Generated Narrative: StructureDefinition MolecularDefinition Name Flags Card. Type Description & Constraints MolecularDefinition 0..* DomainResource Definitional content for a molecular entity Elements defined in Ancestors:id, meta, implicitRules, language, <a href="http://hl7.org/fhir/R5/domainresource.html" title="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.">text, contained, <a href="http://hl7.org/fhir/R5/domainresource.html" title="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 managable, 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.">extension, <a href="http://hl7.org/fhir/R5/domainresource.html" title="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 managable, 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.#xA;#xA;Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).">modifierExtension #xD; identifier Σ 0..* Identifier Unique ID of an instance #xD; description 0..1 markdown Description of the Molecular Definition instance #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.moleculeType" title="The broad physical class of molecule represented by this instance (e.g., DNA, RNA, polypeptide). This element provides a stable, searchable classification of the molecule and is intended to facilitate cross-system querying and to provide domain context for profiles. The terminology binding may be expanded to support additional molecule classes in the future (e.g., peptide nucleic acids, oligosaccharides).">moleculeType Σ 0..1 CodeableConcept The type of molecule (e.g., DNA, RNA, polypeptide) Binding: Molecular Definition Molecule Type (required): The broad physical class of molecule: DNA, RNA, or polypeptide. Codes are drawn from the Sequence Ontology (SO). #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.type" title="Domain-semantic subtype classifications of this molecule instance, providing greater specificity than moleculeType. For example, an instance with moleculeType 'RNA' (SO:0000356) may have a type of 'mRNA' (SO:0000234) or 'miRNA' (SO:0000276). Multiple types may be specified. Note that RNA subtype concepts in the Sequence Ontology are not hierarchically descended from SO:0000356 (RNA); this ValueSet therefore enumerates them explicitly.">type Σ 0..* CodeableConcept Domain-semantic subtype classification of the molecule Binding: Molecular Definition Type (extensible): Domain-semantic subtype of the molecule (e.g., mRNA, genomic_DNA, lncRNA). Codes are drawn from a curated subset of Sequence Ontology (SO). Implementers may use additional SO codes or codes from other systems when no suitable code exists in this set. #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.topology" title="The structural topology of the molecular entity. For nucleotide polymers this specifies the end-to-end configuration of the chain: linear (5'-terminus and 3'-terminus present), circular (no terminal residues), linear-discontiguous (gapped/split representation), or branched. Codes are drawn from the locally defined Molecular Definition Topology CodeSystem.">topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular) Binding: Molecular Definition Topology (required): The structural topology of the molecule (e.g., linear, circular, linear-discontiguous, branched). Codes are drawn from the locally defined Molecular Definition Topology CodeSystem. #xD; member Σ 0..* Reference(Molecular Definition) Constituents of an aggregate molecular concept (e.g., haplotype, genotype) #xD; location Σ 0..* BackboneElement A defined location on a molecular entity #xD; sequenceLocation Σ 0..1 BackboneElement A coordinate-based location on a sequence #xD; sequenceContext Σ 1..1 Reference(Molecular Definition) The sequence on which the location is defined #xD; coordinateInterval Σ 0..1 BackboneElement An interval on a sequence #xD; coordinateSystem Σ 0..1 BackboneElement The coordinate system used to define the location #xD; system Σ 0..1 CodeableConcept The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system type governing position counting. Codes from LOINC answer list LL5323-2 correspond to widely-used systems: LA30100-4 (0-based interval counting, used by UCSC BED, GA4GH VRS, and SPDI), LA30101-2 (0-based character counting), LA30102-0 (1-based character counting, used by HGVS c./g./n./p. and RefSeq), and LA30103-8 (1-based interval counting). #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.origin" title="The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).">origin Σ 0..1 CodeableConcept The location of the origin of the coordinate system Binding: Coordinate System Origin ValueSet (required): The reference landmark from which coordinates are measured. Unambiguous origin specification is essential for correct variant interpretation and cross-system interoperability. #xD; normalizationMethod Σ 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system Binding: Coordinate System Normalization Method ValueSet (required): The normalization convention applied when positioning a variant in a repetitive sequence region (e.g., left-shift for VCF, right-shift for HGVS 3' rule, fully-justified for VOCA/GA4GH). #xD; start[x] Σ 0..1 The start location of the interval #xD; startQuantity Quantity #xD; startRange Range #xD; end[x] Σ 0..1 The end location of the interval #xD; endQuantity Quantity #xD; endRange Range #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.location.sequenceLocation.strand" title="The specific strand at the coordinateInterval, when the interval alone is not sufficient to define a location (e.g., double stranded DNA). 'Forward' corresponds to the plus/sense/Watson strand (5' to 3' in the standard reference orientation); 'reverse' corresponds to the minus/antisense/Crick strand (3' to 5' in the standard reference orientation).">strand 0..1 CodeableConcept The strand orientation of the sequenceLocation Binding: Molecular Definition Strand (required): Strand orientation of a sequenceLocation. 'forward' (SO:0001030) = plus/sense/Watson strand; 'reverse' (SO:0001031) = minus/antisense/Crick strand. #xD; cytobandLocation Σ 0..1 BackboneElement A cytoband-based location on a sequence #xD; genomeAssembly Σ 1..1 BackboneElement Reference Genome #xD; organism 0..1 CodeableConcept Species of the organism Binding: Molecular Definition Organism (extensible): The organism whose genome the assembly describes. Codes are drawn from NCBI Taxonomy (http://www.ncbi.nlm.nih.gov/taxonomy). Common values: 9606 (Homo sapiens), 10090 (Mus musculus). #xD; build 0..1 CodeableConcept Genome assembly build Binding: LOINC Answer List LL1040-6 (extensible): Named genome assembly build. Codes from LOINC LL1040-6 cover established NCBI/Genome Reference Consortium (GRC) assemblies (e.g., LA14029-5 GRCh37, LA14032-9 GRCh38). The extensible binding accommodates newer assemblies such as T2T-CHM13 not yet represented in LL1040-6. #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.location.cytobandLocation.genomeAssembly.accession" title="The NCBI Assembly accession for this genome assembly. Accessions follow the pattern GCF_######.v (RefSeq, e.g., GCF_000001405.40 for GRCh38.p14) or GCA_######.v (GenBank, e.g., GCA_009914755.4 for T2T-CHM13v2.0). Use system http://www.ncbi.nlm.nih.gov/assembly.">accession 0..1 CodeableConcept NCBI Assembly accession Binding Description: (example): NCBI Assembly accession numbers identifying genome assembly versions. Use system http://www.ncbi.nlm.nih.gov/assembly with the accession (e.g., GCF_000001405.40) as the code. #xD; description[x] 0..1 Genome assembly description #xD; descriptionMarkdown markdown #xD; descriptionString string #xD; cytobandInterval Σ 1..1 BackboneElement Cytoband Interval #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.location.cytobandLocation.cytobandInterval.chromosome" title="The chromosome on which this cytoband interval is located. Use a LOINC chromosome answer code from LL2938-0, which covers human autosomes (chromosomes 1-22), sex chromosomes (X, Y), and the mitochondrial chromosome (M). LOINC LA-prefixed codes provide stable identifiers for consistent genomic data exchange. This binding is consistent with the chromosome binding in the genomics-reporting IG (component[chromosome-studied]).">chromosome Σ 1..1 CodeableConcept Human chromosome identifier Binding: LOINC Answer List LL2938-0 (preferred): LOINC answer list LL2938-0: human chromosome identifiers covering autosomes 1-22, sex chromosomes X and Y, and mitochondrial chromosome M. #xD; startCytoband[x] Σ 0..1 Start #xD; startCytobandCodeableConcept CodeableConcept #xD; startCytobandString string #xD; endCytoband[x] Σ 0..1 End #xD; endCytobandCodeableConcept CodeableConcept #xD; endCytobandString string #xD; representation Σ 0..* BackboneElement A representation of a molecular entity #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.focus" title="Identifies which domain concept a given representation instance describes. When multiple representations are present on a single MolecularDefinition instance, this element is the machine-readable discriminator classifying each by role: allele-state (the specific allele being described), reference-state (the reference sequence at this location), alternative-state (an alternate sequence at this location), or context-state (the surrounding genomic sequence context that frames the allele). This element uses a required binding; implementations shall use a code from the MolecularDefinitionRepresentationFocus CodeSystem.">focus Σ 0..1 code Representation focus concept Binding: Molecular Definition Representation Focus VS (required): Classifies the role of a representation within a MolecularDefinition: allele-state, reference-state, alternative-state, or context-state. #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.code" title="A coded identifier for the molecular entity represented by this instance. The most common use is a versioned sequence accession from a public database (e.g., a RefSeq accession such as NC_000010.11 for a genomic sequence, NM_000769.4 for an mRNA transcript, NP_000760.1 for a protein, or NG_008384.3 for a RefSeqGene). Multiple codes may be provided where the same molecule is indexed in more than one database (e.g., both RefSeq and INSDC GenBank for the same sequence). The coding.system should be drawn from a well-known sequence database URI (see the example binding). Implementers should prefer versioned accessions (those including a dot-version, e.g., NC_000010.11) to ensure stable, unambiguous identification of a specific sequence version.">code Σ 0..* CodeableConcept Molecular sequence identifier (e.g., RefSeq accession) Binding: Molecular Definition Representation Code (example): Example molecular sequence identifier systems registered in HL7 terminology: NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq) and LRG (http://www.lrg-sequence.org). #xD; literal Σ 0..1 BackboneElement A molecular entity defined as a string literal #xD; encoding Σ 0..1 CodeableConcept The encoding used in the value Binding: Molecular Definition Literal Encoding VS (extensible) #xD; value Σ 1..1 string A string literal representation of the molecular entity, using the encoding specified in encoding #xD; resolvable Σ 0..1 Reference(DocumentReference) A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.extracted" title="A molecular entity that is represented as a portion of a different entity. For example, this element can represent a subsequence (e.g., genetic region) that is part of and conceptually extracted from a longer sequence (e.g., chromosome sequence). The “parent” entity is specified in startingMolecule and the location of the intended molecular entity on the parent entity is defined by coordinateInterval.">extracted Σ 0..1 BackboneElement A molecular entity that is represented as a portion of a different entity #xD; startingMolecule Σ 1..1 Reference(Molecular Definition) The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived #xD; coordinateInterval Σ 0..1 BackboneElement The interval on startingMolecule that defines the portion to be extracted to produce the intended entity #xD; coordinateSystem Σ 0..1 BackboneElement The coordinate system used to define the location #xD; system Σ 0..1 CodeableConcept The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system type governing position counting. Codes from LOINC answer list LL5323-2 correspond to widely-used systems: LA30100-4 (0-based interval counting, used by UCSC BED, GA4GH VRS, and SPDI), LA30101-2 (0-based character counting), LA30102-0 (1-based character counting, used by HGVS c./g./n./p. and RefSeq), and LA30103-8 (1-based interval counting). #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.origin" title="The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).">origin Σ 0..1 CodeableConcept The location of the origin of the coordinate system Binding: Coordinate System Origin ValueSet (required): The reference landmark from which coordinates are measured. Unambiguous origin specification is essential for correct variant interpretation and cross-system interoperability. #xD; normalizationMethod Σ 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system Binding: Coordinate System Normalization Method ValueSet (required): The normalization convention applied when positioning a variant in a repetitive sequence region (e.g., left-shift for VCF, right-shift for HGVS 3' rule, fully-justified for VOCA/GA4GH). #xD; start[x] Σ 0..1 The start location of the interval #xD; startQuantity Quantity #xD; startRange Range #xD; end[x] Σ 0..1 The end location of the interval #xD; endQuantity Quantity #xD; endRange Range #xD; reverseComplement Σ 0..1 boolean A flag that indicates whether the extracted sequence should be reverse complemented #xD; repeated Σ 0..1 BackboneElement A representation as a repeated motif #xD; sequenceMotif Σ 1..1 Reference(Molecular Definition) The motif that is repeated #xD; copyCount Σ 1..1 integer The number of copies of the motif #xD; concatenated Σ 0..1 BackboneElement An ordered concatenation of molecular entities #xD; sequenceElement Σ 1..* BackboneElement One of the concatenated entities #xD; sequence Σ 1..1 Reference(Molecular Definition) A reference to the sequence that defines this specific concatenated element #xD; ordinalIndex Σ 1..1 integer The ordinal index of the element within the concatenated representation #xD; relative Σ 0..1 BackboneElement A molecular entity represented as an ordered series of edits on a specified starting entity #xD; startingMolecule Σ 1..1 Reference(Molecular Definition) The molecular entity on which edits will be applied #xD; edit Σ 0..* BackboneElement A defined edit (change) to be applied #xD; editOrder 0..1 integer Defines the order of edits when multiple edits are to be applied to the startingMolecule #xD; coordinateInterval Σ 0..1 BackboneElement The interval on startingMolecule that defines the portion to be extracted to produce the intended entity #xD; coordinateSystem Σ 0..1 BackboneElement The coordinate system used to define the location #xD; system Σ 0..1 CodeableConcept The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system type governing position counting. Codes from LOINC answer list LL5323-2 correspond to widely-used systems: LA30100-4 (0-based interval counting, used by UCSC BED, GA4GH VRS, and SPDI), LA30101-2 (0-based character counting), LA30102-0 (1-based character counting, used by HGVS c./g./n./p. and RefSeq), and LA30103-8 (1-based interval counting). #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.origin" title="The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).">origin Σ 0..1 CodeableConcept The location of the origin of the coordinate system Binding: Coordinate System Origin ValueSet (required): The reference landmark from which coordinates are measured. Unambiguous origin specification is essential for correct variant interpretation and cross-system interoperability. #xD; normalizationMethod Σ 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system Binding: Coordinate System Normalization Method ValueSet (required): The normalization convention applied when positioning a variant in a repetitive sequence region (e.g., left-shift for VCF, right-shift for HGVS 3' rule, fully-justified for VOCA/GA4GH). #xD; start[x] Σ 0..1 The start location of the interval #xD; startQuantity Quantity #xD; startRange Range #xD; end[x] Σ 0..1 The end location of the interval #xD; endQuantity Quantity #xD; endRange Range #xD; replacementMolecule Σ 1..1 Reference(Molecular Definition) The molecular entity that serves as the replacement in the edit operation #xD; <a href="StructureDefinition-MolecularDefinition-definitions.html#MolecularDefinition.representation.relative.edit.replacedMolecule" title="The portion of the molecular entity that is replaced by the replacementMolecule as a result of the edit. The value of this element can be derived as the state of the entity at the specified coordinateInterval, prior to the edit being applied. It is provided for convenience.">replacedMolecule Σ 0..1 Reference(Molecular Definition) The portion of the molecular entity that is replaced by the replacementMolecule #xD; Documentation for this format
Definitional content for a molecular entity, such as a nucleotide or protein sequence.
Definitional content for a molecular entity
If the resource is contained in another resource, it SHALL NOT contain nested Resources
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
contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
If a resource is contained in another resource, it SHALL NOT have a security label
When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time.
A resource should have narrative for robust management
Entity. Role, or Act,Entity, Role, or Act
The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
Within the context of the FHIR RESTful interactions, the resource has an id except for cases like the create and conditional update. Otherwise, the use of the resouce id depends on the given use case.
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.
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
A set of rules under which this content was created
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 its narrative along with other profiles, value sets, etc.
This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies its meaning or interpretation
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 summary of the resource, for human interpretation
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 a 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.
These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, nor can they have their own independent transaction scope. This is allowed to be a Parameters resource if and only if it is referenced by a resource that provides context/meaning.
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. Contained resources may be a resource type defined in the FHIR specification, or an [additional resource](http://build.fhir.org/resource.html#additional).
Extensions are always sliced by (at least) url
Additional content defined by implementations
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 managable, 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.
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 managable, 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).
Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](http://build.fhir.org/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
A unique identifier for a particular instance of this resource.
Description of the Molecular Definition instance
A description of the molecular entity in a human friendly format.
The type of molecule (e.g., DNA, RNA, polypeptide)
The broad physical class of molecule represented by this instance (e.g., DNA, RNA, polypeptide). This element provides a stable, searchable classification of the molecule and is intended to facilitate cross-system querying and to provide domain context for profiles. The terminology binding may be expanded to support additional molecule classes in the future (e.g., peptide nucleic acids, oligosaccharides).
The broad physical class of molecule: DNA, RNA, or polypeptide. Codes are drawn from the Sequence Ontology (SO).
Domain-semantic subtype classification of the molecule
Domain-semantic subtype classifications of this molecule instance, providing greater specificity than moleculeType. For example, an instance with moleculeType 'RNA' (SO:0000356) may have a type of 'mRNA' (SO:0000234) or 'miRNA' (SO:0000276). Multiple types may be specified. Note that RNA subtype concepts in the Sequence Ontology are not hierarchically descended from SO:0000356 (RNA); this ValueSet therefore enumerates them explicitly.
Domain-semantic subtype of the molecule (e.g., mRNA, genomic_DNA, lncRNA). Codes are drawn from a curated subset of Sequence Ontology (SO). Implementers may use additional SO codes or codes from other systems when no suitable code exists in this set.
The structural topology of the molecular entity (e.g., linear, circular)
The structural topology of the molecular entity. For nucleotide polymers this specifies the end-to-end configuration of the chain: linear (5'-terminus and 3'-terminus present), circular (no terminal residues), linear-discontiguous (gapped/split representation), or branched. Codes are drawn from the locally defined Molecular Definition Topology CodeSystem.
The structural topology of the molecule (e.g., linear, circular, linear-discontiguous, branched). Codes are drawn from the locally defined Molecular Definition Topology CodeSystem.
Constituents of an aggregate molecular concept (e.g., haplotype, genotype)
Constituents of an aggregate molecular concept (e.g., haplotype, genotype).
A defined location on a molecular entity
A defined location on a molecular entity. Location definitions may vary with respect to coordinate space and precision or level of granularity.
All FHIR elements must have a @value or children or both
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
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 managable, 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.
Extensions that cannot be ignored even if unrecognized
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 managable, 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).
Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
A coordinate-based location on a sequence
A location on a sequence, defined using a nucleotide coordinate system.
The sequence on which the location is defined
A reference to a sequence on which the location is defined.
An interval on a sequence, defined by coordinate-based start and end coordinates.
The coordinate system used to define the location
A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.
Coordinate system type governing position counting. Codes from LOINC answer list LL5323-2 correspond to widely-used systems: LA30100-4 (0-based interval counting, used by UCSC BED, GA4GH VRS, and SPDI), LA30101-2 (0-based character counting), LA30102-0 (1-based character counting, used by HGVS c./g./n./p. and RefSeq), and LA30103-8 (1-based interval counting).
The location of the origin of the coordinate system
The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).
The reference landmark from which coordinates are measured. Unambiguous origin specification is essential for correct variant interpretation and cross-system interoperability.
The normalization method used for determining a location within the coordinate system
The normalization method used for determining a location within the coordinate system. Examples include left shift (e.g., VCF), right shift (e.g., HGVS), or fully justified (e.g., VOCA).
The normalization convention applied when positioning a variant in a repetitive sequence region (e.g., left-shift for VCF, right-shift for HGVS 3' rule, fully-justified for VOCA/GA4GH).
The start location of the interval expressed as a precise coordinate (Quantity) or expressed as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported.
The end location of the interval expressed as a precise coordinate (Quantity) or as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported..
The strand orientation of the sequenceLocation
The specific strand at the coordinateInterval, when the interval alone is not sufficient to define a location (e.g., double stranded DNA). 'Forward' corresponds to the plus/sense/Watson strand (5' to 3' in the standard reference orientation); 'reverse' corresponds to the minus/antisense/Crick strand (3' to 5' in the standard reference orientation).
Strand orientation of a sequenceLocation. 'forward' (SO:0001030) = plus/sense/Watson strand; 'reverse' (SO:0001031) = minus/antisense/Crick strand.
A location on a sequence, defined using cytobands.
The species of the organism whose genome this assembly represents, expressed as an NCBI Taxonomy identifier (e.g., 9606 for Homo sapiens, 10090 for Mus musculus).
The organism whose genome the assembly describes. Codes are drawn from NCBI Taxonomy (http://www.ncbi.nlm.nih.gov/taxonomy). Common values: 9606 (Homo sapiens), 10090 (Mus musculus).
The named genome assembly build, such as GRCh38 or GRCh37. Codes from LOINC answer list LL1040-6 are used here, consistent with the genomics-reporting IG binding for reference-sequence-assembly.
Named genome assembly build. Codes from LOINC LL1040-6 cover established NCBI/Genome Reference Consortium (GRC) assemblies (e.g., LA14029-5 GRCh37, LA14032-9 GRCh38). The extensible binding accommodates newer assemblies such as T2T-CHM13 not yet represented in LL1040-6.
The NCBI Assembly accession for this genome assembly. Accessions follow the pattern GCF_######.v (RefSeq, e.g., GCF_000001405.40 for GRCh38.p14) or GCA_######.v (GenBank, e.g., GCA_009914755.4 for T2T-CHM13v2.0). Use system http://www.ncbi.nlm.nih.gov/assembly.
NCBI Assembly accession numbers identifying genome assembly versions. Use system http://www.ncbi.nlm.nih.gov/assembly with the accession (e.g., GCF_000001405.40) as the code.
The description of this genome assembly.
The chromosome on which this cytoband interval is located. Use a LOINC chromosome answer code from LL2938-0, which covers human autosomes (chromosomes 1-22), sex chromosomes (X, Y), and the mitochondrial chromosome (M). LOINC LA-prefixed codes provide stable identifiers for consistent genomic data exchange. This binding is consistent with the chromosome binding in the genomics-reporting IG (component[chromosome-studied]).
LOINC answer list LL2938-0: human chromosome identifiers covering autosomes 1-22, sex chromosomes X and Y, and mitochondrial chromosome M.
A representation of a molecular entity, specifically including sequence. Note this element is intended to define the entity primarily through computable, discrete elements that express domain semantics rather than replicating a particular file format or relational schema.
Identifies which domain concept a given representation instance describes. When multiple representations are present on a single MolecularDefinition instance, this element is the machine-readable discriminator classifying each by role: allele-state (the specific allele being described), reference-state (the reference sequence at this location), alternative-state (an alternate sequence at this location), or context-state (the surrounding genomic sequence context that frames the allele). This element uses a required binding; implementations shall use a code from the MolecularDefinitionRepresentationFocus CodeSystem.
Classifies the role of a representation within a MolecularDefinition: allele-state, reference-state, alternative-state, or context-state.
Molecular sequence identifier (e.g., RefSeq accession)
A coded identifier for the molecular entity represented by this instance. The most common use is a versioned sequence accession from a public database (e.g., a RefSeq accession such as NC_000010.11 for a genomic sequence, NM_000769.4 for an mRNA transcript, NP_000760.1 for a protein, or NG_008384.3 for a RefSeqGene). Multiple codes may be provided where the same molecule is indexed in more than one database (e.g., both RefSeq and INSDC GenBank for the same sequence). The coding.system should be drawn from a well-known sequence database URI (see the example binding). Implementers should prefer versioned accessions (those including a dot-version, e.g., NC_000010.11) to ensure stable, unambiguous identification of a specific sequence version.
Example molecular sequence identifier systems registered in HL7 terminology: NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq) and LRG (http://www.lrg-sequence.org).
A molecular entity defined as a string literal
A molecular entity defined as a string literal.
The encoding used for the expression of the entity. For a primary sequence, this element represents the alphabet used (e.g., 1 character DNA without ambiguity codes, 3 character amino acid codes).
A string literal representation of the molecular entity, using the encoding specified in encoding
A string literal representation of the molecular entity, using a specific encoding. For example, this may be the primary sequence of a strand of DNA.
A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
A resolvable representation of a molecular entity, which may be specified as a URI and/or attached document (in a defined format).
A molecular entity that is represented as a portion of a different entity
A molecular entity that is represented as a portion of a different entity. For example, this element can represent a subsequence (e.g., genetic region) that is part of and conceptually extracted from a longer sequence (e.g., chromosome sequence). The “parent” entity is specified in startingMolecule and the location of the intended molecular entity on the parent entity is defined by coordinateInterval.
The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
A reference to the molecular entity that serves as the conceptual 'parent' from which the intended entity is derived. For example, this could be a chromosome sequence on which a coordinateInterval is defined.
The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
The interval on startingMolecule that defines the portion to be extracted in order to create the intended entity.
The coordinate system used to define the location, which may vary depending on application or context of use.
A flag that indicates whether the extracted sequence should be reverse complemented
A flag that indicates whether the extracted sequence should be reverse complemented in order to produce the intended entity. This element is only relevant to molecular entities that support the concept of reverse complement (e.g., double stranded DNA).
A representation of a molecular entity that is expressed as a number of copies of a repeated motif.
The motif that is repeated in tandem, which ultimately defines the intended molecular entity.
The number of times the motif is repeated to create the intended molecular entity.
An ordered concatenation of molecular entities
A representation comprised of an ordered concatenation of two or more molecular entities.
One of the concatenated entities within the concatenated representation.
At least two elements are required to represent a concatenated sequence.
A reference to the sequence that defines this specific concatenated element
A reference to the sequence that defines this specific concatenated element.
The ordinal index of the element within the concatenated representation
The ordinal index of the element within the concatenated representation.
0 or 1 based indices are possible, could potentially skip numbers in the sequence, suggest implementers sort numerically prior to concatenating
A molecular entity represented as an ordered series of edits on a specified starting entity
A molecular entity represented as an ordered series of edits on a specified starting entity. This representation can be used to define one entity relative to another.
The molecular entity on which edits will be applied
The molecular entity that serves as the starting point, on which edits will be applied.
A defined edit (change) to be applied to the molecular entity.
Edits are applied sequentially. The sequence that results from one edit operation is used as the 'starting' sequence of the next edit operation.
Defines the order of edits when multiple edits are to be applied to the startingMolecule
Defines the order of edits when multiple edits are to be applied to the startingMolecule. This is important when edits may overlap (intervals) or when edits change the length of the entity.
The molecular entity that serves as the replacement in the edit operation
The molecular entity that serves as the replacement in the edit operation. After the edit has been applied, the state of the entity at the specified coordinateInterval is defined by the state of the replacementMolecule.
The portion of the molecular entity that is replaced by the replacementMolecule
The portion of the molecular entity that is replaced by the replacementMolecule as a result of the edit. The value of this element can be derived as the state of the entity at the specified coordinateInterval, prior to the edit being applied. It is provided for convenience.