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Clinical Genomics Work GroupMaturity Level: 1 Trial Use Compartments: Not linked to any defined compartments

Detailed Descriptions for the elements in the Sequence resource.

Sequence
Element IdSequence
Definition

Raw data describing a biological sequence.

Control1..1
Summarytrue
InvariantsDefined on this element
  • Rule seq-3: Only 0 and 1 are valid for coordinateSystem (expression : coordinateSystem = 1 or coordinateSystem = 0, xpath: count(f:coordinateSystem[@value=0 and @value=1]) = 1)
Sequence.identifier
Element IdSequence.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
Sequence.type
Element IdSequence.type
Definition

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Control0..1
Terminology BindingsequenceType (Example)
Typecode
Summarytrue
Sequence.coordinateSystem
Element IdSequence.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
Sequence.patient
Element IdSequence.patient
Definition

The patient whose sequencing results are described by this resource.

Control0..1
TypeReference(Patient)
Summarytrue
Sequence.specimen
Element IdSequence.specimen
Definition

Specimen used for sequencing.

Control0..1
TypeReference(Specimen)
Summarytrue
Sequence.device
Element IdSequence.device
Definition

The method for sequencing, for example, chip information.

Control0..1
TypeReference(Device)
Summarytrue
Sequence.performer
Element IdSequence.performer
Definition

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

Control0..1
TypeReference(Organization)
Summarytrue
Sequence.quantity
Element IdSequence.quantity
Definition

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

Control0..1
TypeQuantity
Summarytrue
Sequence.referenceSeq
Element IdSequence.referenceSeq
Definition

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

Control0..1
Summarytrue
InvariantsDefined on this element
  • Rule seq-5: GenomeBuild and chromosome must be both contained if either one of them is contained (expression : (chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists()), xpath: (exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild))))
  • Rule seq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; (expression : (genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1, xpath: count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1)
Sequence.referenceSeq.chromosome
Element IdSequence.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
Sequence.referenceSeq.genomeBuild
Element IdSequence.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
Sequence.referenceSeq.orientation
Element IdSequence.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
Sequence.referenceSeq.referenceSeqId
Element IdSequence.referenceSeq.referenceSeqId
Definition

Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.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 BindingENSEMBL (Example)
TypeCodeableConcept
Summarytrue
Sequence.referenceSeq.referenceSeqPointer
Element IdSequence.referenceSeq.referenceSeqPointer
Definition

A Pointer to another Sequence entity as reference sequence.

Control0..1
TypeReference(Sequence)
Summarytrue
Sequence.referenceSeq.referenceSeqString
Element IdSequence.referenceSeq.referenceSeqString
Definition

A string like "ACGT".

Control0..1
Typestring
Summarytrue
Sequence.referenceSeq.strand
Element IdSequence.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
Sequence.referenceSeq.windowStart
Element IdSequence.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.

Control1..1
Typeinteger
Summarytrue
Sequence.referenceSeq.windowEnd
Element IdSequence.referenceSeq.windowEnd
Definition

End position of the window on the reference sequence. If the coordinate system is 0-based then end is 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.

Control1..1
Typeinteger
Summarytrue
Sequence.variant
Element IdSequence.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
Sequence.variant.start
Element IdSequence.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
Sequence.variant.end
Element IdSequence.variant.end
Definition

End position of the variant on the reference sequence.If the coordinate system is 0-based then end is 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
Sequence.variant.observedAllele
Element IdSequence.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
Sequence.variant.referenceAllele
Element IdSequence.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
Sequence.variant.cigar
Element IdSequence.variant.cigar
Definition

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

Control0..1
Typestring
Summarytrue
Sequence.variant.variantPointer
Element IdSequence.variant.variantPointer
Definition

A pointer to an Observation containing variant information.

Control0..1
TypeReference(Observation)
Summarytrue
Sequence.observedSeq
Element IdSequence.observedSeq
Definition

Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.

Control0..1
Typestring
Summarytrue
Sequence.quality
Element IdSequence.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
Sequence.quality.type
Element IdSequence.quality.type
Definition

INDEL / SNP / Undefined variant.

Control1..1
Terminology BindingqualityType (Required)
Typecode
Summarytrue
Sequence.quality.standardSequence
Element IdSequence.quality.standardSequence
Definition

Gold standard sequence used for comparing against.

Control0..1
Terminology BindingFDA-StandardSequence (Example)
TypeCodeableConcept
Summarytrue
Sequence.quality.start
Element IdSequence.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
Sequence.quality.end
Element IdSequence.quality.end
Definition

End position of the sequence.If the coordinate system is 0-based then end is 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
Sequence.quality.score
Element IdSequence.quality.score
Definition

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

Control0..1
TypeQuantity
Summarytrue
Sequence.quality.method
Element IdSequence.quality.method
Definition

Which method is used to get sequence quality.

Control0..1
Terminology BindingFDA-Method (Example)
TypeCodeableConcept
Summarytrue
Sequence.quality.truthTP
Element IdSequence.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
Sequence.quality.queryTP
Element IdSequence.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
Sequence.quality.truthFN
Element IdSequence.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
Sequence.quality.queryFP
Element IdSequence.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
Sequence.quality.gtFP
Element IdSequence.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
Sequence.quality.precision
Element IdSequence.quality.precision
Definition

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

Control0..1
Typedecimal
Summarytrue
Sequence.quality.recall
Element IdSequence.quality.recall
Definition

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

Control0..1
Typedecimal
Summarytrue
Sequence.quality.fScore
Element IdSequence.quality.fScore
Definition

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

Control0..1
Typedecimal
Summarytrue
Sequence.quality.roc
Element IdSequence.quality.roc
Definition

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

Control0..1
Summarytrue
Sequence.quality.roc.score
Element IdSequence.quality.roc.score
Definition

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

Control0..*
Typeinteger
Summarytrue
Sequence.quality.roc.numTP
Element IdSequence.quality.roc.numTP
Definition

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

Control0..*
Typeinteger
Summarytrue
Sequence.quality.roc.numFP
Element IdSequence.quality.roc.numFP
Definition

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

Control0..*
Typeinteger
Summarytrue
Sequence.quality.roc.numFN
Element IdSequence.quality.roc.numFN
Definition

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

Control0..*
Typeinteger
Summarytrue
Sequence.quality.roc.precision
Element IdSequence.quality.roc.precision
Definition

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

Control0..*
Typedecimal
Summarytrue
Sequence.quality.roc.sensitivity
Element IdSequence.quality.roc.sensitivity
Definition

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

Control0..*
Typedecimal
Summarytrue
Sequence.quality.roc.fMeasure
Element IdSequence.quality.roc.fMeasure
Definition

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

Control0..*
Typedecimal
Summarytrue
Sequence.readCoverage
Element IdSequence.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
Sequence.repository
Element IdSequence.repository
Definition

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

Control0..*
Summarytrue
Sequence.repository.type
Element IdSequence.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
Sequence.repository.url
Element IdSequence.repository.url
Definition

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

Control0..1
Typeuri
Summarytrue
Sequence.repository.name
Element IdSequence.repository.name
Definition

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

Control0..1
Typestring
Summarytrue
Sequence.repository.datasetId
Element IdSequence.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
Sequence.repository.variantsetId
Element IdSequence.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
Sequence.repository.readsetId
Element IdSequence.repository.readsetId
Definition

Id of the read in this external repository.

Control0..1
Typestring
Summarytrue
Sequence.pointer
Element IdSequence.pointer
Definition

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

Control0..*
TypeReference(Sequence)
Summarytrue
Sequence.structureVariant
Element IdSequence.structureVariant
Definition

Information about chromosome structure variation.

Control0..*
Summarytrue
Sequence.structureVariant.precision
Element IdSequence.structureVariant.precision
Definition

Identify the exact boundaries of variant sequences. Each type of structure variant requires the DNA duplex to be broken and rejoined, and this creates a new sequence of bases at the rejoined sites, known as breakpoints or boundaries.

Control0..1
Typestring
Summarytrue
Sequence.structureVariant.reportedaCGHRatio
Element IdSequence.structureVariant.reportedaCGHRatio
Definition

Structural Variant reported aCGH ratio.

Control0..1
Typedecimal
Summarytrue
Sequence.structureVariant.length
Element IdSequence.structureVariant.length
Definition

Length of the variant choromosome.

Control0..1
Typeinteger
Summarytrue
Sequence.structureVariant.outer
Element IdSequence.structureVariant.outer
Definition

Structural variant outer.

Control0..1
Summarytrue
Sequence.structureVariant.outer.start
Element IdSequence.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
Sequence.structureVariant.outer.end
Element IdSequence.structureVariant.outer.end
Definition

Structural Variant Outer End. If the coordinate system is 0-based then end is 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
Sequence.structureVariant.inner
Element IdSequence.structureVariant.inner
Definition

Structural variant inner.

Control0..1
Summarytrue
Sequence.structureVariant.inner.start
Element IdSequence.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
Sequence.structureVariant.inner.end
Element IdSequence.structureVariant.inner.end
Definition

Structural Variant Inner End. If the coordinate system is 0-based then end is 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