This page is part of the FHIR Specification (v4.4.0: R5 Preview #2). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4

11.21 Resource SubstanceProtein - Content

Biomedical Research and Regulation

Work Group

Maturity Level: 0

Trial Use

Security 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.

11.21.1 Scope and Usage

11.21.2 References

This resource is referenced by SubstanceDefinition.

This resource does not implement any patterns.

Structure

Name	Flags	Card.	Type	Description & Constraints
SubstanceProtein	Σ TU		DomainResource	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 Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
sequenceType	Σ	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
numberOfSubunits	Σ	0..1	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	Σ	0..*	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	Σ	0..*	BackboneElement	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	Σ	0..1	integer	Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have sequential subscripts
sequence	Σ	0..1	string	The 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	Σ	0..1	integer	Length of linear sequences of amino acids contained in the subunit
sequenceAttachment	Σ	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
nTerminalModificationId	Σ	0..1	Identifier	Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
nTerminalModification	Σ	0..1	string	The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
cTerminalModificationId	Σ	0..1	Identifier	Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
cTerminalModification	Σ	0..1	string	The modification at the C-terminal shall be specified
Documentation for this format

UML Diagram (Legend)

XML Template

<SubstanceProtein xmlns="http://hl7.org/fhir"> 
 <!-- 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

{
  "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/> .


[ 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

SubstanceProtein

No Changes

See the Full Difference for further information

This analysis is available as XML or JSON.