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default
Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.
SubstanceNucleicAcid
Path
SubstanceNucleicAcid
Id
SubstanceNucleicAcid
Cardinality
0 - *
Definition
Nucleic acids are defined by three distinct elements: the base, sugar and linkage. Individual substance/moiety IDs will be created for each of these elements. The nucleotide sequence will be always entered in the 5’-3’ direction.
Comment
Constraint
dom-2 [error]
If the resource is contained in another resource, it SHALL NOT contain nested Resources
dom-3 [error]
If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
dom-4 [error]
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
dom-5 [error]
If a resource is contained in another resource, it SHALL NOT have a security label
dom-6 [warning]
A resource should have narrative for robust management
sequenceType
The type of the sequence shall be specified based on a controlled vocabulary
Path
SubstanceNucleicAcid.sequenceType
Id
SubstanceNucleicAcid.sequenceType
Type
Cardinality
0 - 1
Definition
The type of the sequence shall be specified based on a controlled vocabulary.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding
Id
CodeableConcept.coding
Type
Cardinality
0 - *
Definition
A reference to a code defined by a terminology system.
Comment
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Requirements
Allows for alternative encodings within a code system, and translations to other code systems.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding.Coding.system
Id
Coding.system
Type
Cardinality
0 - 1
Definition
The identification of the code system that defines the meaning of the symbol in the code.
Comment
The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.
Requirements
Need to be unambiguous about the source of the definition of the symbol.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding.Coding.version
Id
Coding.version
Type
Cardinality
0 - 1
Definition
The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
Comment
Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding.Coding.code
Id
Coding.code
Type
Cardinality
0 - 1
Definition
A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).
Comment
Requirements
Need to refer to a particular code in the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding.Coding.display
Id
Coding.display
Type
Cardinality
0 - 1
Definition
A representation of the meaning of the code in the system, following the rules of the system.
Comment
Requirements
Need to be able to carry a human-readable meaning of the code for readers that do not know the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.sequenceType.CodeableConcept.coding.Coding.userSelected
Id
Coding.userSelected
Type
Cardinality
0 - 1
Definition
Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).
Comment
Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.
Requirements
This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
numberOfSubunits
The number of linear sequences of nucleotides linked through phosphodiester bonds shall be described. Subunits would be strands of nucleic acids that are tightly associated typically through Watson-Crick base pairing. NOTE: If not specified in the reference source, the assumption is that there is 1 subunit
Path
SubstanceNucleicAcid.numberOfSubunits
Id
SubstanceNucleicAcid.numberOfSubunits
Type
Cardinality
0 - 1
Definition
The number of linear sequences of nucleotides linked through phosphodiester bonds shall be described. Subunits would be strands of nucleic acids that are tightly associated typically through Watson-Crick base pairing. NOTE: If not specified in the reference source, the assumption is that there is 1 subunit.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
areaOfHybridisation
The area of hybridisation shall be described if applicable for double stranded RNA or DNA. The number associated with the subunit followed by the number associated to the residue shall be specified in increasing order. The underscore “” shall be used as separator as follows: “Subunitnumber Residue”
Path
SubstanceNucleicAcid.areaOfHybridisation
Id
SubstanceNucleicAcid.areaOfHybridisation
Type
Cardinality
0 - 1
Definition
The area of hybridisation shall be described if applicable for double stranded RNA or DNA. The number associated with the subunit followed by the number associated to the residue shall be specified in increasing order. The underscore “” shall be used as separator as follows: “Subunitnumber Residue”.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType
Id
SubstanceNucleicAcid.oligoNucleotideType
Type
Cardinality
0 - 1
Definition
(TBC).
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding
Id
CodeableConcept.coding
Type
Cardinality
0 - *
Definition
A reference to a code defined by a terminology system.
Comment
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Requirements
Allows for alternative encodings within a code system, and translations to other code systems.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding.Coding.system
Id
Coding.system
Type
Cardinality
0 - 1
Definition
The identification of the code system that defines the meaning of the symbol in the code.
Comment
The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.
Requirements
Need to be unambiguous about the source of the definition of the symbol.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding.Coding.version
Id
Coding.version
Type
Cardinality
0 - 1
Definition
The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
Comment
Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding.Coding.code
Id
Coding.code
Type
Cardinality
0 - 1
Definition
A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).
Comment
Requirements
Need to refer to a particular code in the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding.Coding.display
Id
Coding.display
Type
Cardinality
0 - 1
Definition
A representation of the meaning of the code in the system, following the rules of the system.
Comment
Requirements
Need to be able to carry a human-readable meaning of the code for readers that do not know the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.oligoNucleotideType.CodeableConcept.coding.Coding.userSelected
Id
Coding.userSelected
Type
Cardinality
0 - 1
Definition
Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).
Comment
Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.
Requirements
This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
subunit
Subunits are listed in order of decreasing length; sequences of the same length will be ordered by molecular weight; subunits that have identical sequences will be repeated multiple times
Path
SubstanceNucleicAcid.subunit
Id
SubstanceNucleicAcid.subunit
Type
Cardinality
0 - *
Definition
Subunits are listed in order of decreasing length; sequences of the same length will be ordered by molecular weight; subunits that have identical sequences will be repeated multiple times.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
subunit
Index of linear sequences of nucleic acids 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
Path
SubstanceNucleicAcid.subunit.subunit
Id
SubstanceNucleicAcid.subunit.subunit
Type
Cardinality
0 - 1
Definition
Index of linear sequences of nucleic acids 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.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
sequence
Actual nucleotide sequence notation from 5' to 3' end using standard single letter codes. In addition to the base sequence, sugar and type of phosphate or non-phosphate linkage should also be captured
Path
SubstanceNucleicAcid.subunit.sequence
Id
SubstanceNucleicAcid.subunit.sequence
Type
Cardinality
0 - 1
Definition
Actual nucleotide sequence notation from 5' to 3' end using standard single letter codes. In addition to the base sequence, sugar and type of phosphate or non-phosphate linkage should also be captured.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.length
Id
SubstanceNucleicAcid.subunit.length
Type
Cardinality
0 - 1
Definition
The length of the sequence shall be captured.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment
Id
SubstanceNucleicAcid.subunit.sequenceAttachment
Type
Cardinality
0 - 1
Definition
(TBC).
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.contentType
Id
Attachment.contentType
Type
Cardinality
0 - 1
Definition
Identifies the type of the data in the attachment and allows a method to be chosen to interpret or render the data. Includes mime type parameters such as charset where appropriate.
Comment
Requirements
Processors of the data need to be able to know how to interpret the data.
Binding
Strength
required
Description
The mime type of an attachment. Any valid mime type is allowed.
ValueSet
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.data
Id
Attachment.data
Type
Cardinality
0 - 1
Definition
The actual data of the attachment - a sequence of bytes, base64 encoded.
Comment
The base64-encoded data SHALL be expressed in the same character set as the base resource XML or JSON.
Requirements
The data needs to able to be transmitted inline.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.url
Id
Attachment.url
Type
Cardinality
0 - 1
Definition
A location where the data can be accessed.
Comment
If both data and url are provided, the url SHALL point to the same content as the data contains. Urls may be relative references or may reference transient locations such as a wrapping envelope using cid: though this has ramifications for using signatures. Relative URLs are interpreted relative to the service url, like a resource reference, rather than relative to the resource itself. If a URL is provided, it SHALL resolve to actual data.
Requirements
The data needs to be transmitted by reference.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.size
Id
Attachment.size
Type
Cardinality
0 - 1
Definition
The number of bytes of data that make up this attachment (before base64 encoding, if that is done).
Comment
The number of bytes is redundant if the data is provided as a base64binary, but is useful if the data is provided as a url reference.
Requirements
Representing the size allows applications to determine whether they should fetch the content automatically in advance, or refuse to fetch it at all.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.hash
Id
Attachment.hash
Type
Cardinality
0 - 1
Definition
The calculated hash of the data using SHA-1. Represented using base64.
Comment
The hash is calculated on the data prior to base64 encoding, if the data is based64 encoded. The hash is not intended to support digital signatures. Where protection against malicious threats a digital signature should be considered, see [Provenance.signature](provenance-definitions.html#Provenance.signature) for mechanism to protect a resource with a digital signature.
Requirements
Included so that applications can verify that the contents of a location have not changed due to technical failures (e.g., storage rot, transport glitch, incorrect version).
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.title
Id
Attachment.title
Type
Cardinality
0 - 1
Definition
A label or set of text to display in place of the data.
Comment
Requirements
Applications need a label to display to a human user in place of the actual data if the data cannot be rendered or perceived by the viewer.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sequenceAttachment.Attachment.creation
Id
Attachment.creation
Type
Cardinality
0 - 1
Definition
The date that the attachment was first created.
Comment
Requirements
This is often tracked as an integrity issue for use of the attachment.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
fivePrime
The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant
Path
SubstanceNucleicAcid.subunit.fivePrime
Id
SubstanceNucleicAcid.subunit.fivePrime
Type
Cardinality
0 - 1
Definition
The nucleotide present at the 5’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the first position in the sequence. A separate representation would be redundant.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding
Id
CodeableConcept.coding
Type
Cardinality
0 - *
Definition
A reference to a code defined by a terminology system.
Comment
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Requirements
Allows for alternative encodings within a code system, and translations to other code systems.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding.Coding.system
Id
Coding.system
Type
Cardinality
0 - 1
Definition
The identification of the code system that defines the meaning of the symbol in the code.
Comment
The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.
Requirements
Need to be unambiguous about the source of the definition of the symbol.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding.Coding.version
Id
Coding.version
Type
Cardinality
0 - 1
Definition
The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
Comment
Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding.Coding.code
Id
Coding.code
Type
Cardinality
0 - 1
Definition
A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).
Comment
Requirements
Need to refer to a particular code in the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding.Coding.display
Id
Coding.display
Type
Cardinality
0 - 1
Definition
A representation of the meaning of the code in the system, following the rules of the system.
Comment
Requirements
Need to be able to carry a human-readable meaning of the code for readers that do not know the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.fivePrime.CodeableConcept.coding.Coding.userSelected
Id
Coding.userSelected
Type
Cardinality
0 - 1
Definition
Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).
Comment
Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.
Requirements
This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
threePrime
The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant
Path
SubstanceNucleicAcid.subunit.threePrime
Id
SubstanceNucleicAcid.subunit.threePrime
Type
Cardinality
0 - 1
Definition
The nucleotide present at the 3’ terminal shall be specified based on a controlled vocabulary. Since the sequence is represented from the 5' to the 3' end, the 5’ prime nucleotide is the letter at the last position in the sequence. A separate representation would be redundant.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding
Id
CodeableConcept.coding
Type
Cardinality
0 - *
Definition
A reference to a code defined by a terminology system.
Comment
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Requirements
Allows for alternative encodings within a code system, and translations to other code systems.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding.Coding.system
Id
Coding.system
Type
Cardinality
0 - 1
Definition
The identification of the code system that defines the meaning of the symbol in the code.
Comment
The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.
Requirements
Need to be unambiguous about the source of the definition of the symbol.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding.Coding.version
Id
Coding.version
Type
Cardinality
0 - 1
Definition
The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.
Comment
Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding.Coding.code
Id
Coding.code
Type
Cardinality
0 - 1
Definition
A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).
Comment
Requirements
Need to refer to a particular code in the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding.Coding.display
Id
Coding.display
Type
Cardinality
0 - 1
Definition
A representation of the meaning of the code in the system, following the rules of the system.
Comment
Requirements
Need to be able to carry a human-readable meaning of the code for readers that do not know the system.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.threePrime.CodeableConcept.coding.Coding.userSelected
Id
Coding.userSelected
Type
Cardinality
0 - 1
Definition
Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).
Comment
Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.
Requirements
This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage
Id
SubstanceNucleicAcid.subunit.linkage
Type
Cardinality
0 - *
Definition
The linkages between sugar residues will also be captured.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
connectivity
The entity that links the sugar residues together should also be captured for nearly all naturally occurring nucleic acid the linkage is a phosphate group. For many synthetic oligonucleotides phosphorothioate linkages are often seen. Linkage connectivity is assumed to be 3’-5’. If the linkage is either 3’-3’ or 5’-5’ this should be specified
Path
SubstanceNucleicAcid.subunit.linkage.connectivity
Id
SubstanceNucleicAcid.subunit.linkage.connectivity
Type
Cardinality
0 - 1
Definition
The entity that links the sugar residues together should also be captured for nearly all naturally occurring nucleic acid the linkage is a phosphate group. For many synthetic oligonucleotides phosphorothioate linkages are often seen. Linkage connectivity is assumed to be 3’-5’. If the linkage is either 3’-3’ or 5’-5’ this should be specified.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier
Id
SubstanceNucleicAcid.subunit.linkage.identifier
Type
Cardinality
0 - 1
Definition
Each linkage will be registered as a fragment and have an ID.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.use
Id
Identifier.use
Type
Cardinality
0 - 1
Definition
The purpose of this identifier.
Comment
Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.
Requirements
Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.
Binding
Strength
required
Description
Identifies the purpose for this identifier, if known .
ValueSet
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.type
Id
Identifier.type
Type
Cardinality
0 - 1
Definition
A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.
Comment
This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.
Requirements
Allows users to make use of identifiers when the identifier system is not known.
Binding
Strength
extensible
Description
A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
ValueSet
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.system
Id
Identifier.system
Type
Cardinality
0 - 1
Definition
Establishes the namespace for the value - that is, a URL that describes a set values that are unique.
Comment
Identifier.system is always case sensitive.
Requirements
There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.value
Id
Identifier.value
Type
Cardinality
0 - 1
Definition
The portion of the identifier typically relevant to the user and which is unique within the context of the system.
Comment
If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.period
Id
Identifier.period
Type
Cardinality
0 - 1
Definition
Time period during which identifier is/was valid for use.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.identifier.Identifier.assigner
Id
Identifier.assigner
Type
Cardinality
0 - 1
Definition
Organization that issued/manages the identifier.
Comment
The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
name
Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage
Path
SubstanceNucleicAcid.subunit.linkage.name
Id
SubstanceNucleicAcid.subunit.linkage.name
Type
Cardinality
0 - 1
Definition
Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.linkage.residueSite
Id
SubstanceNucleicAcid.subunit.linkage.residueSite
Type
Cardinality
0 - 1
Definition
Residues shall be captured as described in 5.3.6.8.3.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar
Id
SubstanceNucleicAcid.subunit.sugar
Type
Cardinality
0 - *
Definition
5.3.6.8.1 Sugar ID (Mandatory).
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
identifier
The Substance ID of the sugar or sugar-like component that make up the nucleotide
Path
SubstanceNucleicAcid.subunit.sugar.identifier
Id
SubstanceNucleicAcid.subunit.sugar.identifier
Type
Cardinality
0 - 1
Definition
The Substance ID of the sugar or sugar-like component that make up the nucleotide.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.use
Id
Identifier.use
Type
Cardinality
0 - 1
Definition
The purpose of this identifier.
Comment
Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.
Requirements
Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.
Binding
Strength
required
Description
Identifies the purpose for this identifier, if known .
ValueSet
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.type
Id
Identifier.type
Type
Cardinality
0 - 1
Definition
A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.
Comment
This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.
Requirements
Allows users to make use of identifiers when the identifier system is not known.
Binding
Strength
extensible
Description
A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
ValueSet
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.system
Id
Identifier.system
Type
Cardinality
0 - 1
Definition
Establishes the namespace for the value - that is, a URL that describes a set values that are unique.
Comment
Identifier.system is always case sensitive.
Requirements
There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.value
Id
Identifier.value
Type
Cardinality
0 - 1
Definition
The portion of the identifier typically relevant to the user and which is unique within the context of the system.
Comment
If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the [Rendered Value extension](extension-rendered-value.html). Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.period
Id
Identifier.period
Type
Cardinality
0 - 1
Definition
Time period during which identifier is/was valid for use.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.identifier.Identifier.assigner
Id
Identifier.assigner
Type
Cardinality
0 - 1
Definition
Organization that issued/manages the identifier.
Comment
The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
Path
SubstanceNucleicAcid.subunit.sugar.name
Id
SubstanceNucleicAcid.subunit.sugar.name
Type
Cardinality
0 - 1
Definition
The name of the sugar or sugar-like component that make up the nucleotide.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children
residueSite
The residues that contain a given sugar will be captured. The order of given residues will be captured in the 5‘-3‘direction consistent with the base sequences listed above
Path
SubstanceNucleicAcid.subunit.sugar.residueSite
Id
SubstanceNucleicAcid.subunit.sugar.residueSite
Type
Cardinality
0 - 1
Definition
The residues that contain a given sugar will be captured. The order of given residues will be captured in the 5‘-3‘direction consistent with the base sequences listed above.
Comment
Constraint
ele-1 [error]
All FHIR elements must have a @value or children