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10.6 10.7 Resource MolecularSequence - Content

Clinical Genomics icon Work Group Maturity Level : 1   Trial Use Security Category : Patient Compartments : Patient

Raw data describing Representation of a biological molecular sequence.

The Clinical Genomics committee has identified overlaps and redundancies between content in the MolecularSequence resource and content in Observation profiles in the evolving Implementation Guide for Clinical Genomics Reporting found here . The committee is considering options for modifying the resource and anticipates potential changes being brought forward in an upcoming ballot.

10.6.1 10.7.1 Scope and 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 for representing molecular sequences. It can be reported. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. Thus, represent the FHIR MolecularSequence resource avoids large genomic payloads sequence in a manner analogous different ways, allowing implementations to how adopt the FHIR ImagingStudy resource references large images maintained in other systems. For most effective one for their use cases, details on how this resource interact with other Clinical Genomics resources or profiles, please refer to implementation guidance document here . 10.6.1.1 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: case.

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 as much information in this resource for any reported variants, sequences, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize variants sequences over time or across sources. However, these data should not be used to dynamically correct/change variant sequence representations for clinical use outside of the laboratory, due to insufficient information.

Implementers should be aware The MolecularSequence resource is designed to represent a single sequence in an instance. Each sequence might have multiple representations, but implementers SHALL ensure all representations are for the same sequence. This means that if a single MolecularSequence instance contains a literal , two formatted files, and a relative , all four of those representations must represent the same sequence. This can be a challenge across systems, as semantic equivalency of results of genetic variants sequences cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.

10.6.2 10.7.2 Boundaries and Relationships

Focus of the The MolecularSequence resource is should only be used to provide sequencing alignment data immediately relevant capture a molecular sequence. It will not be used for other entities such as variant, variant annotations, genotypes, haplotypes, etc. Those concepts will be captured in Observation profiles found in the Genomics Reporting Implementation Guide icon. The sequence that was observed that led to what the interpretation on clinical decision-making originates from. Hence identification of those concepts can be delivered with this resource, and will be referenced by those observations.

MolecularSequence will not be used to capture data such as precise read of DNA sequences and sequence alignment are not included; such data are nonetheless may be accessible through references to GA4GH icon (Global Alliance for Genomics and Health) API. The MolecularSequence resource will API, and may 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. formatted element.

This resource is referenced by

10.7.3 References to this Resource

10.6.3 10.7.4 Resource Content

Structure

Σ start Σ 0..1 integer Start position of the variant on the reference sequence Σ Extended CIGAR string for aligning the sequence with reference bases An set of value Method to get quality True positives from the perspective of the truth data decimal False negatives queryFP False positives 0..1 F-score Σ Genotype quality score 0..* Roc score false positive numbers 1..1 directlink | openapi | login | oauth Repository's name
Name Flags Card. Type Description & Constraints doco
. . MolecularSequence Σ I TU DomainResource Information about Representation of a biological molecular sequence
+ Rule: Only 0 and 1 are valid for coordinateSystem
Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . . identifier Σ 0..* Identifier Unique ID for this particular sequence. This is a FHIR-defined id sequence

. . . type Σ 0..1 code aa | dna | rna
sequenceType Binding: sequence Type ( Required )
. . coordinateSystem . subject Σ 1..1 0..1 integer Reference ( Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct ) 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) Subject this sequence is associated too
. . . specimen Σ 0..1 Reference ( Specimen ) Specimen used for sequencing
. . . device Σ 0..1 Reference ( Device ) The method for sequencing
. . . performer Σ 0..1 Reference ( Organization ) Who should be responsible for test result
. . quantity . literal Σ 0..1 Quantity string The number of copies of the sequence of interest. (RNASeq) Sequence that was observed
. . referenceSeq . formatted Σ I 0..1 0..* BackboneElement Attachment A Embedded file or a link (URL) which contains content to represent the sequence used as reference
+ Rule: GenomeBuild and chromosome must be both contained if either one of them is contained
+ Rule: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
. . chromosome . relative Σ 0..1 0..* CodeableConcept BackboneElement Chromosome containing genetic finding A sequence defined relative to another sequence
chromosome-human ( Example ) genomeBuild Σ 0..1 string The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' orientation Σ 0..1 code sense | antisense
orientationType ( Required )
. . . . referenceSeqId coordinateSystem Σ 0..1 1..1 CodeableConcept Reference identifier Ways of identifying nucleotides or amino acids within a sequence
Binding: LL5323-2 icon E n s e m b l ( Example ) referenceSeqPointer Σ 0..1 Reference ( MolecularSequence Extensible ) A pointer to another MolecularSequence entity as reference sequence referenceSeqString Σ 0..1 string A string to represent reference sequence strand Σ 0..1 code watson | crick
strandType ( Required )
. . . windowStart Σ 0..1 integer Start position of the window on the reference sequence . windowEnd ordinalPosition 0..1 integer End position of the window on Indicates the reference sequence variant Σ 0..* BackboneElement Variant order in which the sequence should be considered when putting multiple 'relative' elements together
. . . end . sequenceRange 0..1 integer Range End position of the variant on Indicates the reference sequence observedAllele Σ 0..1 string Allele that was observed referenceAllele Σ 0..1 string Allele nucleotide range in the reference composed sequence cigar Σ 0..1 string when multiple 'relative' elements are used together
. . . variantPointer . startingSequence Σ 0..1 Reference ( Observation ) Pointer to observed variant information observedSeq Σ C 0..1 string Sequence that was observed quality Σ 0..* BackboneElement A sequence used as quality of starting sequence
type Σ 1..1 + Rule: Both genomeAssembly and chromosome must be both contained if either one of them is contained code
+ Rule: Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence indel | snp | unknown
qualityType ( Required )
. . . . . standardSequence genomeAssembly Σ C 0..1 CodeableConcept Standard sequence The genome assembly used for comparison starting sequence, e.g. GRCh38
Binding: LL1040-6 icon F d a- standard sequence ( Example Extensible ) start Σ 0..1 integer
Start position of the sequence
. end Σ 0..1 integer End position of the sequence . . . . score chromosome Σ 0..1 Quantity C Quality score for the comparison method Σ 0..1 CodeableConcept Chromosome Identifier
Binding: LL2938-0 icon F d a- method ( Example Required ) truthTP Σ 0..1 decimal
. . . . queryTP . sequence[x] Σ 0..1 decimal C True positives from the perspective of the query data truthFN Σ 0..1 Σ 0..1 decimal The reference sequence that represents the starting sequence
Binding: Multiple bindings acceptable (NCBI or LRG) ( Example )
. gtFP Σ 0..1 decimal False positives where the non-REF alleles in the Truth and Query Call Sets match . . precision Σ 0..1 decimal Precision of comparison . . recall Σ . sequenceCodeableConcept decimal Recall of comparison fScore Σ 0..1 decimal CodeableConcept
. roc Σ 0..1 BackboneElement Receiver Operator Characteristic (ROC) Curve . . . . . score sequenceString 0..* integer string
. . numTP . . Σ . . sequenceReference integer Roc score true positive numbers numFP Σ Reference 0..* integer ( MolecularSequence )
. . numFN Σ 0..* integer Roc score false negative numbers . . . precision windowStart Σ 0..* 0..1 decimal integer Precision Start position of the GQ score sensitivity Σ 0..* decimal Sensitivity of window on the GQ score starting sequence
. . fMeasure Σ 0..* decimal FScore of the GQ score . . . readCoverage windowEnd Σ 0..1 integer Average number End position of reads representing a given nucleotide in the reconstructed window on the starting sequence repository Σ 0..* BackboneElement External repository which contains detailed report related with observedSeq in this resource
. . . . type . orientation Σ 0..1 code sense | other antisense
repositoryType Binding: orientation Type ( Required ) url Σ 0..1 uri URI of the repository name Σ 0..1 string
. datasetId Σ 0..1 string Id of the dataset that used to call for dataset in repository . . . . variantsetId strand Σ 0..1 string Id of the variantset that used to call for variantset in repository readsetId Σ 0..1 string Id of the read pointer Σ code 0..* Reference watson | crick
Binding: strand Type ( MolecularSequence Required ) Pointer to next atomic sequence
. . . . structureVariant edit Σ 0..* BackboneElement Structural variant Changes in sequence from the starting sequence
variantType Σ 0..1 CodeableConcept Structural variant change type
LOINC LL379-9 answerlist ( Required )
. . exact Σ 0..1 boolean Does the structural variant have base pair resolution breakpoints? . . . length start Σ 0..1 integer Structural variant length outer Σ 0..1 BackboneElement Start position of the edit on the starting sequence
Structural variant outer
. . start Σ 0..1 integer Structural variant outer start . . . end Σ 0..1 integer Structural variant outer end End position of the edit on the starting sequence
. . . inner . . replacementSequence Σ 0..1 BackboneElement string Structural variant inner Allele that was observed
. . . . . start replacedSequence Σ 0..1 integer string Structural variant inner start end Σ 0..1 integer Allele in the starting sequence
Structural variant inner end

doco Documentation for this format icon

See the Extensions for this resource

UML Diagram ( Legend )

MolecularSequence ( DomainResource ) A unique identifier for this particular sequence instance. This is a FHIR-defined id instance identifier : Identifier [0..*] Amino Acid Sequence/ DNA Sequence / RNA Sequence type : code [0..1] « Type if a sequence -- DNA, RNA, or amino acid sequence. null (Strength=Required) sequenceType SequenceType ! » Whether Indicates the subject this 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) associated too coordinateSystem subject : integer Reference [1..1] [0..1] « Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct » The actual focus of a molecular sequence when it is not the patient whose sequencing results are described by this resource of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the subject would be the child (proband) and the focus would be the parent focus : Reference [0..1] [0..*] « Patient Any » Specimen used for sequencing specimen : Reference [0..1] « Specimen » The method for sequencing, for example, chip information device : Reference [0..1] « Device » The organization or lab that should be responsible for this result performer : Reference [0..1] « Organization » The number of copies of the sequence of interest. (RNASeq) Sequence that was observed quantity literal : Quantity string [0..1] 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 observed as file content. Can be an actual file contents, or referenced by referenceSeq.windowEnd a URL to an external system observedSeq formatted : string Attachment [0..1] [0..*] Relative Coverage (read depth or depth) is the average number These are different ways of reads representing identifying nucleotides or amino acids within a given nucleotide sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail coordinateSystem : CodeableConcept [1..1] « null (Strength=Extensible) LL5323-2 + » Indicates the order in which the reconstructed sequence should be considered when putting multiple 'relative' elements together readCoverage ordinalPosition : integer [0..1] Pointer to next atomic Indicates the nucleotide range in the composed sequence which at most contains one variant when multiple 'relative' elements are used together pointer sequenceRange : Reference [0..*] « MolecularSequence Range » [0..1] StartingSequence ReferenceSeq The genome assembly used for starting sequence, e.g. GRCh38 genomeAssembly : CodeableConcept [0..1] « null (Strength=Extensible) LL1040-6 + » « This element has or is affected by some invariants C » 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)) chromosome : CodeableConcept [0..1] « Chromosome number for human. (Strength=Example) null (Strength=Required) chromosome-human LL2938-0 ! » « This element has or is affected by some invariants C ?? » 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 reference sequence that represents the starting sequence genomeBuild sequence[x] : DataType [0..1] « CodeableConcept | string | Reference ( MolecularSequence ); null (Strength=Example) Multiple bindings acceptable ...?? » « This element has or is affected by some invariants C » Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem windowStart : integer [0..1] End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem windowEnd : integer [0..1] 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 orientation : code [0..1] « Type for orientation. null (Strength=Required) orientationType OrientationType ! » 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 referenceSeqId : CodeableConcept [0..1] « Reference identifier. (Strength=Example) ENSEMBL ?? » A pointer to another MolecularSequence entity as reference sequence referenceSeqPointer : Reference [0..1] « MolecularSequence » A string like "ACGT" referenceSeqString : string [0..1] 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 strand : code [0..1] « Type for strand. null (Strength=Required) strandType StrandType ! » 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 windowStart : integer [0..1] 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 windowEnd : integer [0..1] Variant Edit Start position of the variant edit on the reference starting sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] End position of the variant edit on the reference starting 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 end : integer [0..1] 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)). Allele that was observed. 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 observedAllele replacementSequence : string [0..1] 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)). Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference starting 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 [0..1] 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) cigar : string [0..1] A pointer to an Observation containing variant information variantPointer : Reference [0..1] « Observation » Quality INDEL / SNP / Undefined variant type : code [1..1] « Type for quality report. (Strength=Required) qualityType ! » Gold standard sequence used for comparing against standardSequence : CodeableConcept [0..1] « Reference identifier of the sequence that used to mark the quality of tested samples. (Strength=Example) FDA-StandardSequence ?? » Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] 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 end : integer [0..1] The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)) score : Quantity [0..1] Which method is used to get sequence quality method : CodeableConcept [0..1] « The method used to evaluate the numerical quality of the observed sequence. (Strength=Example) FDA-Method ?? » 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 truthTP : decimal [0..1] 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 queryTP : decimal [0..1] 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 truthFN : decimal [0..1] 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 queryFP : decimal [0..1] 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) gtFP : decimal [0..1] QUERY.TP / (QUERY.TP + QUERY.FP) precision : decimal [0..1] TRUTH.TP / (TRUTH.TP + TRUTH.FN) recall : decimal [0..1] Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall) fScore : decimal [0..1] Roc Invidual data point representing the GQ (genotype quality) score threshold score : integer [0..*] The number of true positives if the GQ score threshold was set to "score" field value numTP : integer [0..*] The number of false positives if the GQ score threshold was set to "score" field value numFP : integer [0..*] The number of false negatives if the GQ score threshold was set to "score" field value numFN : integer [0..*] Calculated precision if the GQ score threshold was set to "score" field value precision : decimal [0..*] Calculated sensitivity if the GQ score threshold was set to "score" field value sensitivity : decimal [0..*] Calculated fScore if the GQ score threshold was set to "score" field value fMeasure : decimal [0..*] Repository Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource type : code [1..1] « Type for access of external URI. (Strength=Required) repositoryType ! » URI of an external repository which contains further details about the genetics data url : uri [0..1] URI of an external repository which contains further details about the genetics data name : string [0..1] 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 datasetId : string [0..1] 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 variantsetId : string [0..1] Id of the read in this external repository readsetId replacedSequence : string [0..1] StructureVariant Information about chromosome structure variation DNA change type variantType : CodeableConcept [0..1] « DNA change type. (Strength=Required) LOINC LL379-9 answerlist ! » Used to indicate if the outer and inner start-end values have the same meaning exact : boolean [0..1] Length of the variant chromosome length : integer [0..1] Outer Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] 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 end : integer [0..1] Inner Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] 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 end : integer [0..1] A sequence that is used as a reference starting sequence to describe variants that are present in a sequence analyzed referenceSeq startingSequence [0..1] 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 Changes in sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with from the assist of CIGAR string starting sequence variant edit [0..*] Receiver Operator Characteristic (ROC) Curve A sequence defined relative to give sensitivity/specificity tradeoff roc [0..1] 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)) quality [0..*] Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq repository [0..*] Structural variant outer outer [0..1] Structural variant inner inner [0..1] Information about chromosome structure variation another sequence structureVariant relative [0..*]

XML Template 

<

<MolecularSequence xmlns="http://hl7.org/fhir"> doco

 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <</identifier>

 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>

 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <
 <</patient>

 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) Subject this sequence is associated too --></subject>

 <focus><!-- 0..* Reference(Any) What the molecular sequence is about, when it is not about the subject of record --></focus>

 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <</quantity>
 <
  <</chromosome>
  <
  <
  <</referenceSeqId>
  <</referenceSeqPointer>
  <
  <
  <
  <
 </referenceSeq>
 <
  <
  <
  <
  <
  <
  <</variantPointer>
 </variant>
 <
 <
  <
  <</standardSequence>
  <
  <
  <</score>
  <</method>
  <
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  </roc>
 </quality>
 <
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 </repository>
 <</pointer>
 <
  <</variantType>
  <
  <
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  </outer>
  <
   <
   <
  </inner>
 </structureVariant>

 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence icon --></coordinateSystem>
  <ordinalPosition value="[integer]"/><!-- 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together -->
  <sequenceRange><!-- 0..1 Range Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together --></sequenceRange>
  <startingSequence>  <!-- 0..1 A sequence used as starting sequence -->
   <genomeAssembly><!-- I 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38 icon --></genomeAssembly>
   <chromosome><!-- I 0..1 CodeableConcept Chromosome Identifier icon --></chromosome>
   <sequence[x]><!-- I 0..1 CodeableConcept|string|Reference(MolecularSequence) The reference sequence that represents the starting sequence --></sequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the starting sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the starting sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </startingSequence>
  <edit>  <!-- 0..* Changes in sequence from the starting sequence -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the starting sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the starting sequence -->
   <replacementSequence value="[string]"/><!-- 0..1 Allele that was observed -->
   <replacedSequence value="[string]"/><!-- 0..1 Allele in the starting sequence -->
  </edit>
 </relative>

</MolecularSequence>

JSON Template 

{doco
  "resourceType" : "",

  "resourceType" : "MolecularSequence",

  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "

  "identifier" : [{ Identifier }], // Unique ID for this particular sequence

  "type" : "<code>", // aa | dna | rna
  "
  "

  "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) }, // Subject this sequence is associated too

  "focus" : [{ Reference(Any) }], // What the molecular sequence is about, when it is not about the subject of record

  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "
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  },
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  }],
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  }],
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  }],
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  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence icon
    "ordinalPosition" : <integer>, // Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    "sequenceRange" : { Range }, // Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    "startingSequence" : { // A sequence used as starting sequence
      "genomeAssembly" : { CodeableConcept }, // I The genome assembly used for starting sequence, e.g. GRCh38 icon
      "chromosome" : { CodeableConcept }, // I Chromosome Identifier icon
      // sequence[x]: The reference sequence that represents the starting sequence. One of these 3:

      "sequenceCodeableConcept" : { CodeableConcept },
      "sequenceString" : "<string>",
      "sequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the starting sequence
      "windowEnd" : <integer>, // End position of the window on the starting sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick

    },
    "
      "
      "
    }

    "edit" : [{ // Changes in sequence from the starting sequence
      "start" : <integer>, // Start position of the edit on the starting sequence
      "end" : <integer>, // End position of the edit on the starting sequence
      "replacementSequence" : "<string>", // Allele that was observed
      "replacedSequence" : "<string>" // Allele in the starting sequence
    }]

  }]
}

Turtle Template 

@prefix fhir: <http://hl7.org/fhir/> .doco


[ a fhir:;

[ a fhir:MolecularSequence;

  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:
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  ];
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  ], ...;
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    ];
  ], ...;
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    ];
    fhir:
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    ];
  ], ...;

  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular sequence
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 0..1 Subject this sequence is associated too
  fhir:focus  ( [ Reference(Any) ] ... ) ; # 0..* What the molecular sequence is about, when it is not about the subject of record
  fhir:specimen [ Reference(Specimen) ] ; # 0..1 Specimen used for sequencing
  fhir:device [ Reference(Device) ] ; # 0..1 The method for sequencing
  fhir:performer [ Reference(Organization) ] ; # 0..1 Who should be responsible for test result
  fhir:literal [ string ] ; # 0..1 Sequence that was observed
  fhir:formatted  ( [ Attachment ] ... ) ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:relative ( [ # 0..* A sequence defined relative to another sequence
    fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:ordinalPosition [ integer ] ; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:sequenceRange [ Range ] ; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:genomeAssembly [ CodeableConcept ] ; # 0..1 I The genome assembly used for starting sequence, e.g. GRCh38
      fhir:chromosome [ CodeableConcept ] ; # 0..1 I Chromosome Identifier
      # sequence[x] : 0..1 I The reference sequence that represents the starting sequence. One of these 3
        fhir:sequence [  a fhir:CodeableConcept ; CodeableConcept ]
        fhir:sequence [  a fhir:string ; string ]
        fhir:sequence [  a fhir:Reference ; Reference(MolecularSequence) ]
      fhir:windowStart [ integer ] ; # 0..1 Start position of the window on the starting sequence
      fhir:windowEnd [ integer ] ; # 0..1 End position of the window on the starting sequence
      fhir:orientation [ code ] ; # 0..1 sense | antisense
      fhir:strand [ code ] ; # 0..1 watson | crick
    ] ;
    fhir:edit ( [ # 0..* Changes in sequence from the starting sequence
      fhir:start [ integer ] ; # 0..1 Start position of the edit on the starting sequence
      fhir:end [ integer ] ; # 0..1 End position of the edit on the starting sequence
      fhir:replacementSequence [ string ] ; # 0..1 Allele that was observed
      fhir:replacedSequence [ string ] ; # 0..1 Allele in the starting sequence
    ] ... ) ;
  ] ... ) ;

]

Changes since R3 This resource did not exist in Release 2 This analysis is available as XML or JSON . See R3 <--> from both R4 Conversion Maps (status = 14 tests that all execute ok. All tests pass round-trip testing and all r3 resources are valid.) Structure R4B

Name Flags Card. Type Description & Constraints Σ I TU DomainResource identifier Σ 0..* type Σ 0..1 coordinateSystem Σ 1..1 patient Σ specimen device Σ performer Σ quantity Σ 0..1 referenceSeq BackboneElement A sequence used as reference Σ 0..1 Σ 0..1 Σ 0..1 Σ 0..1 referenceSeqPointer Σ Σ 0..1 Σ 0..1 Σ 0..1 Σ 0..1 integer Σ 0..* Σ 0..1 integer Σ
MolecularSequence
MolecularSequence.subject
    Information about a biological sequence
  • Renamed from patient to subject
    • + Rule: Only 0 and 1 are valid for coordinateSystem
  • Type Reference: Added Target Types Group, Substance, BiologicallyDerivedProduct, NutritionProduct
    • Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
MolecularSequence.focus Identifier
  • Added Element
    • Unique ID for this particular sequence. This is a FHIR-defined id
MolecularSequence.literal code
  • Added Element
    • aa | dna | rna
sequenceType ( Required )
MolecularSequence.formatted
    integer
  • Added Element
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)
MolecularSequence.relative 0..1
  • Added Element
    • Reference ( Patient )
Who and/or what this is about
MolecularSequence.relative.coordinateSystem Σ
  • 0..1 Added Mandatory Element
    • Reference ( Specimen )
Specimen used for sequencing
MolecularSequence.relative.ordinalPosition 0..1
  • Added Element
    • Reference ( Device )
The method for sequencing
MolecularSequence.relative.sequenceRange 0..1
  • Added Element
    • Reference ( Organization )
Who should be responsible for test result
MolecularSequence.relative.startingSequence
    Quantity
  • Added Element
The number of copies of the sequence of interest. (RNASeq)
MolecularSequence.relative.startingSequence.genomeAssembly Σ
    I
  • Added Element
0..1
MolecularSequence.relative.startingSequence.chromosome + Rule: GenomeBuild and chromosome must be both contained if either one of them is contained
  • Added Element
    • + Rule: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
MolecularSequence.relative.startingSequence.sequence[x]
    chromosome
  • Added Element
MolecularSequence.relative.startingSequence.windowStart CodeableConcept
  • Added Element
    • Chromosome containing genetic finding
chromosome-human ( Example )
MolecularSequence.relative.startingSequence.windowEnd
    genomeBuild
  • Added Element
MolecularSequence.relative.startingSequence.orientation
    string
  • Added Element
The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
MolecularSequence.relative.startingSequence.strand
    orientation
  • Added Element
MolecularSequence.relative.edit code
  • Added Element
    • sense | antisense
orientationType ( Required )
MolecularSequence.relative.edit.start
    referenceSeqId
  • Added Element
MolecularSequence.relative.edit.end CodeableConcept
  • Added Element
    • Reference identifier
E n s e m b l ( Example )
MolecularSequence.relative.edit.replacementSequence 0..1
  • Added Element
    • Reference ( MolecularSequence )
A pointer to another MolecularSequence entity as reference sequence
MolecularSequence.relative.edit.replacedSequence
    referenceSeqString
  • Added Element
MolecularSequence.coordinateSystem
    string
  • Deleted (>relative.coordinateSystem)
A string to represent reference sequence
MolecularSequence.quantity
    strand
  • Deleted (Removed. Covered by the Variant Profile in the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
MolecularSequence.referenceSeq code
  • Deleted (->relative.startingSequence.sequence[x])
    • watson | crick
strandType ( Required )
MolecularSequence.variant
    windowStart
  • Deleted (Removed. Covered by the Variant Profile in the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
MolecularSequence.observedSeq
    integer
  • Deleted (->relative.startingSequence.sequenceString)
Start position of the window on the reference sequence
MolecularSequence.quality
    windowEnd
  • Deleted (Removed from the resource.)
MolecularSequence.readCoverage
    End position of
  • Deleted (Removed. Covered by the window on RegionStudied Profile in the reference sequence variant CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
MolecularSequence.repository BackboneElement
  • Deleted (->formatted)
    • Variant in sequence
MolecularSequence.pointer
    start
  • Deleted (->relative)
MolecularSequence.structureVariant
    Start position of
  • Deleted (Removed. Covered by the variant on Variant Profile in the reference sequence end CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)

See the Full Difference 0..1 integer for further information

This analysis is available for R4 as XML End position of the variant on the reference sequence observedAllele or JSON and for R4B as XML Σ or JSON .

See R4 <--> R5 Conversion Maps (status = See Conversions Summary .)

0..1 string

Allele that was observed Structure

referenceAllele cigar 0..1 observedSeq Sequence that was observed truthTP Σ Σ Σ Repository's name Σ Id of the dataset that used to call for dataset in repository Σ Pointer to next atomic sequence
Name Σ Flags 0..1 string Card. Allele in the reference sequence Type Σ Description & Constraints 0..1 doco string Extended CIGAR string for aligning the sequence with reference bases
variantPointer . . MolecularSequence Σ Reference ( Observation TU ) Pointer to observed variant information Σ DomainResource 0..1 Representation of a molecular sequence
string
Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . quality . identifier Σ 0..* BackboneElement Identifier An set of value as quality of Unique ID for this particular sequence

. . . type Σ 1..1 0..1 code indel aa | snp dna | unknown rna
qualityType Binding: sequence Type ( Required )
. . standardSequence . subject Σ 0..1 CodeableConcept Standard sequence for comparison F d a- standard sequence Reference ( Example ) start Σ 0..1 integer Patient Start position of the sequence end | Group | Substance Σ | BiologicallyDerivedProduct 0..1 integer | NutritionProduct ) End position of the Subject this sequence is associated too
. . queryFP . specimen Σ 0..1 decimal Reference ( Specimen ) False positives Specimen used for sequencing
. . gtFP . device Σ 0..1 decimal Reference ( Device ) False positives where the non-REF alleles in the Truth and Query Call Sets match The method for sequencing
. . precision . performer Σ 0..1 decimal Reference ( Organization ) Precision of comparison Who should be responsible for test result
. . . recall literal Σ 0..1 decimal Recall of comparison fScore Σ 0..1 decimal F-score roc Σ string 0..1 BackboneElement Sequence that was observed
Receiver Operator Characteristic (ROC) Curve
. . score . formatted Σ 0..* integer Attachment Genotype quality score Embedded file or a link (URL) which contains content to represent the sequence

. . numTP . relative Σ 0..* integer BackboneElement Roc score true positive numbers A sequence defined relative to another sequence

. . . numFP . coordinateSystem Σ 0..* 1..1 integer CodeableConcept Roc score false positive numbers Ways of identifying nucleotides or amino acids within a sequence
Binding: LL5323-2 icon ( Extensible )
. . . . numFN ordinalPosition 0..* 0..1 integer Roc score false negative numbers Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
. . . precision . sequenceRange 0..* 0..1 decimal Range Precision of Indicates the GQ score nucleotide range in the composed sequence when multiple 'relative' elements are used together
. . . sensitivity . startingSequence Σ C 0..* 0..1 decimal BackboneElement Sensitivity of the GQ score A sequence used as starting sequence
fMeasure Σ 0..* decimal + Rule: Both genomeAssembly and chromosome must be both contained if either one of them is contained
FScore + Rule: Have and only have one of the GQ score following elements in startingSequence: 1. genomeAssembly; 2 sequence
. readCoverage Σ 0..1 integer Average number of reads representing a given nucleotide in the reconstructed sequence . . . repository . genomeAssembly Σ C 0..* 0..1 BackboneElement CodeableConcept External repository which contains detailed report related with observedSeq in this resource The genome assembly used for starting sequence, e.g. GRCh38
Binding: LL1040-6 icon ( Extensible )
. . . . type . chromosome Σ C 1..1 0..1 code CodeableConcept directlink | openapi | login | oauth | other Chromosome Identifier
Binding: LL2938-0 icon repositoryType ( Required )
. . . . url . sequence[x] Σ C 0..1 uri URI of The reference sequence that represents the repository starting sequence
Binding: Multiple bindings acceptable (NCBI or LRG) ( Example )
. . . . name . . sequenceCodeableConcept 0..1 string CodeableConcept
. . . . . . datasetId sequenceString 0..1 string
. variantsetId Σ 0..1 string Id of the variantset that used to call for variantset in repository . . . . readsetId Σ 0..1 string Id of the read . pointer sequenceReference 0..* Reference ( MolecularSequence )
. . structureVariant . . . windowStart Σ 0..* 0..1 BackboneElement integer Structural variant Start position of the window on the starting sequence
. . . . variantType . windowEnd Σ 0..1 CodeableConcept integer Structural variant change type End position of the window on the starting sequence
LOINC LL379-9 answerlist ( Required )
. . . . . exact orientation Σ 0..1 boolean code Does the structural variant have base pair resolution breakpoints? sense | antisense
Binding: orientation Type ( Required )
. . . . . length strand Σ 0..1 integer code Structural variant length watson | crick
Binding: strand Type ( Required )
. . . . outer edit Σ 0..1 0..* BackboneElement Structural variant outer Changes in sequence from the starting sequence

. . . . . start Σ 0..1 integer Structural variant outer start Start position of the edit on the starting sequence
. . . . . end Σ 0..1 integer Structural variant outer end End position of the edit on the starting sequence
. . . inner . . replacementSequence Σ 0..1 BackboneElement string Structural variant inner Allele that was observed
. . . . . start replacedSequence Σ 0..1 integer string Structural variant inner start end Σ 0..1 integer Allele in the starting sequence
Structural variant inner end

doco Documentation for this format icon

See the Extensions for this resource

UML Diagram ( Legend )

MolecularSequence ( DomainResource ) A unique identifier for this particular sequence instance. This is a FHIR-defined id instance identifier : Identifier [0..*] Amino Acid Sequence/ DNA Sequence / RNA Sequence type : code [0..1] « Type if a sequence -- DNA, RNA, or amino acid sequence. null (Strength=Required) sequenceType SequenceType ! » Whether Indicates the subject this 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) associated too coordinateSystem subject : integer Reference [1..1] [0..1] « Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct » The actual focus of a molecular sequence when it is not the patient whose sequencing results are described by this resource of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the subject would be the child (proband) and the focus would be the parent focus : Reference [0..1] [0..*] « Patient Any » Specimen used for sequencing specimen : Reference [0..1] « Specimen » The method for sequencing, for example, chip information device : Reference [0..1] « Device » The organization or lab that should be responsible for this result performer : Reference [0..1] « Organization » The number of copies of the sequence of interest. (RNASeq) Sequence that was observed quantity literal : Quantity string [0..1] 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 observed as file content. Can be an actual file contents, or referenced by referenceSeq.windowEnd a URL to an external system observedSeq formatted : string Attachment [0..1] [0..*] Relative Coverage (read depth or depth) is the average number These are different ways of reads representing identifying nucleotides or amino acids within a given nucleotide sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail coordinateSystem : CodeableConcept [1..1] « null (Strength=Extensible) LL5323-2 + » Indicates the order in which the reconstructed sequence should be considered when putting multiple 'relative' elements together readCoverage ordinalPosition : integer [0..1] Pointer to next atomic Indicates the nucleotide range in the composed sequence which at most contains one variant when multiple 'relative' elements are used together pointer sequenceRange : Reference [0..*] « MolecularSequence Range » [0..1] StartingSequence ReferenceSeq The genome assembly used for starting sequence, e.g. GRCh38 genomeAssembly : CodeableConcept [0..1] « null (Strength=Extensible) LL1040-6 + » « This element has or is affected by some invariants C » 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)) chromosome : CodeableConcept [0..1] « Chromosome number for human. (Strength=Example) null (Strength=Required) chromosome-human LL2938-0 ! » « This element has or is affected by some invariants C ?? » 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 reference sequence that represents the starting sequence genomeBuild sequence[x] : DataType [0..1] « CodeableConcept | string | Reference ( MolecularSequence ); null (Strength=Example) Multiple bindings acceptable ...?? » « This element has or is affected by some invariants C » Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem windowStart : integer [0..1] End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem windowEnd : integer [0..1] 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 orientation : code [0..1] « Type for orientation. null (Strength=Required) orientationType OrientationType ! » 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 referenceSeqId : CodeableConcept [0..1] « Reference identifier. (Strength=Example) ENSEMBL ?? » A pointer to another MolecularSequence entity as reference sequence referenceSeqPointer : Reference [0..1] « MolecularSequence » A string like "ACGT" referenceSeqString : string [0..1] 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 strand : code [0..1] « Type for strand. null (Strength=Required) strandType StrandType ! » 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 windowStart : integer [0..1] 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 windowEnd : integer [0..1] Variant Edit Start position of the variant edit on the reference starting sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] End position of the variant edit on the reference starting 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 end : integer [0..1] 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)). Allele that was observed. 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 observedAllele replacementSequence : string [0..1] 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)). Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference starting 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 replacedSequence : string [0..1] 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) cigar : string [0..1] A pointer sequence that is used as a starting sequence to an Observation containing variant information describe variants that are present in a sequence analyzed variantPointer : Reference startingSequence [0..1] « Observation » Changes in sequence from the starting sequence edit Quality [0..*] INDEL / SNP / Undefined variant type : code [1..1] « Type for quality report. (Strength=Required) qualityType ! » Gold standard sequence used for comparing against standardSequence : CodeableConcept [0..1] « Reference identifier of the A sequence that used defined relative to mark the quality of tested samples. (Strength=Example) another sequence FDA-StandardSequence relative ?? » [0..*]
Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1]

XML Template 

<MolecularSequence xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) Subject this sequence is associated too --></subject>

 <focus><!-- 0..* Reference(Any) What the molecular sequence is about, when it is not about the subject of record --></focus>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence icon --></coordinateSystem>
  <ordinalPosition value="[integer]"/><!-- 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together -->
  <sequenceRange><!-- 0..1 Range Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together --></sequenceRange>
  <startingSequence>  <!-- 0..1 A sequence used as starting sequence -->
   <genomeAssembly><!-- I 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38 icon --></genomeAssembly>
   <chromosome><!-- I 0..1 CodeableConcept Chromosome Identifier icon --></chromosome>
   <sequence[x]><!-- I 0..1 CodeableConcept|string|Reference(MolecularSequence) The reference sequence that represents the starting sequence --></sequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the starting sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the starting sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </startingSequence>
  <edit>  <!-- 0..* Changes in sequence from the starting sequence -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the starting sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the starting sequence -->
   <replacementSequence value="[string]"/><!-- 0..1 Allele that was observed -->
   <replacedSequence value="[string]"/><!-- 0..1 Allele in the starting sequence -->
  </edit>
 </relative>
</MolecularSequence>
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 end : integer [0..1]

JSON Template 

{doco
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // aa | dna | rna
  "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) }, // Subject this sequence is associated too

  "focus" : [{ Reference(Any) }], // What the molecular sequence is about, when it is not about the subject of record
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence icon
    "ordinalPosition" : <integer>, // Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    "sequenceRange" : { Range }, // Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    "startingSequence" : { // A sequence used as starting sequence
      "genomeAssembly" : { CodeableConcept }, // I The genome assembly used for starting sequence, e.g. GRCh38 icon
      "chromosome" : { CodeableConcept }, // I Chromosome Identifier icon
      // sequence[x]: The reference sequence that represents the starting sequence. One of these 3:

      "sequenceCodeableConcept" : { CodeableConcept },
      "sequenceString" : "<string>",
      "sequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the starting sequence
      "windowEnd" : <integer>, // End position of the window on the starting sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick
    },
    "edit" : [{ // Changes in sequence from the starting sequence
      "start" : <integer>, // Start position of the edit on the starting sequence
      "end" : <integer>, // End position of the edit on the starting sequence
      "replacementSequence" : "<string>", // Allele that was observed
      "replacedSequence" : "<string>" // Allele in the starting sequence
    }]
  }]
}
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)) score : Quantity [0..1]

Turtle Template 

@prefix fhir: <http://hl7.org/fhir/> .doco


[ a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular sequence
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 0..1 Subject this sequence is associated too
  fhir:focus  ( [ Reference(Any) ] ... ) ; # 0..* What the molecular sequence is about, when it is not about the subject of record
  fhir:specimen [ Reference(Specimen) ] ; # 0..1 Specimen used for sequencing
  fhir:device [ Reference(Device) ] ; # 0..1 The method for sequencing
  fhir:performer [ Reference(Organization) ] ; # 0..1 Who should be responsible for test result
  fhir:literal [ string ] ; # 0..1 Sequence that was observed
  fhir:formatted  ( [ Attachment ] ... ) ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:relative ( [ # 0..* A sequence defined relative to another sequence
    fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:ordinalPosition [ integer ] ; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:sequenceRange [ Range ] ; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:genomeAssembly [ CodeableConcept ] ; # 0..1 I The genome assembly used for starting sequence, e.g. GRCh38
      fhir:chromosome [ CodeableConcept ] ; # 0..1 I Chromosome Identifier
      # sequence[x] : 0..1 I The reference sequence that represents the starting sequence. One of these 3
        fhir:sequence [  a fhir:CodeableConcept ; CodeableConcept ]
        fhir:sequence [  a fhir:string ; string ]
        fhir:sequence [  a fhir:Reference ; Reference(MolecularSequence) ]
      fhir:windowStart [ integer ] ; # 0..1 Start position of the window on the starting sequence
      fhir:windowEnd [ integer ] ; # 0..1 End position of the window on the starting sequence
      fhir:orientation [ code ] ; # 0..1 sense | antisense
      fhir:strand [ code ] ; # 0..1 watson | crick
    ] ;
    fhir:edit ( [ # 0..* Changes in sequence from the starting sequence
      fhir:start [ integer ] ; # 0..1 Start position of the edit on the starting sequence
      fhir:end [ integer ] ; # 0..1 End position of the edit on the starting sequence
      fhir:replacementSequence [ string ] ; # 0..1 Allele that was observed
      fhir:replacedSequence [ string ] ; # 0..1 Allele in the starting sequence
    ] ... ) ;
  ] ... ) ;
]

Which method is used to get sequence quality method : CodeableConcept [0..1] « Changes from both R4 and R4B The method used to evaluate the numerical quality of the observed sequence. (Strength=Example) FDA-Method ?? »

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 queryFP : decimal [0..1] QUERY.TP / (QUERY.TP + QUERY.FP) precision : decimal [0..1] TRUTH.TP / (TRUTH.TP + TRUTH.FN) recall : decimal [0..1] Invidual data point representing the GQ (genotype quality) score threshold score : integer [0..*] The number of true positives if the GQ score threshold was set to "score" field value numTP : integer [0..*] The number of false negatives if the GQ score threshold was set to "score" field value numFN : integer [0..*] Calculated fScore if the GQ score threshold was set to "score" field value fMeasure : decimal [0..*] Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource type : code [1..1] « Type for access of external URI. (Strength=Required) repositoryType ! » URI of an external repository which contains further details about the genetics data name : string [0..1] Id of the read in this external repository readsetId : string [0..1] StructureVariant Used to indicate if the outer and inner start-end values have the same meaning exact : boolean [0..1] Length of the variant chromosome length : integer [0..1] Outer 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 end : integer [0..1] Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1] [0..1] 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 variant An experimental feature attribute that defines the quality of Configurations of Structural variant outer outer [0..1] Structural variant inner inner [0..*] XML Template Turtle Template @prefix fhir: <http://hl7.org/fhir/> . [ a fhir:; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from # from fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: ]; fhir: fhir: fhir: fhir: fhir: fhir: fhir: ], ...; fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: ]; ], ...; fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: ], ...; fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: ]; fhir: fhir: fhir: ]; ], ...; ] Changes since Release 3
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 truthTP : decimal MolecularSequence [0..1] True positives,
MolecularSequence.subject
  • Renamed 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 queryTP : decimal [0..1] patient to subject
  • Type Reference: Added Target Types Group, Substance, BiologicallyDerivedProduct, NutritionProduct
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 truthFN : decimal [0..1]
MolecularSequence.focus
    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) gtFP : decimal [0..1]
  • Added Element
MolecularSequence.literal
  • Added Element
    • Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall) fScore : decimal [0..1]
MolecularSequence.formatted
    Roc
  • Added Element
MolecularSequence.relative
  • Added Element
    • The number of false positives if the GQ score threshold was set to "score" field value numFP : integer [0..*]
MolecularSequence.relative.coordinateSystem Calculated precision if the GQ score threshold was set to "score" field value precision : decimal [0..*]
  • Added Mandatory Element Calculated sensitivity if the GQ score threshold was set to "score" field value sensitivity : decimal [0..*]
MolecularSequence.relative.ordinalPosition
  • Added Element
Repository
MolecularSequence.relative.sequenceRange
  • Added Element
    • URI of an external repository which contains further details about the genetics data url : uri [0..1]
MolecularSequence.relative.startingSequence 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 datasetId : string [0..1]
  • Added Element
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 variantsetId : string [0..1]
MolecularSequence.relative.startingSequence.genomeAssembly
  • Added Element
MolecularSequence.relative.startingSequence.chromosome Information about chromosome structure variation DNA change type variantType : CodeableConcept [0..1] «
    DNA change type. (Strength=Required) LOINC LL379-9 answerlist ! »
  • Added Element
MolecularSequence.relative.startingSequence.sequence[x]
  • Added Element
MolecularSequence.relative.startingSequence.windowStart
    Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive start : integer [0..1]
  • Added Element
MolecularSequence.relative.startingSequence.windowEnd
  • Added Element
Inner
MolecularSequence.relative.startingSequence.orientation
    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 end : integer [0..1]
  • Added Element
MolecularSequence.relative.startingSequence.strand
  • Added Element
A sequence that is used as a reference to describe variants that are present in a sequence analyzed referenceSeq
MolecularSequence.relative.edit
  • Added Element
MolecularSequence.relative.edit.start [0..*]
  • Added Element
MolecularSequence.relative.edit.end
    Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff roc
  • Added Element
[0..1]
MolecularSequence.relative.edit.replacementSequence
  • Added Element
MolecularSequence.relative.edit.replacedSequence
  • Added Element
MolecularSequence.coordinateSystem
  • Deleted (>relative.coordinateSystem)
MolecularSequence.quantity
  • Deleted (Removed. Covered by the feature Variant Profile in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)) quality the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
[0..*]
MolecularSequence.referenceSeq
  • Deleted (->relative.startingSequence.sequence[x])
MolecularSequence.variant
  • Deleted (Removed. Covered by the external repository. The repository shall store target's observedSeq or records related with target's observedSeq repository Variant Profile in the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
[0..*]
MolecularSequence.observedSeq
  • Deleted (->relative.startingSequence.sequenceString)
MolecularSequence.quality
  • Deleted (Removed from the resource.)
MolecularSequence.readCoverage
    [0..1]
  • Deleted (Removed. Covered by the RegionStudied Profile in the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)
MolecularSequence.repository
  • Deleted (->formatted)
    • Information about chromosome structure variation structureVariant
MolecularSequence.pointer < <!-- from --> <!-- from --> <</identifier> < < <</patient> <</specimen> <</device> <</performer> <</quantity> < <</chromosome> < < <</referenceSeqId> <</referenceSeqPointer> < < < < </referenceSeq> < < < < < < <</variantPointer> </variant> < < < <</standardSequence> < < <</score> <</method> < < < < < < < < < < < < < < < < </roc> </quality> < < < < < < < < </repository> <</pointer> < <</variantType> < < < < < </outer> < < < </inner> </structureVariant> </MolecularSequence>
  • Deleted (->relative)
    • JSON Template
{ "resourceType" : "", // from // from " " " " " " " " " " " " " " " " " " }, " " " " " " " }], " " " " " " " " " " " " " " " " " " " " " " " " } }], " " " " " " " " }], " " " " " " " " }, " " " } }] }
MolecularSequence.structureVariant This resource did not exist
  • Deleted (Removed. Covered by the Variant Profile in Release 2 the CG IG: http://hl7.org/fhir/uv/genomics-reporting/index.html)

See the Full Difference for further information

This analysis is available for R4 as XML or JSON and for R4B as XML or JSON .

See R3 <--> R4 <--> R5 Conversion Maps (status = 14 tests that all execute ok. All tests pass round-trip testing and all r3 resources are valid.) See Conversions Summary .)

 

See the Profiles & Extensions and the alternate Additional definitions: Master Definition XML + JSON , XML Schema / Schematron + JSON Schema , ShEx (for Turtle ) + see the extensions , the spreadsheet version & the dependency analysis

10.6.3.1 10.7.4.1 Terminology Bindings

MolecularSequence.referenceSeq.chromosome MolecularSequence.referenceSeq.orientation Type for orientation. MolecularSequence.referenceSeq.referenceSeqId MolecularSequence.quality.type MolecularSequence.quality.standardSequence MolecularSequence.quality.method The method used to evaluate the numerical quality of the observed sequence. Example MolecularSequence.repository.type Type for access of external URI. MolecularSequence.structureVariant.variantType
Path Definition ValueSet Type Reference Documentation
MolecularSequence.type Type if a sequence -- DNA, RNA, or amino acid sequence. SequenceType Required sequenceType

Type if a sequence -- DNA, RNA, or amino acid sequence.

MolecularSequence.relative.coordinateSystem Chromosome number for human. Example http://loinc.org/LL5323-2/ icon chromosome-human Required Extensible orientationType
MolecularSequence.relative.startingSequence.genomeAssembly Reference identifier. http://loinc.org/LL1040-6/ icon Example ENSEMBL MolecularSequence.referenceSeq.strand Type for strand. Required Extensible strandType
MolecularSequence.relative.startingSequence.chromosome Type for quality report. http://loinc.org/LL2938-0/ icon Required qualityType
MolecularSequence.relative.startingSequence.sequence[x] Reference identifier of the sequence that used to mark the quality of tested samples. ?? Example FDA-StandardSequence
MolecularSequence.relative.startingSequence.orientation FDA-Method OrientationType Required repositoryType

Type for orientation.

MolecularSequence.relative.startingSequence.strand DNA change type. StrandType Required http://loinc.org/vs/LL379-9

Type for strand.

10.6.3.2 10.7.4.2 Constraints

id UniqueKey Level Location Description Expression
msq-3 Rule (base) Only 0 and 1 are valid for coordinateSystem coordinateSystem = 1 or coordinateSystem = 0 msq-5 img  msq-5 Rule MolecularSequence.referenceSeq MolecularSequence.relative.startingSequence GenomeBuild Both genomeAssembly and chromosome must be both contained if either one of them is contained (chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists()) chromosome.exists() = genomeAssembly.exists()
msq-6 img  msq-6 Rule MolecularSequence.referenceSeq MolecularSequence.relative.startingSequence Have and only have one of the following elements in referenceSeq : startingSequence: 1. genomeBuild ; genomeAssembly; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; sequence (genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1 genomeAssembly.exists() xor sequence.exists()

10.6.4 10.7.5 Notes: Notes

10.6.4.1 10.7.5.1 MolecularSequence Coordinate System Representing the Sequence

When saving the variant information, the nucleic acid will be numbered with order. Some files are using 0-based coordinates (e.g. BCD This resource supports three patterns for representing a sequence of interest:

  • By providing a literal string of IUPAC codes representing nucleotides or amino acids.
  • By linking to a formatted file format) while some files are using 1-based coordinates or link containing the sequence information (e.g. VCF FASTA file format). or GA4GH sequence repository).
  • By providing a list of edits from a starting sequence.

The element coordinateSystem in MolecularSequence resource contains this information. is designed to represent a single sequence in an instance. Each sequence might have multiple representations, but implementers SHALL ensure all representations are for the same sequence.

10.7.5.1.1 Sequence as a literal string

MolecularSequence.coordinateSystem constraints within two possible values: 0 for 0-based system, which will mark literal : This string element can be used to hold the sequence as a string of characters.

10.7.5.1.2 Sequence as a file or URL

formatted : This Attachment is used to refer to the sequence as embedded file content or via a URL reference.

This method can be used to refer to sequence data from number 0, while 1 for 1-based system, which will begin marking in an external source. If the first position with number 1. The significant difference between two system sequence is referring to a GA4GH repository, the end position. In 0-based system, the end position formatted.url should refer to a GA4GH compliant endpoint that conforms to GA4GH data models.

10.7.5.1.3 Sequence as a series of edits from a known sequence

relative : This complex element is exclusive , which means used for encoding sequence. When the last position information of starting sequence and edits are provided, the observed sequence will not be contained derived. Here is a picture below:

null
10.7.5.1.3.1 Composing multiple relative sequences into one new sequence

relative.ordinalPosition : Indicates the order in which the sequence window while should be considered when putting multiple relative instances together.

relative.sequenceRange : Indicates the nucleotide range in 1-based system, the end position composed sequence when multiple relative instances are used together.

These attributes help to clarify what sequence is inclusive , which means being represented with less computation/inference on the last position recipient side. Implementers SHOULD use sequenceRange first to determine order as the most reliable. If sequenceRange is included not present then ordinalPosition SHOULD be used. Finally, if both sequenceRange and ordinalPosition are absent, then the order of the relative data elements SHOULD be used to calculate a composition. It is the responsibility of the data sender to ensure the message can be consistently understood. Additionally, gaps in sequenceRange are considered intentional (i.e. the composed sequence window. Note both systems has an inclusive start position. contains a sequence of N's, the placeholder nucleotide, for the gap range).

For example, ACGTGCAT will In a FGFR2:MET Fusion use case, where the fusion was uncovered through RNA sequencing, a partial representation can be numbered from 1 found here .

10.7.5.1.3.2 Representing the Starting Sequence

relative.startingSequence : There are four optional ways to 8 represent a starting sequence in 1-based system MolecularSequence resource:

  1. relative.startingSequence.sequenceCodeableConcept : Starting sequence id in public database;
  2. relative.startingSequence.sequenceString : Starting sequence string;
  3. relative.startingSequence.sequenceReference : Reference to starting sequence stored in another sequence entity;
  4. relative.startingSequence.genomeAssembly , relative.startingSequence.chromosome : The combination of genome assembly and chromosome.

The relative.startingSequence.windowStart and relative.startingSequence.windowEnd defines a range from the starting sequence that is used to define a subsequence used as the starting sequence.

10.7.5.1.3.3 Coordinate System

When saving the sequence information, the nucleic acid will be numbered from 0 to 8 in with order. Some representations use a 0-based system to mark flanks (i.e. place between two Nucleotide). So the interval [3,5] in (e.g. GA4GH API, BAM files) while some use a 1-based system is GTG while interval [2,5) in (e.g. VCF file format). The element coordinateSystem contains this information.

relative.coordinateSystem binds to a LOINC answer list, please review those answers here icon as well as the detailed description found here icon.

Here are two examples:

  • 0-based system is same segment GTG. example: here
  • 1-based example: here

10.6.4.2 10.7.5.1.3.4 Choice of Strand

There are lots of definition many considerations concerning with the Directionality directionality of DNA or RNA. Here we are using referenceSeq.orientation relative.startingSequence.orientation and relative.startingSequence.strand . referenceSeq.strand . orientation Orientation represents the sense of the sequence, which has different meanings depending on the type . MolecularSequence.type . strand Strand represents the sequence writing order. Watson strand refers to 5' to 3' top strand (5' -> 3'), whereas Crick strand refers to 5' to 3' bottom strand (3' <- 5').

10.6.4.3 String usage for reference sequence and observed sequence

We hope that string of observedSeq Only two possible values can be constrained more than just any normal string but with notation tables. Here we present what made by strand, watson and crick . Since the nucleotide acid directionality of the sequence string should might be constrained within the range: represented in different ways in different omics scenario, below are examples of how to map other expressions into its correlated value:

A --> adenosine M --> A C (amino) U --> uridine H --> A C T V --> G C A
Watson Crick
C --> cytidine S --> G C (strong) D --> G A T 5′-to-3′ direction K --> G T (keto) 3′-to-5′ direction
G --> guanine W --> A T (weak) R --> G A (purine) +1 N --> A G C T (any) -1
T --> thymidine Sense B --> G T C Antisense
Y --> T C (pyrimidine) Positive - --> gap of indeterminate length Negative
while

10.7.5.2 Character usage for sequence as strings

There are attributes where the amino acid sequence is represented as a string of characters.

  • relative.startingSequence.sequenceString
  • relative.edit.replacementSequence
  • relative.edit.replacedSequence
  • literal

The characters used in these string representations of a sequence should be constrained within to the range: A alanine P proline B aspartate or asparagine Q glutamine C cystine R arginine D aspartate S serine E glutamate T threonine F phenylalanine U selenocysteine G glycine V valine H histidine W tryptophan I isoleucine Y tyrosine K lysine Z glutamate or glutamine L leucine X any M methionine * translation stop N asparagine - gap of indeterminate length IUPAC codes found here https://www.bioinformatics.org/sms2/iupac.html icon.

10.6.5 10.7.6 Search Parameters

Search parameters for this resource. See also the full list of search parameters for this resource , and check the Extensions registry for search parameters on extensions related to this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

Reference Sequence of the sequence MolecularSequence.referenceSeq.referenceSeqId 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
Name Type Description Expression In Common
chromosome token focus Chromosome number of the reference sequence MolecularSequence.referenceSeq.chromosome chromosome-variant-coordinate composite reference 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 What the gene or whole genome sequence. For example, a search for molecular sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means is about, when 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 is not about 0-based v.s. 1-based above. On MolecularSequence.variant:   chromosome: %resource.referenceSeq.chromosome   variant-start: start   variant-end: end 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 subject 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. record On MolecularSequence.referenceSeq:   chromosome: chromosome   window-start: windowStart MolecularSequence.focus
  window-end: windowEnd (Any)
identifier token The unique identity for a particular sequence MolecularSequence.identifier 65 Resources
patient reference The subject that the observation sequence is about MolecularSequence.patient MolecularSequence.subject.where(resolve() is Patient)
( Patient ) 		referenceseqid token 66 Resources
referenceseqid-variant-coordinate composite subject 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. On MolecularSequence.variant:   referenceseqid: %resource.referenceSeq.referenceSeqId   variant-start: start   variant-end: end referenceseqid-window-coordinate composite reference 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 The subject 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 is about 0-based v.s. 1-based above. On MolecularSequence.referenceSeq:   referenceseqid: referenceSeqId   window-start: windowStart MolecularSequence.subject
  window-end: windowEnd ( Group , BiologicallyDerivedProduct , NutritionProduct , Patient , Substance )
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 11 Resources