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Clinical Genomics Work Group | 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. | ||||||||||||
Short Display | 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. | ||||||||||||
Short Display | Unique ID for this particular sequence | ||||||||||||
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. | ||||||||||||
Short Display | aa | dna | rna | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | sequenceType (Required) | ||||||||||||
Type | code | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.subject | |||||||||||||
Element Id | MolecularSequence.subject | ||||||||||||
Definition | Indicates the subject this sequence is associated too. | ||||||||||||
Short Display | Subject this sequence is associated too | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.specimen | |||||||||||||
Element Id | MolecularSequence.specimen | ||||||||||||
Definition | Specimen used for sequencing. | ||||||||||||
Short Display | 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. | ||||||||||||
Short Display | The method for sequencing | ||||||||||||
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. | ||||||||||||
Short Display | Who should be responsible for test result | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Reference(Organization) | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.literal | |||||||||||||
Element Id | MolecularSequence.literal | ||||||||||||
Definition | Sequence that was observed. | ||||||||||||
Short Display | 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. | ||||||||||||
Short Display | Embedded file or a link (URL) which contains content to represent the sequence | ||||||||||||
Cardinality | 0..* | ||||||||||||
Type | Attachment | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative | |||||||||||||
Element Id | MolecularSequence.relative | ||||||||||||
Definition | A sequence defined relative to another sequence. | ||||||||||||
Short Display | 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. | ||||||||||||
Short Display | Ways of identifying nucleotides or amino acids within a sequence | ||||||||||||
Cardinality | 1..1 | ||||||||||||
Terminology Binding | LL5323-2 : | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.ordinalPosition | |||||||||||||
Element Id | MolecularSequence.relative.ordinalPosition | ||||||||||||
Definition | Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together. | ||||||||||||
Short Display | Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | false | ||||||||||||
MolecularSequence.relative.sequenceRange | |||||||||||||
Element Id | MolecularSequence.relative.sequenceRange | ||||||||||||
Definition | Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together. | ||||||||||||
Short Display | Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | Range | ||||||||||||
Summary | false | ||||||||||||
MolecularSequence.relative.startingSequence | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence | ||||||||||||
Definition | A sequence that is used as a starting sequence to describe variants that are present in a sequence analyzed. | ||||||||||||
Short Display | A sequence used as starting sequence | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Summary | true | ||||||||||||
Invariants |
| ||||||||||||
MolecularSequence.relative.startingSequence.genomeAssembly | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.genomeAssembly | ||||||||||||
Definition | The genome assembly used for starting sequence, e.g. GRCh38. | ||||||||||||
Short Display | The genome assembly used for starting sequence, e.g. GRCh38 | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | LL1040-6 : | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.startingSequence.chromosome | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.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 ). | ||||||||||||
Short Display | Chromosome Identifier | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | LL2938-0 : | ||||||||||||
Type | CodeableConcept | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.startingSequence.sequence[x] | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.sequence[x] | ||||||||||||
Definition | The reference sequence that represents the starting sequence. | ||||||||||||
Short Display | 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 Datatypes for further information about how to use [x] | ||||||||||||
Summary | true | ||||||||||||
Comments | A starting sequence may be represented in one of three ways:
| ||||||||||||
MolecularSequence.relative.startingSequence.windowStart | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.windowStart | ||||||||||||
Definition | Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem. | ||||||||||||
Short Display | Start position of the window on the starting sequence | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.startingSequence.windowEnd | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.windowEnd | ||||||||||||
Definition | End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem. | ||||||||||||
Short Display | End position of the window on the starting sequence | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.startingSequence.orientation | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.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. | ||||||||||||
Short Display | sense | antisense | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Terminology Binding | orientationType (Required) | ||||||||||||
Type | code | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.startingSequence.strand | |||||||||||||
Element Id | MolecularSequence.relative.startingSequence.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. | ||||||||||||
Short Display | watson | crick | ||||||||||||
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 starting sequence. | ||||||||||||
Short Display | Changes in sequence from the starting sequence | ||||||||||||
Cardinality | 0..* | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.start | |||||||||||||
Element Id | MolecularSequence.relative.edit.start | ||||||||||||
Definition | Start position of the edit on the starting sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | ||||||||||||
Short Display | Start position of the edit on the starting sequence | ||||||||||||
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 starting 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. | ||||||||||||
Short Display | End position of the edit on the starting sequence | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | integer | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.replacementSequence | |||||||||||||
Element Id | MolecularSequence.relative.edit.replacementSequence | ||||||||||||
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. | ||||||||||||
Short Display | Allele that was observed | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | string | ||||||||||||
Summary | true | ||||||||||||
MolecularSequence.relative.edit.replacedSequence | |||||||||||||
Element Id | MolecularSequence.relative.edit.replacedSequence | ||||||||||||
Definition | Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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. | ||||||||||||
Short Display | Allele in the starting sequence | ||||||||||||
Cardinality | 0..1 | ||||||||||||
Type | string | ||||||||||||
Summary | true |