Name Flags Card. Type Description & Constraints MolecularSequence 0..* DomainResource Molecular Sequence name 0..1 string Name of sequence type 1..1 CodeableConcept The type of sequence (genomic, mRNA, protein, ...) identifier[x] 0..* Identifier(s) for the sequence identifierHttp://hl7.org/fhir/uv/cg-model/StructureDefinition/GenomeSequenceDesignation http://hl7.org/fhir/uv/cg-model/StructureDefinition/GenomeSequenceDesignation identifierHttp://hl7.org/fhir/uv/cg-model/StructureDefinition/IdentifierSequenceDesignation http://hl7.org/fhir/uv/cg-model/StructureDefinition/IdentifierSequenceDesignation representations 0..* BackboneElement Represents the many different ways a molecular sequence could be represented literal 0..1 BackboneElement Literal sequence encoding 0..1 CodeableConcept The coding system (alphabet) used by the sequence value 1..1 string The literal sequence expressed as a string formatted 0..1 BackboneElement A formatted sequence file 1..1 Attachment Attached file resolveable 0..1 BackboneElement A sequenced retrieved from a URI uri 1..1 uri A URI that, when resolved, will return the sequence format 0..1 code The format of the resolved sequence relative 0..1 BackboneElement A Sequence defined relative to another Sequence(s) startingSequence[x] 1..1 The starting Sequence startingSequenceString string startingSequenceReference Reference(Molecular Sequence) edits 1..* BackboneElement The edits to apply to the starting sequence interval 1..1 http://hl7.org/fhir/uv/cg-model/StructureDefinition/MolecularPreciseInterval The interval on the current Sequence that defines the region to be replaced referenceSequence[x] 0..1 Contents of the sequence that will be edited referenceSequenceString string referenceSequenceReference Reference(Molecular Sequence) replacementSequence[x] 1..1 The content used in the replacement replacementSequenceString string replacementSequenceReference Reference(Molecular Sequence) relationship 0..* BackboneElement Relationship between two Sequences type 1..1 CodeableConcept Relationship type description 0..1 string Relationship description sequence 1..1 Reference(Molecular Sequence) The target of the sequence relationship Documentation for this format
Next version of MolecularSequence resource
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
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 in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))
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()
not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
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.
The only time that a resource does not have an id is when it is being submitted to the server using a create operation.
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 it's 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 it's 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 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, 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.
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 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.
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
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).
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://hl7.org/fhir/R4/extensibility.html#modifierExtension).
Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
The human-readable name of the sequence.
The type of sequence (genomic, mRNA, protein, ...)
The type of the sequence. Ideally, a code from an ontology would be used to designate genomic (including plasmid and short oligonucleotides), RNA (including mRNA, tRNA, ncRNA, etc), and protein (including short peptides). The bindings for this element have not yet been determined.
Represents the many different ways a molecular sequence could be represented
This element allows a single instance of Sequence to be represented in many different ways, including different file formats.
A sequence represented as a literal string
The coding system (alphabet) used by the sequence
The coding system (alphabet) used by the sequence. While IUPAC symbols are frequently assumed, this attribute can denote whether an amino acid sequence is encoded as single letter or 3-letter abbreviations. Ideally, a value set defining common coding systewould be developed.
The literal sequence expressed as a string
A sequence expressed in a pre-defined format. The attached sequence can be processed using existing software tools designed for the given format.
A file containing the formatted sequence.
Reference to a sequence that is not explicitly provided within this instance of Sequence, but which can be retrieved by resolving the URI
A URI that, when resolved, will return the sequence
A resolvable, absolute address that, when accessed, will return the Sequence
The format of the resolved sequence. The codes for this element should be the same as those for a Formatted Sequence.
A Sequence defined relative to another Sequence(s)
The definition of a new sequence that is represented by applying an ordered series of edits to one or more other Sequences.
A reference to the Sequence used as the starting "base" of the Sequence that is to be derived.
The edits to apply to the starting sequence
An ordered series of edits to apply to the starting sequence
The interval on the current Sequence that defines the region to be replaced
The coordinate interval that defines the region of Sequence to be replaced during the current edit operation
Contents of the sequence that will be edited
The content of the sub-Sequence that will be replaced in the current edit operation
The replacement Sequence used in the current edit operation
This element captures information about the relationship between two Sequences. Ideally, the relationship will be codified using concepts from an ontology.
The relationship between two sequences. For example: transcribed to, transcribed from, translated to, translated from. Ideally, the concepts used to express the relationship should be defined in an ontology.
A description of the relationship between two sequences.
A reference to a Sequence that represents the object of a defined relationship.