This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
See the Directory of published versions
Clinical Genomics ![]() | Maturity Level: 1 | Trial Use | Security Category: Patient | Compartments: Patient |
Detailed Descriptions for the elements in the MolecularSequence resource.
MolecularSequence | |||||||||||||
Element Id | MolecularSequence | ||||||||||||
Definition | Representation of a molecular sequence. | ||||||||||||
Cardinality | 0..* | ||||||||||||
Type | DomainResource | ||||||||||||
Summary | false | ||||||||||||
MolecularSequence.identifier | |||||||||||||
Element Id | MolecularSequence.identifier | ||||||||||||
Definition | A unique identifier for this particular sequence instance. | ||||||||||||
Note | This is a business identifier, not a resource identifier (see discussion) | ||||||||||||
Cardinality | 0..* | ||||||||||||
Type | Identifier | ||||||||||||
Requirements | Allows sequences to be distinguished and referenced. | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.type | |||||||||||||
Element Id | MolecularSequence.type | ||||||||||||
Definition | Amino Acid Sequence/ DNA Sequence / RNA Sequence. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | sequenceType (Required) | ||||||||||||
Type | code | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.patient | |||||||||||||
Element Id | MolecularSequence.patient | ||||||||||||
Definition | Indicates the patient this sequence is associated too. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Patient) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.specimen | |||||||||||||
Element Id | MolecularSequence.specimen | ||||||||||||
Definition | Specimen used for sequencing. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Specimen) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.device | |||||||||||||
Element Id | MolecularSequence.device | ||||||||||||
Definition | The method for sequencing, for example, chip information. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Device) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.performer | |||||||||||||
Element Id | MolecularSequence.performer | ||||||||||||
Definition | The organization or lab that should be responsible for this result. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Organization) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.literal | |||||||||||||
Element Id | MolecularSequence.literal | ||||||||||||
Definition | Sequence that was observed. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | string | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.formatted | |||||||||||||
Element Id | MolecularSequence.formatted | ||||||||||||
Definition | Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system. | ||||||||||||
Cardinality | 0..* | ||||||||||||
Type | Attachment | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative | |||||||||||||
Element Id | MolecularSequence.relative | ||||||||||||
Definition | A sequence defined relative to another sequence. | ||||||||||||
Cardinality | 0..* | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.coordinateSystem | |||||||||||||
Element Id | MolecularSequence.relative.coordinateSystem | ||||||||||||
Definition | These are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail. | ||||||||||||
Cardinality | 1..1 | ||||||||||||
Terminology Binding | LL5323-2 ![]() | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference | |||||||||||||
Element Id | MolecularSequence.relative.reference | ||||||||||||
Definition | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Summary | true | ||||||||||||
Invariants |
| ||||||||||||
MolecularSequence.relative.reference.referenceSequenceAssembly | |||||||||||||
Element Id | MolecularSequence.relative.reference.referenceSequenceAssembly | ||||||||||||
Definition | The reference assembly used for reference, e.g. GRCh38. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | LL1040-6 ![]() | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference.chromosome | |||||||||||||
Element Id | MolecularSequence.relative.reference.chromosome | ||||||||||||
Definition | Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340 | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | LL2938-0 ![]() | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference.referenceSequence[x] | |||||||||||||
Element Id | MolecularSequence.relative.reference.referenceSequence[x] | ||||||||||||
Definition | The reference sequence that represents the starting sequence. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | Multiple bindings acceptable (NCBI or LRG): | ||||||||||||
Type | CodeableConcept|string|Reference(MolecularSequence) | ||||||||||||
[x] Note | See Choice of Data Types for further information about how to use [x] | ||||||||||||
Summary | true | ||||||||||||
Comments | A reference sequnce may be represented in one of three ways:
| ||||||||||||
MolecularSequence.relative.reference.windowStart | |||||||||||||
Element Id | MolecularSequence.relative.reference.windowStart | ||||||||||||
Definition | Start position of the window on the reference sequence. This value should honor the rules of the coordinateSystem. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference.windowEnd | |||||||||||||
Element Id | MolecularSequence.relative.reference.windowEnd | ||||||||||||
Definition | End position of the window on the reference sequence. This value should honor the rules of the coordinateSystem. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference.orientation | |||||||||||||
Element Id | MolecularSequence.relative.reference.orientation | ||||||||||||
Definition | A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | orientationType (Required) | ||||||||||||
Type | code | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.reference.strand | |||||||||||||
Element Id | MolecularSequence.relative.reference.strand | ||||||||||||
Definition | An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | strandType (Required) | ||||||||||||
Type | code | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit | |||||||||||||
Element Id | MolecularSequence.relative.edit | ||||||||||||
Definition | Changes in sequence from the reference. | ||||||||||||
Cardinality | 0..* | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.start | |||||||||||||
Element Id | MolecularSequence.relative.edit.start | ||||||||||||
Definition | Start position of the edit on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.end | |||||||||||||
Element Id | MolecularSequence.relative.edit.end | ||||||||||||
Definition | End position of the edit on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.observedAllele | |||||||||||||
Element Id | MolecularSequence.relative.edit.observedAllele | ||||||||||||
Definition | Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | string | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.referenceAllele | |||||||||||||
Element Id | MolecularSequence.relative.edit.referenceAllele | ||||||||||||
Definition | Allele in the reference sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end. | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | string | ||||||||||||
Summary | true |