MolecularSequence
Raw data describing a biological sequence.
- Backends
- PostgreSQLElasticsearch
- Interactions
- CreateReadUpdatePatchDelete
- Search
- 9 of 13 parameters tested
Structure
| Element | Card. | Type | Description |
|---|---|---|---|
identifierΣ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id |
typeΣ | 0..1 | code | aa | dna | rnaBinding (required): sequence-type |
coordinateSystemRequiredΣ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) |
patientΣ | 0..1 | Reference(Patient) | Who and/or what this is about |
specimenΣ | 0..1 | Reference(Specimen) | Specimen used for sequencing |
deviceΣ | 0..1 | Reference(Device) | The method for sequencing |
performerΣ | 0..1 | Reference(Organization) | Who should be responsible for test result |
quantityΣ | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq) |
referenceSeqΣ | 0..1 | BackboneElement | A sequence used as reference |
chromosomeΣ | 0..1 | CodeableConcept | Chromosome containing genetic findingBinding (example): chromosome-human |
genomeBuildΣ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
orientationΣ | 0..1 | code | sense | antisenseBinding (required): orientation-type |
referenceSeqIdΣ | 0..1 | CodeableConcept | Reference identifierBinding (example): sequence-referenceSeq |
referenceSeqPointerΣ | 0..1 | Reference(MolecularSequence) | A pointer to another MolecularSequence entity as reference sequence |
referenceSeqStringΣ | 0..1 | string | A string to represent reference sequence |
strandΣ | 0..1 | code | watson | crickBinding (required): strand-type |
windowStartΣ | 0..1 | integer | Start position of the window on the reference sequence |
windowEndΣ | 0..1 | integer | End position of the window on the reference sequence |
variantΣ | 0..* | BackboneElement | Variant in sequence |
startΣ | 0..1 | integer | Start position of the variant on the reference sequence |
endΣ | 0..1 | integer | End position of the variant on the reference sequence |
observedAlleleΣ | 0..1 | string | Allele that was observed |
referenceAlleleΣ | 0..1 | string | Allele in the reference sequence |
cigarΣ | 0..1 | string | Extended CIGAR string for aligning the sequence with reference bases |
variantPointerΣ | 0..1 | Reference(Observation) | Pointer to observed variant information |
observedSeqΣ | 0..1 | string | Sequence that was observed |
qualityΣ | 0..* | BackboneElement | An set of value as quality of sequence |
typeRequiredΣ | 1..1 | code | indel | snp | unknownBinding (required): quality-type |
standardSequenceΣ | 0..1 | CodeableConcept | Standard sequence for comparisonBinding (example): sequence-quality-standardSequence |
startΣ | 0..1 | integer | Start position of the sequence |
endΣ | 0..1 | integer | End position of the sequence |
scoreΣ | 0..1 | Quantity | Quality score for the comparison |
methodΣ | 0..1 | CodeableConcept | Method to get qualityBinding (example): sequence-quality-method |
truthTPΣ | 0..1 | decimal | True positives from the perspective of the truth data |
queryTPΣ | 0..1 | decimal | True positives from the perspective of the query data |
truthFNΣ | 0..1 | decimal | False negatives |
queryFPΣ | 0..1 | decimal | False positives |
gtFPΣ | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match |
precisionΣ | 0..1 | decimal | Precision of comparison |
recallΣ | 0..1 | decimal | Recall of comparison |
fScoreΣ | 0..1 | decimal | F-score |
rocΣ | 0..1 | BackboneElement | Receiver Operator Characteristic (ROC) Curve |
scoreΣ | 0..* | integer | Genotype quality score |
numTPΣ | 0..* | integer | Roc score true positive numbers |
numFPΣ | 0..* | integer | Roc score false positive numbers |
numFNΣ | 0..* | integer | Roc score false negative numbers |
precisionΣ | 0..* | decimal | Precision of the GQ score |
sensitivityΣ | 0..* | decimal | Sensitivity of the GQ score |
fMeasureΣ | 0..* | decimal | FScore of the GQ score |
readCoverageΣ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence |
repositoryΣ | 0..* | BackboneElement | External repository which contains detailed report related with observedSeq in this resource |
typeRequiredΣ | 1..1 | code | directlink | openapi | login | oauth | otherBinding (required): repository-type |
urlΣ | 0..1 | uri | URI of the repository |
nameΣ | 0..1 | string | Repository's name |
datasetIdΣ | 0..1 | string | Id of the dataset that used to call for dataset in repository |
variantsetIdΣ | 0..1 | string | Id of the variantset that used to call for variantset in repository |
readsetIdΣ | 0..1 | string | Id of the read |
pointerΣ | 0..* | Reference(MolecularSequence) | Pointer to next atomic sequence |
structureVariantΣ | 0..* | BackboneElement | Structural variant |
variantTypeΣ | 0..1 | CodeableConcept | Structural variant change typeBinding (required): LL379-9 |
exactΣ | 0..1 | boolean | Does the structural variant have base pair resolution breakpoints? |
lengthΣ | 0..1 | integer | Structural variant length |
outerΣ | 0..1 | BackboneElement | Structural variant outer |
startΣ | 0..1 | integer | Structural variant outer start |
endΣ | 0..1 | integer | Structural variant outer end |
innerΣ | 0..1 | BackboneElement | Structural variant inner |
startΣ | 0..1 | integer | Structural variant inner start |
endΣ | 0..1 | integer | Structural variant inner end |
Σ in _summary results · ?! modifier element · 1.. required · inherited elements in grey
Search parameters
Query with GET [base]/MolecularSequence?[parameter]=[value]. Type decides which modifiers and prefixes apply, see search features.
| Parameter | Type | Description | PG | ES |
|---|---|---|---|---|
chromosome | token | Chromosome number of the reference sequence MolecularSequence.referenceSeq.chromosome | ||
chromosome-variant-coordinate | composite | Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as MolecularSequence.variant | ||
chromosome-window-coordinate | composite | Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as MolecularSequence.referenceSeq | ||
identifier | token | The unique identity for a particular sequence MolecularSequence.identifier | ||
patient | reference | The subject that the observation is about MolecularSequence.patient | ||
referenceseqid | token | Reference Sequence of the sequence MolecularSequence.referenceSeq.referenceSeqId | ||
referenceseqid-variant-coordinate | composite | Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as MolecularSequence.variant | ||
referenceseqid-window-coordinate | composite | Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as MolecularSequence.referenceSeq | ||
type | token | Amino Acid Sequence/ DNA Sequence / RNA Sequence MolecularSequence.type | ||
variant-end | number | End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant. MolecularSequence.variant.end | ||
variant-start | number | Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant. MolecularSequence.variant.start | ||
window-end | number | End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence. MolecularSequence.referenceSeq.windowEnd | ||
window-start | number | Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence. MolecularSequence.referenceSeq.windowStart |
PG: PostgreSQL, ES: Elasticsearch. passes its TestScript checks, fails, not tested yet. The author of the resource Logical id of this artifact When the resource version last changed Profiles this resource claims to conform to Security Labels applied to this resource Identifies where the resource comes from Tags applied to this resource Derived from the R4B DefinitionCommon parameters on every resource (8)
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