MolecularSequence
ClinicalRaw data describing a biological sequence.
| Path | Card. | Type | Description & Constraints |
|---|---|---|---|
| MolecularSequence | 0..* | — | Information about a biological sequence |
| .idΣ | 0..1 | String | Logical id of this artifact |
| .metaΣ | 0..1 | Meta | Metadata about the resource |
| .implicitRules?!Σ | 0..1 | uri | A set of rules under which this content was created |
| .language | 0..1 | code | Language of the resource content Bindinglanguages(preferred) |
| .text | 0..1 | Narrative | Text summary of the resource, for human interpretation |
| .contained | 0..* | Resource | Contained, inline Resources |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?! | 0..* | Extension | Extensions that cannot be ignored |
| .identifierΣ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id |
| .typeΣ | 0..1 | code | aa | dna | rna Bindingsequence-type(required) |
| .coordinateSystemΣ | 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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .chromosomeΣ | 0..1 | CodeableConcept | Chromosome containing genetic finding Bindingchromosome-human(example) |
| .genomeBuildΣ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' |
| .orientationΣ | 0..1 | code | sense | antisense Bindingorientation-type(required) |
| .referenceSeqIdΣ | 0..1 | CodeableConcept | Reference identifier Bindingsequence-referenceSeq(example) |
| .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 | crick Bindingstrand-type(required) |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .typeΣ | 1..1 | code | indel | snp | unknown Bindingquality-type(required) |
| .standardSequenceΣ | 0..1 | CodeableConcept | Standard sequence for comparison Bindingsequence-quality-standardSequence(example) |
| .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 quality Bindingsequence-quality-method(example) |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .typeΣ | 1..1 | code | directlink | openapi | login | oauth | other Bindingrepository-type(required) |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .variantTypeΣ | 0..1 | CodeableConcept | Structural variant change type BindingLL379-9(required) |
| .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 |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .startΣ | 0..1 | integer | Structural variant outer start |
| .endΣ | 0..1 | integer | Structural variant outer end |
| .innerΣ | 0..1 | BackboneElement | Structural variant inner |
| .id | 0..1 | String | Unique id for inter-element referencing |
| .extension | 0..* | Extension | Additional content defined by implementations |
| .modifierExtension?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| .startΣ | 0..1 | integer | Structural variant inner start |
| .endΣ | 0..1 | integer | Structural variant inner end |