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11.23 Resource SubstanceProtein - Content

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

A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators.

This resource is referenced by SubstanceSpecification

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstanceProtein ΣTUDomainResourceA SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... sequenceType Σ0..1CodeableConceptThe SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
... numberOfSubunits Σ0..1integerNumber of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
... disulfideLinkage Σ0..*stringThe disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
... subunit Σ0..*BackboneElementThis subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
.... subunit Σ0..1integerIndex 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 Σ0..1stringThe sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
.... length Σ0..1integerLength of linear sequences of amino acids contained in the subunit
.... sequenceAttachment Σ0..1AttachmentThe sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
.... nTerminalModificationId Σ0..1IdentifierUnique identifier for molecular fragment modification based on the ISO 11238 Substance ID
.... nTerminalModification Σ0..1stringThe name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
.... cTerminalModificationId Σ0..1IdentifierUnique identifier for molecular fragment modification based on the ISO 11238 Substance ID
.... cTerminalModification Σ0..1stringThe modification at the C-terminal shall be specified

doco Documentation for this format

UML Diagram (Legend)

SubstanceProtein (DomainResource)The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequencesequenceType : CodeableConcept [0..1]Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variablenumberOfSubunits : integer [0..1]The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positionsdisulfideLinkage : string [0..*]SubunitIndex 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 subscriptssubunit : integer [0..1]The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequencesequence : string [0..1]Length of linear sequences of amino acids contained in the subunitlength : integer [0..1]The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequencesequenceAttachment : Attachment [0..1]Unique identifier for molecular fragment modification based on the ISO 11238 Substance IDnTerminalModificationId : Identifier [0..1]The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specifiednTerminalModification : string [0..1]Unique identifier for molecular fragment modification based on the ISO 11238 Substance IDcTerminalModificationId : Identifier [0..1]The modification at the C-terminal shall be specifiedcTerminalModification : string [0..1]This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple timessubunit[0..*]

XML Template

<SubstanceProtein xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <sequenceType><!-- 0..1 CodeableConcept The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence --></sequenceType>
 <numberOfSubunits value="[integer]"/><!-- 0..1 Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable -->
 <disulfideLinkage value="[string]"/><!-- 0..* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions -->
 <subunit>  <!-- 0..* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times -->
  <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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished 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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence --></sequenceAttachment>
  <nTerminalModificationId><!-- 0..1 Identifier Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID --></nTerminalModificationId>
  <nTerminalModification value="[string]"/><!-- 0..1 The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified -->
  <cTerminalModificationId><!-- 0..1 Identifier Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID --></cTerminalModificationId>
  <cTerminalModification value="[string]"/><!-- 0..1 The modification at the C-terminal shall be specified -->
 </subunit>
</SubstanceProtein>

JSON Template

{doco
  "resourceType" : "SubstanceProtein",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "sequenceType" : { CodeableConcept }, // The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
  "numberOfSubunits" : <integer>, // Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
  "disulfideLinkage" : ["<string>"], // The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
  "subunit" : [{ // This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
    "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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    "length" : <integer>, // Length of linear sequences of amino acids contained in the subunit
    "sequenceAttachment" : { Attachment }, // The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    "nTerminalModificationId" : { Identifier }, // Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    "nTerminalModification" : "<string>", // The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
    "cTerminalModificationId" : { Identifier }, // Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    "cTerminalModification" : "<string>" // The modification at the C-terminal shall be specified
  }]
}

Turtle Template

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


[ a fhir:SubstanceProtein;
  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:SubstanceProtein.sequenceType [ CodeableConcept ]; # 0..1 The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
  fhir:SubstanceProtein.numberOfSubunits [ integer ]; # 0..1 Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
  fhir:SubstanceProtein.disulfideLinkage [ string ], ... ; # 0..* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
  fhir:SubstanceProtein.subunit [ # 0..* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
    fhir:SubstanceProtein.subunit.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:SubstanceProtein.subunit.sequence [ string ]; # 0..1 The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    fhir:SubstanceProtein.subunit.length [ integer ]; # 0..1 Length of linear sequences of amino acids contained in the subunit
    fhir:SubstanceProtein.subunit.sequenceAttachment [ Attachment ]; # 0..1 The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    fhir:SubstanceProtein.subunit.nTerminalModificationId [ Identifier ]; # 0..1 Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    fhir:SubstanceProtein.subunit.nTerminalModification [ string ]; # 0..1 The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
    fhir:SubstanceProtein.subunit.cTerminalModificationId [ Identifier ]; # 0..1 Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    fhir:SubstanceProtein.subunit.cTerminalModification [ string ]; # 0..1 The modification at the C-terminal shall be specified
  ], ...;
]

Changes since R3

This resource did not exist in Release 2

This analysis is available as XML or JSON.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. SubstanceProtein ΣTUDomainResourceA SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic, recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors, peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... sequenceType Σ0..1CodeableConceptThe SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
... numberOfSubunits Σ0..1integerNumber of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
... disulfideLinkage Σ0..*stringThe disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
... subunit Σ0..*BackboneElementThis subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
.... subunit Σ0..1integerIndex 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 Σ0..1stringThe sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
.... length Σ0..1integerLength of linear sequences of amino acids contained in the subunit
.... sequenceAttachment Σ0..1AttachmentThe sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
.... nTerminalModificationId Σ0..1IdentifierUnique identifier for molecular fragment modification based on the ISO 11238 Substance ID
.... nTerminalModification Σ0..1stringThe name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
.... cTerminalModificationId Σ0..1IdentifierUnique identifier for molecular fragment modification based on the ISO 11238 Substance ID
.... cTerminalModification Σ0..1stringThe modification at the C-terminal shall be specified

doco Documentation for this format

UML Diagram (Legend)

SubstanceProtein (DomainResource)The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequencesequenceType : CodeableConcept [0..1]Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variablenumberOfSubunits : integer [0..1]The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positionsdisulfideLinkage : string [0..*]SubunitIndex 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 subscriptssubunit : integer [0..1]The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequencesequence : string [0..1]Length of linear sequences of amino acids contained in the subunitlength : integer [0..1]The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequencesequenceAttachment : Attachment [0..1]Unique identifier for molecular fragment modification based on the ISO 11238 Substance IDnTerminalModificationId : Identifier [0..1]The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specifiednTerminalModification : string [0..1]Unique identifier for molecular fragment modification based on the ISO 11238 Substance IDcTerminalModificationId : Identifier [0..1]The modification at the C-terminal shall be specifiedcTerminalModification : string [0..1]This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple timessubunit[0..*]

XML Template

<SubstanceProtein xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <sequenceType><!-- 0..1 CodeableConcept The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence --></sequenceType>
 <numberOfSubunits value="[integer]"/><!-- 0..1 Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable -->
 <disulfideLinkage value="[string]"/><!-- 0..* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions -->
 <subunit>  <!-- 0..* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times -->
  <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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished 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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence --></sequenceAttachment>
  <nTerminalModificationId><!-- 0..1 Identifier Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID --></nTerminalModificationId>
  <nTerminalModification value="[string]"/><!-- 0..1 The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified -->
  <cTerminalModificationId><!-- 0..1 Identifier Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID --></cTerminalModificationId>
  <cTerminalModification value="[string]"/><!-- 0..1 The modification at the C-terminal shall be specified -->
 </subunit>
</SubstanceProtein>

JSON Template

{doco
  "resourceType" : "SubstanceProtein",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "sequenceType" : { CodeableConcept }, // The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
  "numberOfSubunits" : <integer>, // Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
  "disulfideLinkage" : ["<string>"], // The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
  "subunit" : [{ // This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
    "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 sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    "length" : <integer>, // Length of linear sequences of amino acids contained in the subunit
    "sequenceAttachment" : { Attachment }, // The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    "nTerminalModificationId" : { Identifier }, // Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    "nTerminalModification" : "<string>", // The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
    "cTerminalModificationId" : { Identifier }, // Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    "cTerminalModification" : "<string>" // The modification at the C-terminal shall be specified
  }]
}

Turtle Template

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


[ a fhir:SubstanceProtein;
  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:SubstanceProtein.sequenceType [ CodeableConcept ]; # 0..1 The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is available or derivable from a nucleic acid sequence
  fhir:SubstanceProtein.numberOfSubunits [ integer ]; # 0..1 Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the SubstanceProtein shall be described. It is possible that the number of subunits can be variable
  fhir:SubstanceProtein.disulfideLinkage [ string ], ... ; # 0..* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage positions shall actually contain the amino acid Cysteine at the respective positions
  fhir:SubstanceProtein.subunit [ # 0..* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
    fhir:SubstanceProtein.subunit.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:SubstanceProtein.subunit.sequence [ string ]; # 0..1 The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    fhir:SubstanceProtein.subunit.length [ integer ]; # 0..1 Length of linear sequences of amino acids contained in the subunit
    fhir:SubstanceProtein.subunit.sequenceAttachment [ Attachment ]; # 0..1 The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids that are not represented with a single letter code an X should be used within the sequence. The modified amino acids will be distinguished by their position in the sequence
    fhir:SubstanceProtein.subunit.nTerminalModificationId [ Identifier ]; # 0..1 Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    fhir:SubstanceProtein.subunit.nTerminalModification [ string ]; # 0..1 The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
    fhir:SubstanceProtein.subunit.cTerminalModificationId [ Identifier ]; # 0..1 Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
    fhir:SubstanceProtein.subunit.cTerminalModification [ string ]; # 0..1 The modification at the C-terminal shall be specified
  ], ...;
]

Changes since Release 3

This resource did not exist in Release 2

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 dependency analysis