MolecularSequence | Medplum

Elements

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
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. 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. 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).
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
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
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). 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. 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. 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
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).
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. 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. 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. 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. 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. 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. 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. 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. 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 of the variant.	MolecularSequence.variant.end
variant-start	number	Start position of the variant.	MolecularSequence.variant.start
window-end	number	End position of the reference sequence.	MolecularSequence.referenceSeq.windowEnd
window-start	number	Start position of the reference sequence.	MolecularSequence.referenceSeq.windowStart
chromosome-variant-coordinate	composite	Search parameter by chromosome and variant coordinate.	MolecularSequence.variant
chromosome-window-coordinate	composite	Search parameter by chromosome and window.	MolecularSequence.referenceSeq
referenceseqid-variant-coordinate	composite	Search parameter by reference sequence and variant coordinate.	MolecularSequence.variant
referenceseqid-window-coordinate	composite	Search parameter by reference sequence and window.	MolecularSequence.referenceSeq

Inherited Elements

Name	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.
language	code	Language of the resource content Details The base language in which the resource is written.
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.
contained	Resource[]	Contained, inline Resources Details These resources do not have an independent existence apart from the resource that contains them.
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.
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.

The MolecularSequence resource is designed to describe an atomic sequence which contains the alignment sequencing test result and multiple variations. This resource aims to provide complete genetic sequence information, with specific genetic variations reported by reference to the GA4GH repository. It is constructed to avoid large genomic payloads similar to how the FHIR ImagingStudy resource references large images maintained in other systems. Implementers should also be aware that semantic equivalency of results of genetic variants cannot be guaranteed without an agreed standard between sending and receiving systems.