MolecularSequence
Raw data describing a biological sequence.
- Schema
- Usage
- Relationships
- Referenced By
Elements
Name | Required | Type | Description |
---|---|---|---|
identifier | Identifier[] | Unique ID for this particular sequence. This is a FHIR-defined id DetailsA unique identifier for this particular sequence instance. This is a FHIR-defined id. | |
type | code | aa | dna | rna DetailsAmino Acid Sequence/ DNA Sequence / RNA Sequence. | |
coordinateSystem | ✓ | 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) DetailsWhether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end). |
patient | Reference<Patient> | Who and/or what this is about DetailsThe patient whose sequencing results are described by this resource. | |
specimen | Reference<Specimen> | Specimen used for sequencing DetailsSpecimen used for sequencing. | |
device | Reference<Device> | The method for sequencing DetailsThe method for sequencing, for example, chip information. | |
performer | Reference<Organization> | Who should be responsible for test result DetailsThe organization or lab that should be responsible for this result. | |
quantity | Quantity | The number of copies of the sequence of interest. (RNASeq) DetailsThe number of copies of the sequence of interest. (RNASeq). | |
referenceSeq | MolecularSequencereferenceSeq | A sequence used as reference DetailsA sequence that is used as a reference to describe variants that are present in a sequence analyzed. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
chromosome | CodeableConcept | Chromosome containing genetic finding DetailsStructural 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)). | |
genomeBuild | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' DetailsThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used. | |
orientation | code | sense | antisense DetailsA 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. | |
referenceSeqId | CodeableConcept | Reference identifier DetailsReference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences. | |
referenceSeqPointer | Reference<MolecularSequence> | A pointer to another MolecularSequence entity as reference sequence DetailsA pointer to another MolecularSequence entity as reference sequence. | |
referenceSeqString | string | A string to represent reference sequence DetailsA string like "ACGT". | |
strand | code | watson | crick DetailsAn 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. | |
windowStart | integer | Start position of the window on the reference sequence DetailsStart position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | |
windowEnd | integer | End position of the window on the reference sequence DetailsEnd position of the window 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. | |
variant | MolecularSequencevariant[] | Variant in sequence DetailsThe definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
start | integer | Start position of the variant on the reference sequence DetailsStart position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | |
end | integer | End position of the variant on the reference sequence DetailsEnd position of the variant 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. | |
observedAllele | string | Allele that was observed DetailsAn allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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. | |
referenceAllele | string | Allele in the reference sequence DetailsAn allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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. | |
cigar | string | Extended CIGAR string for aligning the sequence with reference bases DetailsExtended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm). | |
variantPointer | Reference<Observation> | Pointer to observed variant information DetailsA pointer to an Observation containing variant information. | |
observedSeq | string | Sequence that was observed DetailsSequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd. | |
quality | MolecularSequencequality[] | An set of value as quality of sequence DetailsAn experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)). | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
type | ✓ | code | indel | snp | unknown DetailsINDEL / SNP / Undefined variant. |
standardSequence | CodeableConcept | Standard sequence for comparison DetailsGold standard sequence used for comparing against. | |
start | integer | Start position of the sequence DetailsStart position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | |
end | integer | End position of the sequence DetailsEnd position of the 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. | |
score | Quantity | Quality score for the comparison DetailsThe score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)). | |
method | CodeableConcept | Method to get quality DetailsWhich method is used to get sequence quality. | |
truthTP | decimal | True positives from the perspective of the truth data DetailsTrue positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event. | |
queryTP | decimal | True positives from the perspective of the query data DetailsTrue positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event. | |
truthFN | decimal | False negatives DetailsFalse negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here. | |
queryFP | decimal | False positives DetailsFalse positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here. | |
gtFP | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match DetailsThe number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar). | |
precision | decimal | Precision of comparison DetailsQUERY.TP / (QUERY.TP + QUERY.FP). | |
recall | decimal | Recall of comparison DetailsTRUTH.TP / (TRUTH.TP + TRUTH.FN). | |
fScore | decimal | F-score DetailsHarmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall). | |
roc | MolecularSequencequalityroc | Receiver Operator Characteristic (ROC) Curve DetailsReceiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
score | integer[] | Genotype quality score DetailsInvidual data point representing the GQ (genotype quality) score threshold. | |
numTP | integer[] | Roc score true positive numbers DetailsThe number of true positives if the GQ score threshold was set to "score" field value. | |
numFP | integer[] | Roc score false positive numbers DetailsThe number of false positives if the GQ score threshold was set to "score" field value. | |
numFN | integer[] | Roc score false negative numbers DetailsThe number of false negatives if the GQ score threshold was set to "score" field value. | |
precision | decimal[] | Precision of the GQ score DetailsCalculated precision if the GQ score threshold was set to "score" field value. | |
sensitivity | decimal[] | Sensitivity of the GQ score DetailsCalculated sensitivity if the GQ score threshold was set to "score" field value. | |
fMeasure | decimal[] | FScore of the GQ score DetailsCalculated fScore if the GQ score threshold was set to "score" field value. | |
readCoverage | integer | Average number of reads representing a given nucleotide in the reconstructed sequence DetailsCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. | |
repository | MolecularSequencerepository[] | External repository which contains detailed report related with observedSeq in this resource DetailsConfigurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
type | ✓ | code | directlink | openapi | login | oauth | other DetailsClick and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource. |
url | uri | URI of the repository DetailsURI of an external repository which contains further details about the genetics data. | |
name | string | Repository's name DetailsURI of an external repository which contains further details about the genetics data. | |
datasetId | string | Id of the dataset that used to call for dataset in repository DetailsId of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository. | |
variantsetId | string | Id of the variantset that used to call for variantset in repository DetailsId of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository. | |
readsetId | string | Id of the read DetailsId of the read in this external repository. | |
pointer | Reference<MolecularSequence>[] | Pointer to next atomic sequence DetailsPointer to next atomic sequence which at most contains one variant. | |
structureVariant | MolecularSequencestructureVariant[] | Structural variant DetailsInformation about chromosome structure variation. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
variantType | CodeableConcept | Structural variant change type DetailsInformation about chromosome structure variation DNA change type. | |
exact | boolean | Does the structural variant have base pair resolution breakpoints? DetailsUsed to indicate if the outer and inner start-end values have the same meaning. | |
length | integer | Structural variant length DetailsLength of the variant chromosome. | |
outer | MolecularSequencestructureVariantouter | Structural variant outer DetailsStructural variant outer. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
start | integer | Structural variant outer start DetailsStructural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | |
end | integer | Structural variant outer end DetailsStructural variant outer end. 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. | |
inner | MolecularSequencestructureVariantinner | Structural variant inner DetailsStructural variant inner. | |
id | string | Unique id for inter-element referencing DetailsUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored even if unrecognized DetailsMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
start | integer | Structural variant inner start DetailsStructural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive. | |
end | integer | Structural variant inner end DetailsStructural variant inner end. 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. |
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 Elements
Name | Required | Type | Description |
---|---|---|---|
id | string | Logical id of this artifact DetailsThe logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. The only time that a resource does not have an id is when it is being submitted to the server using a create operation. | |
meta | Meta | Metadata about the resource DetailsThe metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. | |
implicitRules | uri | A set of rules under which this content was created DetailsA reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. | |
language | code | Language of the resource content DetailsThe base language in which the resource is written. Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). | |
text | Narrative | Text summary of the resource, for human interpretation DetailsA human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. | |
contained | Resource[] | Contained, inline Resources DetailsThese resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. | |
extension | Extension[] | Additional content defined by implementations DetailsMay be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. | |
modifierExtension | Extension[] | Extensions that cannot be ignored DetailsMay be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. |
The MolecularSequence resource is designed to describe an atomic sequence which contains the alignment sequencing test result and multiple variations. Atomic sequences can be connected by link element and they will lead to sequence graph. By this method, a sequence can be reported. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. Thus, the FHIR MolecularSequence resource avoids large genomic payloads in a manner analogous to how the FHIR ImagingStudy resource references large images maintained in other systems. For use cases, details on how this resource interact with other Clinical Genomics resources or profiles, please refer to implementation guidance document here.
Genetic Standards and Resources include:
This resource is designed to describe sequence variations with clinical significance with information such as:
- Name of the variation represented
- Type of the variation
- Gene region occupied by the variation
- Tissue source used to determine genotype of the variation
- Quality of the result
It is strongly encouraged to provide all available information in this resource for any reported variants, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize variants over time or across sources. However, these data should not be used to dynamically correct/change variant representations for clinical use outside of the laboratory, due to insufficient information.
Implementers should be aware that semantic equivalency of results of genetic variants cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.
Focus of the resource is to provide sequencing alignment data immediately relevant to what the interpretation on clinical decision-making originates from. Hence data such as precise read of DNA sequences and sequence alignment are not included; such data are nonetheless accessible through references to GA4GH (Global Alliance for Genomics and Health) API. The MolecularSequence resource will be referenced by Observation to provide variant information. As clinical assessments/diagnosis of a patient are typically captured in the Condition resource or the ClinicalImpression resource, the MolecularSequence resource can be referenced by the Condition resource to provide specific genetic data to support assertions. This is analogous to how Condition references other resources, such as AllergyIntolerance, Procedure, and Questionnaire resources.