MolecularSequence
MolecularSequence
Raw data describing a biological sequence.
Properties
| Name | Required | Type | Description |
|---|---|---|---|
| identifier | No | Identifier[] | Unique ID for this particular sequence. This is a FHIR-defined id |
| type | No | code | aa / dna / rna |
| coordinateSystem | Yes | 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) |
| patient | No | Reference<Patient> | Who and/or what this is about |
| specimen | No | Reference<Specimen> | Specimen used for sequencing |
| device | No | Reference<Device> | The method for sequencing |
| performer | No | Reference<Organization> | Who should be responsible for test result |
| quantity | No | Quantity | The number of copies of the sequence of interest. (RNASeq) |
| referenceSeq | No | MolecularSequenceReferenceSeq | A sequence used as reference |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - chromosome | No | CodeableConcept | Chromosome containing genetic finding |
| - genomeBuild | No | string | The Genome Build used for reference, following GRCh build versions e.g. ‘GRCh 37’ |
| - orientation | No | code | sense / antisense |
| - referenceSeqId | No | CodeableConcept | Reference identifier |
| - referenceSeqPointer | No | Reference<MolecularSequence> | A pointer to another MolecularSequence entity as reference sequence |
| - referenceSeqString | No | string | A string to represent reference sequence |
| - strand | No | code | watson / crick |
| - windowStart | No | integer | Start position of the window on the reference sequence |
| - windowEnd | No | integer | End position of the window on the reference sequence |
| variant | No | MolecularSequenceVariant | Variant in sequence |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - start | No | integer | Start position of the variant on the reference sequence |
| - end | No | integer | End position of the variant on the reference sequence |
| - observedAllele | No | string | Allele that was observed |
| - referenceAllele | No | string | Allele in the reference sequence |
| - cigar | No | string | Extended CIGAR string for aligning the sequence with reference bases |
| - variantPointer | No | Reference<Observation> | Pointer to observed variant information |
| observedSeq | No | string | Sequence that was observed |
| quality | No | MolecularSequenceQuality | An set of value as quality of sequence |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - type | Yes | code | indel / snp / unknown |
| - standardSequence | No | CodeableConcept | Standard sequence for comparison |
| - start | No | integer | Start position of the sequence |
| - end | No | integer | End position of the sequence |
| - score | No | Quantity | Quality score for the comparison |
| - method | No | CodeableConcept | Method to get quality |
| - truthTP | No | decimal | True positives from the perspective of the truth data |
| - queryTP | No | decimal | True positives from the perspective of the query data |
| - truthFN | No | decimal | False negatives |
| - queryFP | No | decimal | False positives |
| - gtFP | No | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match |
| - precision | No | decimal | Precision of comparison |
| - recall | No | decimal | Recall of comparison |
| - fScore | No | decimal | F-score |
| - roc | No | MolecularSequenceQualityRoc | Receiver Operator Characteristic (ROC) Curve |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - score | No | integer[] | Genotype quality score |
| - numTP | No | integer[] | Roc score true positive numbers |
| - numFP | No | integer[] | Roc score false positive numbers |
| - numFN | No | integer[] | Roc score false negative numbers |
| - precision | No | decimal[] | Precision of the GQ score |
| - sensitivity | No | decimal[] | Sensitivity of the GQ score |
| - fMeasure | No | decimal[] | FScore of the GQ score |
| readCoverage | No | integer | Average number of reads representing a given nucleotide in the reconstructed sequence |
| repository | No | MolecularSequenceRepository | External repository which contains detailed report related with observedSeq in this resource |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - type | Yes | code | directlink / openapi / login / oauth / other |
| - url | No | uri | URI of the repository |
| - name | No | string | Repository’s name |
| - datasetId | No | string | Id of the dataset that used to call for dataset in repository |
| - variantsetId | No | string | Id of the variantset that used to call for variantset in repository |
| - readsetId | No | string | Id of the read |
| pointer | No | Reference<MolecularSequence>[] | Pointer to next atomic sequence |
| structureVariant | No | MolecularSequenceStructureVariant | Structural variant |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - variantType | No | CodeableConcept | Structural variant change type |
| - exact | No | boolean | Does the structural variant have base pair resolution breakpoints? |
| - length | No | integer | Structural variant length |
| - outer | No | MolecularSequenceStructureVariantOuter | Structural variant outer |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - start | No | integer | Structural variant outer start |
| - end | No | integer | Structural variant outer end |
| - inner | No | MolecularSequenceStructureVariantInner | Structural variant inner |
| - id | No | string | Unique id for inter-element referencing |
| - extension | No | Extension[] | Additional content defined by implementations |
| - modifierExtension | No | Extension[] | Extensions that cannot be ignored even if unrecognized |
| - start | No | integer | Structural variant inner start |
| - end | No | integer | Structural variant inner end |
Search Parameters
| Name | Type | Description | Expression |
|---|---|---|---|
| chromosome | token | Chromosome number of the reference sequence | MolecularSequence.referenceSeq.chromosome |
| 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 |
| 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 |
| 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 chromosome-variant-coordinate=1$lt345$gt123, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | 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 chromosome-window-coordinate=1$lt345$gt123, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.referenceSeq |
| 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 referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | 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 referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. | MolecularSequence.referenceSeq |
Inherited Properties
| Name | Required | Type | Description |
|---|---|---|---|
| id | No | string | Logical id of this artifact |
| meta | No | Meta | Metadata about the resource |
| implicitRules | No | uri | A set of rules under which this content was created |
| language | No | code | Language of the resource content |
| text | No | Narrative | Text summary of the resource, for human interpretation |
| contained | No | Resource[] | Contained, inline Resources |
| extension | No | Extension[] | Additional content defined by implementations |
| modifierExtension | No | Extension[] | Extensions that cannot be ignored |
To view the FHIR specification for this resource, see MolecularSequence.