SubstanceNucleicAcid

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.

Schema

Elements

Name	Required	Type	Description
sequenceType		CodeableConcept	The type of the sequence shall be specified based on a controlled vocabulary Details The type of the sequence shall be specified based on a controlled vocabulary.
numberOfSubunits		integer	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 Details 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.
areaOfHybridisation		string	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” Details 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”.
oligoNucleotideType		CodeableConcept	(TBC) Details (TBC).
subunit		SubstanceNucleicAcidSubunit[]	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 Details 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.
id		string	Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
extension		Extension[]	Additional content defined by implementations Details May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
modifierExtension		Extension[]	Extensions that cannot be ignored even if unrecognized Details May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
subunit		integer	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 Details 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.
sequence		string	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 Details 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.
length		integer	The length of the sequence shall be captured Details The length of the sequence shall be captured.
sequenceAttachment		Attachment	(TBC) Details (TBC).
fivePrime		CodeableConcept	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 Details 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.
threePrime		CodeableConcept	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 Details 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.
linkage		SubstanceNucleicAcidSubunitLinkage[]	The linkages between sugar residues will also be captured Details The linkages between sugar residues will also be captured.
id		string	Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
extension		Extension[]	Additional content defined by implementations Details May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
modifierExtension		Extension[]	Extensions that cannot be ignored even if unrecognized Details May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
connectivity		string	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 Details 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.
identifier		Identifier	Each linkage will be registered as a fragment and have an ID Details Each linkage will be registered as a fragment and have an ID.
name		string	Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage Details Each linkage will be registered as a fragment and have at least one name. A single name shall be assigned to each linkage.
residueSite		string	Residues shall be captured as described in 5.3.6.8.3 Details Residues shall be captured as described in 5.3.6.8.3.
sugar		SubstanceNucleicAcidSubunitSugar[]	5.3.6.8.1 Sugar ID (Mandatory) Details 5.3.6.8.1 Sugar ID (Mandatory).
id		string	Unique id for inter-element referencing Details Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
extension		Extension[]	Additional content defined by implementations Details May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
modifierExtension		Extension[]	Extensions that cannot be ignored even if unrecognized Details May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
identifier		Identifier	The Substance ID of the sugar or sugar-like component that make up the nucleotide Details The Substance ID of the sugar or sugar-like component that make up the nucleotide.
name		string	The name of the sugar or sugar-like component that make up the nucleotide Details The name of the sugar or sugar-like component that make up the nucleotide.
residueSite		string	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 Details 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.

Search Parameters

None

Inherited Elements

Name	Required	Type	Description
id		string	Logical id of this artifact Details The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. The only time that a resource does not have an id is when it is being submitted to the server using a create operation.
meta		Meta	Metadata about the resource Details The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
implicitRules		uri	A set of rules under which this content was created Details A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.
language		code	Language of the resource content Details The base language in which the resource is written. Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).
text		Narrative	Text summary of the resource, for human interpretation Details A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.
contained		Resource[]	Contained, inline Resources Details These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.
extension		Extension[]	Additional content defined by implementations Details May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
modifierExtension		Extension[]	Extensions that cannot be ignored Details May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Usage

Referenced By

• SubstanceSpecification