MolecularSequence

Raw data describing a biological sequence.

Schema

Properties

Name	Required	Type	Description
identifier		Identifier[]	Unique ID for this particular sequence. This is a FHIR-defined id Details A unique identifier for this particular sequence instance. This is a FHIR-defined id.
type		code	aa | dna | rna Details Amino 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) Details Whether 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 Details The patient whose sequencing results are described by this resource.
specimen		Reference<Specimen>	Specimen used for sequencing Details Specimen used for sequencing.
device		Reference<Device>	The method for sequencing Details The method for sequencing, for example, chip information.
performer		Reference<Organization>	Who should be responsible for test result Details The organization or lab that should be responsible for this result.
quantity		Quantity	The number of copies of the sequence of interest. (RNASeq) Details The number of copies of the sequence of interest. (RNASeq).
referenceSeq		MolecularSequenceReferenceSeq	A sequence used as reference Details A 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 Details Unique 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 Details May 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 Details May 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 Details 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](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' Details The 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 Details 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.
referenceSeqId		CodeableConcept	Reference identifier Details Reference 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 Details A pointer to another MolecularSequence entity as reference sequence.
referenceSeqString		string	A string to represent reference sequence Details A string like "ACGT".
strand		code	watson | crick Details 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.
windowStart		integer	Start position of the window on the reference sequence Details Start 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 Details End 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 Details The 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 Details Unique 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 Details May 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 Details May 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 Details Start 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 Details End 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 Details An 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 Details An 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 Details Extended 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 Details A pointer to an Observation containing variant information.
observedSeq		string	Sequence that was observed Details Sequence 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 Details An 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 Details Unique 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 Details May 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 Details May 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 Details INDEL / SNP / Undefined variant.
standardSequence		CodeableConcept	Standard sequence for comparison Details Gold standard sequence used for comparing against.
start		integer	Start position of the sequence Details Start 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 Details End 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 Details The 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 Details Which method is used to get sequence quality.
truthTP		decimal	True positives from the perspective of the truth data Details True 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 Details True 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 Details False 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 Details False 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 Details The 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 Details QUERY.TP / (QUERY.TP + QUERY.FP).
recall		decimal	Recall of comparison Details TRUTH.TP / (TRUTH.TP + TRUTH.FN).
fScore		decimal	F-score Details Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).
roc		MolecularSequenceQualityRoc	Receiver Operator Characteristic (ROC) Curve Details Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
id		string	Unique id for inter-element referencing Details Unique 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 Details May 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 Details May 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 Details Invidual data point representing the GQ (genotype quality) score threshold.
numTP		integer[]	Roc score true positive numbers Details The number of true positives if the GQ score threshold was set to "score" field value.
numFP		integer[]	Roc score false positive numbers Details The number of false positives if the GQ score threshold was set to "score" field value.
numFN		integer[]	Roc score false negative numbers Details The number of false negatives if the GQ score threshold was set to "score" field value.
precision		decimal[]	Precision of the GQ score Details Calculated precision if the GQ score threshold was set to "score" field value.
sensitivity		decimal[]	Sensitivity of the GQ score Details Calculated sensitivity if the GQ score threshold was set to "score" field value.
fMeasure		decimal[]	FScore of the GQ score Details Calculated 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 Details Coverage (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 Details Configurations 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 Details Unique 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 Details May 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 Details May 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 Details Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.
url		uri	URI of the repository Details URI of an external repository which contains further details about the genetics data.
name		string	Repository's name Details URI 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 Details Id 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 Details Id 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 Details Id of the read in this external repository.
pointer		Reference<MolecularSequence>[]	Pointer to next atomic sequence Details Pointer to next atomic sequence which at most contains one variant.
structureVariant		MolecularSequenceStructureVariant[]	Structural variant Details Information about chromosome structure variation.
id		string	Unique id for inter-element referencing Details Unique 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 Details May 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 Details May 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 Details Information about chromosome structure variation DNA change type.
exact		boolean	Does the structural variant have base pair resolution breakpoints? Details Used to indicate if the outer and inner start-end values have the same meaning.
length		integer	Structural variant length Details Length of the variant chromosome.
outer		MolecularSequenceStructureVariantOuter	Structural variant outer Details Structural variant outer.
id		string	Unique id for inter-element referencing Details Unique 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 Details May 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 Details May 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 Details Structural 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 Details Structural 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 Details Structural variant inner.
id		string	Unique id for inter-element referencing Details Unique 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 Details May 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 Details May 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 Details Structural 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 Details Structural 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 Properties

Name	Required	Type	Description
id		string	Logical id of this artifact Details The 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 Details The 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 Details A 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 Details The 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 Details A 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 Details These 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 Details May 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 Details May 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.

Usage

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:

• Variant Databases: dbSNP , ClinVar , and COSMIC
• Reference Sequences: RefSeq and ENSEMBL

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.

Relationships

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.

Referenced By

• Observation