Generated Narrative: StructureDefinition allele Name Flags Card. Type Description & Constraints MolecularDefinition 0..* MolecularDefinition Definitional content for a molecular entity #xD; type S 1..1 CodeableConcept Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type ValueSet (required) #xD; topology 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (required) #xD; member 0..0 Constituents of an aggregate molecular concept (e.g., haplotype, genotype) #xD; location 1..1 BackboneElement Genomic location of the specified allele #xD; sequenceLocation #xD; sequenceContext 1..1 Reference(Sequence) The sequence on which the location is defined #xD; coordinateInterval #xD; coordinateSystem #xD; origin 0..1 CodeableConcept The location of the origin of the coordinate system Binding: Coordinate Origin ValueSet (required) #xD; normalizationMethod 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system Binding: Normalization Method ValueSet (required) #xD; strand 0..1 CodeableConcept The strand at the coordinateInterval Binding: Strand Orientation ValueSet (required) #xD; Slices for representation 1..* BackboneElement A representation of a molecular entity Slice: Unordered, Open by value:focus #xD; representation:All Slices Content/Rules for all slices #xD; literal #xD; encoding 0..1 CodeableConcept The encoding used in the value Binding: Molecular Definition Encodings ValueSet (required) #xD; value 1..1 string A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding. Additional Bindings Purpose Nucleotide DNA 1-letter Unambiguous Symbols ValueSet Extensible Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet Extensible Nucleotide DNA 1-letter Ambiguous Symbols ValueSet Extensible Nucleotide RNA 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Ambiguous Symbols ValueSet Extensible Amino Acid 3-letter Unambiguous Symbols ValueSet Extensible Amino Acid 3-letter Ambiguous Symbols ValueSet Extensible #xD; representation:contextState S 0..1 BackboneElement A representation of a molecular entity #xD; focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: context-state #xD; display 1..1 string Representation defined by the system Fixed Value: Context State #xD; representation:alleleState S 1..1 BackboneElement A representation of a molecular entity #xD; focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following #xD; coding 1..* Coding Code defined by a terminology system Fixed Value: (Complex) #xD; system 1..1 uri Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus #xD; code 1..1 code Symbol in syntax defined by the system Fixed Value: allele-state #xD; display 1..1 string Representation defined by the system Fixed Value: Allele State #xD; Documentation for this format
Allele profile of the MolecularDefinition resource.
Definitional content for a molecular entity
Definitional content for a molecular entity, such as a nucleotide or protein sequence.
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
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).
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, amino acid)
The type of molecule (e.g., DNA, RNA, amino acid). This is a broad concept that refers to the general physical composition of the molecule, intended to facilitate searching and to provide domain context for profiles and instances. The terminology binding may be expanded to support additional types of molecules in the future (e.g., peptide nucleic acids, oligosaccharides).
Classification of the molecule into types other than those defined by moleculeType
Classifications of an instance of the resource into arbitrary types, based on domain semantics. For example, this element could indicate that an instance of moleculeType 'RNA' could have a type of 'mRNA' or 'siRNA'.
The structural topology of the molecular entity (e.g., linear, circular)
The structural topology of the molecular entity. For sequences (e.g., DNA), this could specify 'linear' and 'circular'. More complex entities might be branched or have a quaternary structure.
Constituents of an aggregate molecular concept (e.g., haplotype, genotype)
Constituents of an aggregate molecular concept (e.g., haplotype, genotype).
Genomic location of the specified allele
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.
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 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 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 specific strand at the coordinateInterval, when the interval alone is not sufficient to define a location (e.g., double stranded DNA). Example values include 'forward' and 'reverse'.
A location on a sequence, defined using cytobands.
The build number of this genome assemble.
The description of this genome assembly.
The chromosome where this cytoband interval occurs.
Slice based on the representation.focus value to differentiate between Context and Allele states.
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.
The domain concept that is the focus of a given instance of the representation
The domain concept that is the focus of the representation. This element is used to disambiguate the representations of the “reference” and the “alternate” alleles at a given location, for example.
A code (e.g., sequence accession number) used to represent a molecular entity
A code (e.g., sequence accession number) used to represent a molecular entity.
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.
Refer to the addtional bindings for the literal encoding.
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.