linked, network or dendritic
... modification Σ0..1stringTodo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
... monomerSet Σ0..*BackboneElementTodo
.... ratioType Σ0..1CodeableConceptCaptures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
.... startingMaterial Σ0..*BackboneElementThe starting materials - monomer(s) used in the synthesis of the polymer
..... code Σ0..1CodeableConceptThe type of substance for this starting material
..... category Σ0..1CodeableConceptSubstance high level category, e.g. chemical substance
..... isDefining Σ0..1booleanUsed to specify whether the attribute described is a defining element for the unique identification of the polymer
..... amount Σ0..1QuantityA percentage
... repeat Σ0..*BackboneElementSpecifies and quantifies the repeated units and their configuration
.... averageMolecularFormula Σ0..1stringA representation of an (average) molecular formula from a polymer
.... repeatUnitAmountType Σ0..1CodeableConceptHow the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
.... repeatUnit Σ0..*BackboneElementAn SRU - Structural Repeat Unit
..... unit Σ0..1stringStructural repeat units are essential elements for defining polymers
..... orientation Σ0..1CodeableConceptThe orientation of the polymerisation, e.g. head-tail, head-head, random
..... amount Σ0..1integerNumber of repeats of this unit
..... degreeOfPolymerisation Σ0..*BackboneElementApplies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
...... type Σ0..1CodeableConceptThe type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratio
...... average Σ0..1integerAn average amount of polymerisation
...... low Σ0..1integerA low expected limit of the amount
...... high Σ0..1integerA high expected limit of the amount
..... structuralRepresentation Σ0..*BackboneElementA graphical structure for this SRU
...... type Σ0..1CodeableConceptThe type of structure (e.g. Full, Partial, Representative)
...... representation Σ0..1stringThe structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
...... format Σ0..1CodeableConceptThe format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
...... attachment Σ0..1AttachmentAn attached file with the structural representation

doco Documentation for this format

UML Diagram (Legend)

SubstancePolymer (DomainResource)A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifieridentifier : Identifier [0..1]Overall type of the polymerclass : CodeableConcept [0..1]Polymer geometry, e.g. linear, branched, cross-linked, network or dendriticgeometry : CodeableConcept [0..1]Descrtibes the copolymer sequence type (polymer connectivity)copolymerConnectivity : CodeableConcept [0..*]Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholdermodification : string [0..1]MonomerSetCaptures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer RatioratioType : CodeableConcept [0..1]StartingMaterialThe type of substance for this starting materialcode : CodeableConcept [0..1]Substance high level category, e.g. chemical substancecategory : CodeableConcept [0..1]Used to specify whether the attribute described is a defining element for the unique identification of the polymerisDefining : boolean [0..1]A percentageamount : Quantity [0..1]RepeatA representation of an (average) molecular formula from a polymeraverageMolecularFormula : string [0..1]How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)repeatUnitAmountType : CodeableConcept [0..1]RepeatUnitStructural repeat units are essential elements for defining polymersunit : string [0..1]The orientation of the polymerisation, e.g. head-tail, head-head, randomorientation : CodeableConcept [0..1]Number of repeats of this unitamount : integer [0..1]DegreeOfPolymerisationThe type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratiotype : CodeableConcept [0..1]An average amount of polymerisationaverage : integer [0..1]A low expected limit of the amountlow : integer [0..1]A high expected limit of the amounthigh : integer [0..1]StructuralRepresentationThe type of structure (e.g. Full, Partial, Representative)type : CodeableConcept [0..1]The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIFrepresentation : string [0..1]The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIFformat : CodeableConcept [0..1]An attached file with the structural representationattachment : Attachment [0..1]The starting materials - monomer(s) used in the synthesis of the polymerstartingMaterial[0..*]TodomonomerSet[0..*]Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be describeddegreeOfPolymerisation[0..*]A graphical structure for this SRUstructuralRepresentation[0..*]An SRU - Structural Repeat UnitrepeatUnit[0..*]Specifies and quantifies the repeated units and their configurationrepeat[0..*]

XML Template

<SubstancePolymer xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..1 Identifier A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier --></identifier>
 <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 Descrtibes the copolymer sequence type (polymer connectivity) --></copolymerConnectivity>
 <modification value="[string]"/><!-- 0..1 Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder -->
 <monomerSet>  <!-- 0..* Todo -->
  <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 CodeableConcept The type of substance for this starting material --></code>
   <category><!-- 0..1 CodeableConcept Substance high level category, e.g. chemical substance --></category>
   <isDefining value="[boolean]"/><!-- 0..1 Used to specify whether the attribute described is a defining element for the unique identification of the polymer -->
   <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 Structural repeat units are essential elements for defining polymers -->
   <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 the degree of polymerisation shall be described, 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..* A graphical structure for this SRU -->
    <type><!-- 0..1 CodeableConcept The type of structure (e.g. Full, Partial, Representative) --></type>
    <representation value="[string]"/><!-- 0..1 The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF -->
    <format><!-- 0..1 CodeableConcept The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF --></format>
    <attachment><!-- 0..1 Attachment An attached file with the structural representation --></attachment>
   </structuralRepresentation>
  </repeatUnit>
 </repeat>
</SubstancePolymer>

JSON Template

{doco
  "resourceType" : "SubstancePolymer",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : { Identifier }, // A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
  "class" : { CodeableConcept }, // Overall type of the polymer
  "geometry" : { CodeableConcept }, // Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
  "copolymerConnectivity" : [{ CodeableConcept }], // Descrtibes the copolymer sequence type (polymer connectivity)
  "modification" : "<string>", // Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
  "monomerSet" : [{ // Todo
    "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" : { CodeableConcept }, // The type of substance for this starting material
      "category" : { CodeableConcept }, // Substance high level category, e.g. chemical substance
      "isDefining" : <boolean>, // Used to specify whether the attribute described is a defining element for the unique identification of the polymer
      "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>", // Structural repeat units are essential elements for defining polymers
      "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 the degree of polymerisation shall be described, 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" : [{ // A graphical structure for this SRU
        "type" : { CodeableConcept }, // The type of structure (e.g. Full, Partial, Representative)
        "representation" : "<string>", // The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        "format" : { CodeableConcept }, // The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        "attachment" : { Attachment } // An attached file with the structural representation
      }]
    }]
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:SubstancePolymer.identifier [ Identifier ]; # 0..1 A business idenfier for this polymer, but typically this is handled by a SubstanceDefinition identifier
  fhir:SubstancePolymer.class [ CodeableConcept ]; # 0..1 Overall type of the polymer
  fhir:SubstancePolymer.geometry [ CodeableConcept ]; # 0..1 Polymer geometry, e.g. linear, branched, cross-linked, network or dendritic
  fhir:SubstancePolymer.copolymerConnectivity [ CodeableConcept ], ... ; # 0..* Descrtibes the copolymer sequence type (polymer connectivity)
  fhir:SubstancePolymer.modification [ string ]; # 0..1 Todo - this is intended to connect to a repeating full modification structure, also used by Protein and Nucleic Acid . String is just a placeholder
  fhir:SubstancePolymer.monomerSet [ # 0..* Todo
    fhir:SubstancePolymer.monomerSet.ratioType [ CodeableConcept ]; # 0..1 Captures the type of ratio to the entire polymer, e.g. Monomer/Polymer ratio, SRU/Polymer Ratio
    fhir:SubstancePolymer.monomerSet.startingMaterial [ # 0..* The starting materials - monomer(s) used in the synthesis of the polymer
      fhir:SubstancePolymer.monomerSet.startingMaterial.code [ CodeableConcept ]; # 0..1 The type of substance for this starting material
      fhir:SubstancePolymer.monomerSet.startingMaterial.category [ CodeableConcept ]; # 0..1 Substance high level category, e.g. chemical substance
      fhir:SubstancePolymer.monomerSet.startingMaterial.isDefining [ boolean ]; # 0..1 Used to specify whether the attribute described is a defining element for the unique identification of the polymer
      fhir:SubstancePolymer.monomerSet.startingMaterial.amount [ Quantity ]; # 0..1 A percentage
    ], ...;
  ], ...;
  fhir:SubstancePolymer.repeat [ # 0..* Specifies and quantifies the repeated units and their configuration
    fhir:SubstancePolymer.repeat.averageMolecularFormula [ string ]; # 0..1 A representation of an (average) molecular formula from a polymer
    fhir:SubstancePolymer.repeat.repeatUnitAmountType [ CodeableConcept ]; # 0..1 How the quantitative amount of Structural Repeat Units is captured (e.g. Exact, Numeric, Average)
    fhir:SubstancePolymer.repeat.repeatUnit [ # 0..* An SRU - Structural Repeat Unit
      fhir:SubstancePolymer.repeat.repeatUnit.unit [ string ]; # 0..1 Structural repeat units are essential elements for defining polymers
      fhir:SubstancePolymer.repeat.repeatUnit.orientation [ CodeableConcept ]; # 0..1 The orientation of the polymerisation, e.g. head-tail, head-head, random
      fhir:SubstancePolymer.repeat.repeatUnit.amount [ integer ]; # 0..1 Number of repeats of this unit
      fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation [ # 0..* Applies to homopolymer and block co-polymers where the degree of polymerisation within a block can be described
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.type [ CodeableConcept ]; # 0..1 The type of the degree of polymerisation shall be described, e.g. SRU/Polymer Ratio
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.average [ integer ]; # 0..1 An average amount of polymerisation
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.low [ integer ]; # 0..1 A low expected limit of the amount
        fhir:SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.high [ integer ]; # 0..1 A high expected limit of the amount
      ], ...;
      fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation [ # 0..* A graphical structure for this SRU
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.type [ CodeableConcept ]; # 0..1 The type of structure (e.g. Full, Partial, Representative)
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.representation [ string ]; # 0..1 The structural representation as text string in a standard format e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.format [ CodeableConcept ]; # 0..1 The format of the representation e.g. InChI, SMILES, MOLFILE, CDX, SDF, PDB, mmCIF
        fhir:SubstancePolymer.repeat.repeatUnit.structuralRepresentation.attachment [ Attachment ]; # 0..1 An attached file with the structural representation
      ], ...;
    ], ...;
  ], ...;
]

Changes since Release 3

SubstancePolymer
SubstancePolymer.identifier
  • Added Element
SubstancePolymer.modification
  • Max Cardinality changed from * to 1
SubstancePolymer.monomerSet.startingMaterial.code
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.category
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.amount
  • Type changed from SubstanceAmount to Quantity
SubstancePolymer.repeat.repeatUnit.unit
  • Added Element
SubstancePolymer.repeat.repeatUnit.orientation
  • Added Element
SubstancePolymer.repeat.repeatUnit.amount
  • Type changed from SubstanceAmount to integer
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.type
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.average
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.low
  • Added Element
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.high
  • Added Element
SubstancePolymer.repeat.repeatUnit.structuralRepresentation.format
  • Added Element
SubstancePolymer.monomerSet.startingMaterial.material
  • deleted
SubstancePolymer.monomerSet.startingMaterial.type
  • deleted
SubstancePolymer.repeat.numberOfUnits
  • deleted
SubstancePolymer.repeat.repeatUnit.orientationOfPolymerisation
  • deleted
SubstancePolymer.repeat.repeatUnit.repeatUnit
  • deleted
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.degree
  • deleted
SubstancePolymer.repeat.repeatUnit.degreeOfPolymerisation.amount
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

 

See the Profiles & Extensions and the alternate definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis a