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Clinical Genomics Work GroupMaturity Level: 1 Trial Use Compartments: Patient

Подробное описание элементов ресурса MolecularSequence.

MolecularSequence
Element IdMolecularSequence
Definition

Raw data describing a biological sequence.

Control0..*
TypeDomainResource
Summarytrue
Invariants
Defined on this element
msq-3Rule Only 0 and 1 are valid for coordinateSystemcoordinateSystem = 1 or coordinateSystem = 0
MolecularSequence.identifier
Element IdMolecularSequence.identifier
Definition

A unique identifier for this particular sequence instance. This is a FHIR-defined id.

NoteThis is a business identifer, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
Requirements

Allows sequences to be distinguished and referenced.

Summarytrue
MolecularSequence.type
Element IdMolecularSequence.type
Definition

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Control0..1
Terminology BindingsequenceType (Required)
Typecode
Summarytrue
MolecularSequence.coordinateSystem
Element IdMolecularSequence.coordinateSystem
Definition

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).

Control1..1
Typeinteger
Summarytrue
MolecularSequence.patient
Element IdMolecularSequence.patient
Definition

The patient whose sequencing results are described by this resource.

Control0..1
TypeReference(Patient)
Summarytrue
MolecularSequence.specimen
Element IdMolecularSequence.specimen
Definition

Specimen used for sequencing.

Control0..1
TypeReference(Specimen)
Summarytrue
MolecularSequence.device
Element IdMolecularSequence.device
Definition

The method for sequencing, for example, chip information.

Control0..1
TypeReference(Device)
Summarytrue
MolecularSequence.performer
Element IdMolecularSequence.performer
Definition

The organization or lab that should be responsible for this result.

Control0..1
TypeReference(Organization)
Summarytrue
MolecularSequence.quantity
Element IdMolecularSequence.quantity
Definition

The number of copies of the sequence of interest. (RNASeq).

Control0..1
TypeQuantity
Summarytrue
MolecularSequence.referenceSeq
Element IdMolecularSequence.referenceSeq
Definition

A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

Control0..1
Summarytrue
Invariants
Defined on this element
msq-5Rule GenomeBuild and chromosome must be both contained if either one of them is contained(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())
msq-6Rule Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1
MolecularSequence.referenceSeq.chromosome
Element IdMolecularSequence.referenceSeq.chromosome
Definition

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 ).

Control0..1
Terminology Bindingchromosome-human (Example)
TypeCodeableConcept
Summarytrue
MolecularSequence.referenceSeq.genomeBuild
Element IdMolecularSequence.referenceSeq.genomeBuild
Definition

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.

Control0..1
Typestring
Summarytrue
MolecularSequence.referenceSeq.orientation
Element IdMolecularSequence.referenceSeq.orientation
Definition

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.

Control0..1
Terminology BindingorientationType (Required)
Typecode
Summarytrue
MolecularSequence.referenceSeq.referenceSeqId
Element IdMolecularSequence.referenceSeq.referenceSeqId
Definition

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.

Control0..1
Terminology BindingE n s e m b l (Example)
TypeCodeableConcept
Summarytrue
MolecularSequence.referenceSeq.referenceSeqPointer
Element IdMolecularSequence.referenceSeq.referenceSeqPointer
Definition

A pointer to another MolecularSequence entity as reference sequence.

Control0..1
TypeReference(MolecularSequence)
Summarytrue
MolecularSequence.referenceSeq.referenceSeqString
Element IdMolecularSequence.referenceSeq.referenceSeqString
Definition

A string like "ACGT".

Control0..1
Typestring
Summarytrue
MolecularSequence.referenceSeq.strand
Element IdMolecularSequence.referenceSeq.strand
Definition

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.

Control0..1
Terminology BindingstrandType (Required)
Typecode
Summarytrue
MolecularSequence.referenceSeq.windowStart
Element IdMolecularSequence.referenceSeq.windowStart
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.referenceSeq.windowEnd
Element IdMolecularSequence.referenceSeq.windowEnd
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.variant
Element IdMolecularSequence.variant
Definition

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.

Control0..*
Summarytrue
MolecularSequence.variant.start
Element IdMolecularSequence.variant.start
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.variant.end
Element IdMolecularSequence.variant.end
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.variant.observedAllele
Element IdMolecularSequence.variant.observedAllele
Definition

An allele is one of a set of coexisting sequence variants of a gene (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.

Control0..1
Typestring
Summarytrue
MolecularSequence.variant.referenceAllele
Element IdMolecularSequence.variant.referenceAllele
Definition

An allele is one of a set of coexisting sequence variants of a gene (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.

Control0..1
Typestring
Summarytrue
MolecularSequence.variant.cigar
Element IdMolecularSequence.variant.cigar
Definition

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here .

Control0..1
Typestring
Summarytrue
MolecularSequence.variant.variantPointer
Element IdMolecularSequence.variant.variantPointer
Definition

A pointer to an Observation containing variant information.

Control0..1
TypeReference(Observation)
Summarytrue
MolecularSequence.observedSeq
Element IdMolecularSequence.observedSeq
Definition

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.

Control0..1
Typestring
Summarytrue
MolecularSequence.quality
Element IdMolecularSequence.quality
Definition

An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score (SO:0001686 ).

Control0..*
Summarytrue
MolecularSequence.quality.type
Element IdMolecularSequence.quality.type
Definition

INDEL / SNP / Undefined variant.

Control1..1
Terminology BindingqualityType (Required)
Typecode
Summarytrue
MolecularSequence.quality.standardSequence
Element IdMolecularSequence.quality.standardSequence
Definition

Gold standard sequence used for comparing against.

Control0..1
Terminology BindingF d a- standard sequence (Example)
TypeCodeableConcept
Summarytrue
MolecularSequence.quality.start
Element IdMolecularSequence.quality.start
Definition

Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.quality.end
Element IdMolecularSequence.quality.end
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.quality.score
Element IdMolecularSequence.quality.score
Definition

The score of an experimentally derived feature such as a p-value (SO:0001685 ).

Control0..1
TypeQuantity
Summarytrue
MolecularSequence.quality.method
Element IdMolecularSequence.quality.method
Definition

Which method is used to get sequence quality.

Control0..1
Terminology BindingF d a- method (Example)
TypeCodeableConcept
Summarytrue
MolecularSequence.quality.truthTP
Element IdMolecularSequence.quality.truthTP
Definition

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.

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.queryTP
Element IdMolecularSequence.quality.queryTP
Definition

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.

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.truthFN
Element IdMolecularSequence.quality.truthFN
Definition

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.

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.queryFP
Element IdMolecularSequence.quality.queryFP
Definition

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.

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.gtFP
Element IdMolecularSequence.quality.gtFP
Definition

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).

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.precision
Element IdMolecularSequence.quality.precision
Definition

QUERY.TP / (QUERY.TP + QUERY.FP).

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.recall
Element IdMolecularSequence.quality.recall
Definition

TRUTH.TP / (TRUTH.TP + TRUTH.FN).

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.fScore
Element IdMolecularSequence.quality.fScore
Definition

Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).

Control0..1
Typedecimal
Summarytrue
MolecularSequence.quality.roc
Element IdMolecularSequence.quality.roc
Definition

Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.

Control0..1
Summarytrue
MolecularSequence.quality.roc.score
Element IdMolecularSequence.quality.roc.score
Definition

Invidual data point representing the GQ (genotype quality) score threshold.

Control0..*
Typeinteger
Summarytrue
MolecularSequence.quality.roc.numTP
Element IdMolecularSequence.quality.roc.numTP
Definition

The number of true positives if the GQ score threshold was set to "score" field value.

Control0..*
Typeinteger
Summarytrue
MolecularSequence.quality.roc.numFP
Element IdMolecularSequence.quality.roc.numFP
Definition

The number of false positives if the GQ score threshold was set to "score" field value.

Control0..*
Typeinteger
Summarytrue
MolecularSequence.quality.roc.numFN
Element IdMolecularSequence.quality.roc.numFN
Definition

The number of false negatives if the GQ score threshold was set to "score" field value.

Control0..*
Typeinteger
Summarytrue
MolecularSequence.quality.roc.precision
Element IdMolecularSequence.quality.roc.precision
Definition

Calculated precision if the GQ score threshold was set to "score" field value.

Control0..*
Typedecimal
Summarytrue
MolecularSequence.quality.roc.sensitivity
Element IdMolecularSequence.quality.roc.sensitivity
Definition

Calculated sensitivity if the GQ score threshold was set to "score" field value.

Control0..*
Typedecimal
Summarytrue
MolecularSequence.quality.roc.fMeasure
Element IdMolecularSequence.quality.roc.fMeasure
Definition

Calculated fScore if the GQ score threshold was set to "score" field value.

Control0..*
Typedecimal
Summarytrue
MolecularSequence.readCoverage
Element IdMolecularSequence.readCoverage
Definition

Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.repository
Element IdMolecularSequence.repository
Definition

Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

Control0..*
Summarytrue
MolecularSequence.repository.type
Element IdMolecularSequence.repository.type
Definition

Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource.

Control1..1
Terminology BindingrepositoryType (Required)
Typecode
Summarytrue
MolecularSequence.repository.url
Element IdMolecularSequence.repository.url
Definition

URI of an external repository which contains further details about the genetics data.

Control0..1
Typeuri
Summarytrue
MolecularSequence.repository.name
Element IdMolecularSequence.repository.name
Definition

URI of an external repository which contains further details about the genetics data.

Control0..1
Typestring
Summarytrue
MolecularSequence.repository.datasetId
Element IdMolecularSequence.repository.datasetId
Definition

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.

Control0..1
Typestring
Summarytrue
MolecularSequence.repository.variantsetId
Element IdMolecularSequence.repository.variantsetId
Definition

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.

Control0..1
Typestring
Summarytrue
MolecularSequence.repository.readsetId
Element IdMolecularSequence.repository.readsetId
Definition

Id of the read in this external repository.

Control0..1
Typestring
Summarytrue
MolecularSequence.pointer
Element IdMolecularSequence.pointer
Definition

Pointer to next atomic sequence which at most contains one variant.

Control0..*
TypeReference(MolecularSequence)
Summarytrue
MolecularSequence.structureVariant
Element IdMolecularSequence.structureVariant
Definition

Information about chromosome structure variation.

Control0..*
Summarytrue
MolecularSequence.structureVariant.variantType
Element IdMolecularSequence.structureVariant.variantType
Definition

Information about chromosome structure variation DNA change type.

Control0..1
Terminology BindingLOINC LL379-9 answerlist :
TypeCodeableConcept
Summarytrue
MolecularSequence.structureVariant.exact
Element IdMolecularSequence.structureVariant.exact
Definition

Used to indicate if the outer and inner start-end values have the same meaning.

Control0..1
Typeboolean
Summarytrue
MolecularSequence.structureVariant.length
Element IdMolecularSequence.structureVariant.length
Definition

Length of the variant chromosome.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.structureVariant.outer
Element IdMolecularSequence.structureVariant.outer
Definition

Structural variant outer.

Control0..1
Summarytrue
MolecularSequence.structureVariant.outer.start
Element IdMolecularSequence.structureVariant.outer.start
Definition

Structural Variant Outer Start.If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.structureVariant.outer.end
Element IdMolecularSequence.structureVariant.outer.end
Definition

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.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.structureVariant.inner
Element IdMolecularSequence.structureVariant.inner
Definition

Structural variant inner.

Control0..1
Summarytrue
MolecularSequence.structureVariant.inner.start
Element IdMolecularSequence.structureVariant.inner.start
Definition

Structural Variant Inner Start.If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Control0..1
Typeinteger
Summarytrue
MolecularSequence.structureVariant.inner.end
Element IdMolecularSequence.structureVariant.inner.end
Definition

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.

Control0..1
Typeinteger
Summarytrue