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This page is part of the FHIR Specification (v4.3.0: R4B (v5.0.0-ballot: R5 Ballot - STU see ballot notes ). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4

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.

10.6.1 10.7.1 Scope and Usage

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.

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 representions 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.

10.6.3 10.7.3 References to this Resource

This resource is referenced by

10.6.4 10.7.4 Resource Content

Structure

Who and/or what chromosome Σ 0..1 CodeableConcept Chromosome containing genetic finding chromosome-human ( Example ) Start position of the sequence True positives from the perspective of the truth data 0..1 decimal False positives where the non-REF alleles in the Truth and Query Call Sets match Receiver Operator Characteristic (ROC) Curve Roc score true positive numbers Average number Id of the dataset that used to call for dataset in repository structureVariant Σ 0..* BackboneElement Structural variant Structural variant length outer Σ 0..1
Name Flags Card. Type Description & Constraints doco
. . MolecularSequence 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 ( Required )
. . coordinateSystem . subject Σ 1..1 integer Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) patient Σ 0..1 Reference ( Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct ) Subject this sequence is about associated too
. . . device Σ 0..1 Reference ( Device ) The method for sequencing
. . . performer Σ 0..1 Reference ( Organization ) Who should be responsible for test result quantity Σ 0..1 Quantity The number of copies of the sequence of interest. (RNASeq) referenceSeq Σ I 0..1 BackboneElement A 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;
. . . genomeBuild literal Σ 0..1 string The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' Sequence that was observed
. . orientation . formatted Σ 0..1 0..* code Attachment sense | antisense Embedded file or a link (URL) which contains content to represent the sequence

orientationType ( Required )
. . referenceSeqId . relative Σ 0..1 0..* CodeableConcept BackboneElement Reference identifier ENSEMBL ( Example ) referenceSeqPointer Σ 0..1 Reference ( MolecularSequence ) A pointer sequence defined relative to another MolecularSequence entity as reference sequence referenceSeqString Σ 0..1 string

A string to represent reference sequence
. . . strand . coordinateSystem Σ 0..1 1..1 code CodeableConcept watson | crick Ways of identifying nucleotides or amino acids within a sequence
strandType LL5323-2 icon ( Required Extensible )
. . . . windowStart ordinalPosition Σ 0..1 integer Start position of Indicates the window on order in which the reference sequence should be considered when putting multiple 'relative' elements together
. . . windowEnd . sequenceRange Σ 0..1 integer Range End position of Indicates the window on nucleotide range in the reference composed sequence when multiple 'relative' elements are used together
. . . . variant startingSequence Σ C 0..* 0..1 BackboneElement Variant in A sequence used as starting sequence
start Σ 0..1 integer Start position + Rule: Both genomeAssembly and chromosome must be both contained if either one of the variant on the reference sequence end Σ 0..1 integer them is contained
End position + Rule: Have and only have one of the variant on the reference following elements in startingSequence: 1. genomeAssembly; 2 sequence observedAllele Σ 0..1 string
Allele that was observed
. referenceAllele Σ 0..1 string Allele in the reference sequence . . . cigar . genomeAssembly Σ 0..1 string CodeableConcept Extended CIGAR string The genome assembly used for aligning the sequence with reference bases variantPointer Σ 0..1 starting sequence, e.g. GRCh38
LL1040-6 icon Reference ( Observation Extensible ) Pointer to observed variant information observedSeq Σ 0..1 string Sequence that was observed quality Σ 0..* BackboneElement An set of value as quality of sequence
. type Σ 1..1 code indel | snp | unknown qualityType ( Required ) . . . . standardSequence chromosome Σ 0..1 CodeableConcept Standard sequence for comparison Chromosome Identifier
FDA-StandardSequence LL2938-0 icon ( Example Required ) start Σ 0..1 integer
. end Σ 0..1 integer End position of the sequence . . . score . sequence[x] Σ 0..1 Quantity Quality score for The reference sequence that represents the comparison method Σ 0..1 CodeableConcept Method to get quality starting sequence
FDA-Method Multiple bindings acceptable (NCBI or LRG) ( Example ) truthTP Σ 0..1 decimal
. queryTP Σ 0..1 decimal True positives from the perspective of the query data . . truthFN Σ 0..1 decimal False negatives . . queryFP . sequenceCodeableConcept Σ 0..1 decimal False positives gtFP Σ CodeableConcept
. precision Σ 0..1 decimal Precision of comparison . . . . . recall Σ sequenceString 0..1 decimal Recall of comparison fScore Σ 0..1 decimal F-score roc Σ string 0..1 BackboneElement
. . . score . . . sequenceReference Σ 0..* integer Genotype quality score numTP Σ Reference 0..* integer ( MolecularSequence )
. . numFP Σ 0..* integer Roc score false positive numbers . . . numFN windowStart Σ 0..* 0..1 integer Roc score false negative numbers precision Σ 0..* decimal Precision Start position of the GQ score window on the starting sequence
. . sensitivity Σ 0..* decimal Sensitivity of the GQ score . . . fMeasure windowEnd Σ 0..* decimal FScore of the GQ score readCoverage Σ 0..1 integer 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 1..1 0..1 code directlink | openapi | login | oauth sense | other antisense
repositoryType orientationType ( Required ) url Σ 0..1 uri URI of the repository name Σ 0..1 string Repository's name datasetId Σ 0..1 string
. variantsetId Σ 0..1 string Id of the variantset that used to call for variantset in repository . . . . readsetId strand Σ 0..1 string code Id of the read pointer Σ 0..* watson | crick
Reference strandType ( MolecularSequence Required ) Pointer to next atomic sequence
. . . variantType . edit Σ 0..1 0..* CodeableConcept BackboneElement Structural variant change type Changes in sequence from the starting sequence
LOINC LL379-9 answerlist
( Required )
. . . . . exact start Σ 0..1 boolean Does the structural variant have base pair resolution breakpoints? length Σ 0..1 integer Start position of the edit on the starting sequence
BackboneElement Structural variant outer
. . . . . start end Σ 0..1 integer Structural variant outer start end Σ 0..1 integer Structural variant outer end inner Σ 0..1 BackboneElement End position of the edit on the starting sequence
Structural variant inner
. . . . . start replacementSequence Σ 0..1 integer string Structural variant inner start Allele that was observed
. . . . . end replacedSequence Σ 0..1 integer string Structural variant inner end Allele in the starting sequence

doco Documentation for this format

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] « null (Strength=Required) 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) coordinateSystem : integer [1..1] The patient whose sequencing results are described by this resource associated too patient subject : Reference [0..1] « Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct » 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] ReferenceSeq StartingSequence The genome assembly used for starting sequence, e.g. GRCh38 genomeAssembly : CodeableConcept [0..1] « null (Strength=Extensible) LL1040-6 + » 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] « null (Strength=Example) (Strength=Required) chromosome-human ?? LL2938-0 ! » 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 ...?? » 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] « null (Strength=Required) 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] « null (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] « null (Strength=Required) 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] « null (Strength=Required) qualityType ! » Gold standard sequence used for comparing against standardSequence : CodeableConcept [0..1] « null (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] « null (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] « null (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] « null (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|Device|Group|Location|
   Medication|NutritionProduct|Organization|Patient|Practitioner|Procedure|
   Substance) Subject this sequence is associated too --></subject>
 <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>
 <
  <
  <
  <
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  <
  <</variantPointer>
 </variant>
 <
 <
  <
  <</standardSequence>
  <
  <
  <</score>
  <</method>
  <
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  </roc>
 </quality>
 <
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 </repository>
 <</pointer>
 <
  <</variantType>
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  </outer>
  <
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   <
  </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><!-- 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38 icon --></genomeAssembly>
   <chromosome><!-- 0..1 CodeableConcept Chromosome Identifier icon --></chromosome>
   <sequence[x]><!-- 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|Device|Group|Location|
   Medication|NutritionProduct|Organization|Patient|Practitioner|Procedure|
   Substance) }, // Subject this sequence is associated too
  "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 }, // The genome assembly used for starting sequence, e.g. GRCh38 icon
      "chromosome" : { CodeableConcept }, // 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:

  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence

  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:
  fhir:

  fhir:MolecularSequence.subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|Medication|NutritionProduct|
  Organization|Patient|Practitioner|Procedure|Substance) ]; # 0..1 Subject this sequence is associated too
  fhir:MolecularSequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:MolecularSequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:MolecularSequence.performer [ Reference(Organization) ]; # 0..1 Who should be responsible for test result
  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:MolecularSequence.literal [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.formatted [ Attachment ], ... ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:MolecularSequence.relative [ # 0..* A sequence defined relative to another sequence
    fhir:MolecularSequence.relative.coordinateSystem [ CodeableConcept ]; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:MolecularSequence.relative.ordinalPosition [ integer ]; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:MolecularSequence.relative.sequenceRange [ Range ]; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:MolecularSequence.relative.startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:MolecularSequence.relative.startingSequence.genomeAssembly [ CodeableConcept ]; # 0..1 The genome assembly used for starting sequence, e.g. GRCh38
      fhir:MolecularSequence.relative.startingSequence.chromosome [ CodeableConcept ]; # 0..1 Chromosome Identifier
      # MolecularSequence.relative.startingSequence.sequence[x] : 0..1 The reference sequence that represents the starting sequence. One of these 3
        fhir:MolecularSequence.relative.startingSequence.sequenceCodeableConcept [ CodeableConcept ]
        fhir:MolecularSequence.relative.startingSequence.sequenceString [ string ]
        fhir:MolecularSequence.relative.startingSequence.sequenceReference [ Reference(MolecularSequence) ]
      fhir:MolecularSequence.relative.startingSequence.windowStart [ integer ]; # 0..1 Start position of the window on the starting sequence
      fhir:MolecularSequence.relative.startingSequence.windowEnd [ integer ]; # 0..1 End position of the window on the starting sequence
      fhir:MolecularSequence.relative.startingSequence.orientation [ code ]; # 0..1 sense | antisense
      fhir:MolecularSequence.relative.startingSequence.strand [ code ]; # 0..1 watson | crick

    ];
    fhir:MolecularSequence.relative.edit [ # 0..* Changes in sequence from the starting sequence
      fhir:MolecularSequence.relative.edit.start [ integer ]; # 0..1 Start position of the edit on the starting sequence
      fhir:MolecularSequence.relative.edit.end [ integer ]; # 0..1 End position of the edit on the starting sequence
      fhir:MolecularSequence.relative.edit.replacementSequence [ string ]; # 0..1 Allele that was observed
      fhir:MolecularSequence.relative.edit.replacedSequence [ string ]; # 0..1 Allele in the starting sequence
    ], ...;

  ], ...;
]

Changes since R4

MolecularSequence
MolecularSequence.subject
  • No Changes Added Element
MolecularSequence.literal
  • Added Element
MolecularSequence.formatted
  • Added Element
MolecularSequence.relative
  • Added Element
MolecularSequence.relative.coordinateSystem
  • Added Mandatory Element
MolecularSequence.relative.ordinalPosition
  • Added Element
MolecularSequence.relative.sequenceRange
  • Added Element
MolecularSequence.relative.startingSequence
  • Added Element
MolecularSequence.relative.startingSequence.genomeAssembly
  • Added Element
MolecularSequence.relative.startingSequence.chromosome
  • Added Element
MolecularSequence.relative.startingSequence.sequence[x]
  • Added Element
MolecularSequence.relative.startingSequence.windowStart
  • Added Element
MolecularSequence.relative.startingSequence.windowEnd
  • Added Element
MolecularSequence.relative.startingSequence.orientation
  • Added Element
MolecularSequence.relative.startingSequence.strand
  • Added Element
MolecularSequence.relative.edit
  • Added Element
MolecularSequence.relative.edit.start
  • Added Element
MolecularSequence.relative.edit.end
  • Added Element
MolecularSequence.relative.edit.replacementSequence
  • Added Element
MolecularSequence.relative.edit.replacedSequence
  • Added Element
MolecularSequence.coordinateSystem
  • deleted
MolecularSequence.patient
  • deleted
MolecularSequence.quantity
  • deleted
MolecularSequence.referenceSeq
  • deleted
MolecularSequence.variant
  • deleted
MolecularSequence.observedSeq
  • deleted
MolecularSequence.quality
  • deleted
MolecularSequence.readCoverage
  • deleted
MolecularSequence.repository
  • deleted
MolecularSequence.pointer
  • deleted
MolecularSequence.structureVariant
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON .

Conversions between R3 and R4

Structure

Who and/or what chromosome Σ 0..1 CodeableConcept Chromosome containing genetic finding chromosome-human ( Example ) 0..1 decimal False positives where the non-REF alleles in the Truth and Query Call Sets match Receiver Operator Characteristic (ROC) Curve Roc score true positive numbers Average number datasetId Σ 0..1 string Id of the dataset that used to call for dataset in repository structureVariant Σ 0..* BackboneElement Structural variant Structural variant length outer Σ 0..1 Structural variant outer
Name Flags Card. Type Description & Constraints doco
. . MolecularSequence 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 ( Required )
. . coordinateSystem . subject Σ 1..1 integer Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) patient Σ 0..1 Reference ( Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct ) Subject this sequence is about associated too
. . . device Σ 0..1 Reference ( Device ) The method for sequencing
. . . performer Σ 0..1 Reference ( Organization ) Who should be responsible for test result quantity Σ 0..1 Quantity The number of copies of the sequence of interest. (RNASeq) referenceSeq Σ I 0..1 BackboneElement A 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;
. . . genomeBuild literal Σ 0..1 string The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' Sequence that was observed
. . orientation . formatted Σ 0..1 0..* code Attachment sense | antisense Embedded file or a link (URL) which contains content to represent the sequence

orientationType ( Required )
. . referenceSeqId . relative Σ 0..1 0..* CodeableConcept BackboneElement Reference identifier ENSEMBL ( Example ) referenceSeqPointer Σ 0..1 Reference ( MolecularSequence ) A pointer sequence defined relative to another MolecularSequence entity as reference sequence referenceSeqString Σ 0..1 string

A string to represent reference sequence
. . . strand . coordinateSystem Σ 0..1 1..1 code CodeableConcept watson | crick Ways of identifying nucleotides or amino acids within a sequence
strandType LL5323-2 icon ( Required Extensible )
. . . . windowStart ordinalPosition Σ 0..1 integer Start position of Indicates the window on order in which the reference sequence should be considered when putting multiple 'relative' elements together
. . . windowEnd . sequenceRange Σ 0..1 integer Range End position of Indicates the window on nucleotide range in the reference composed sequence when multiple 'relative' elements are used together
. . . . variant startingSequence Σ C 0..* 0..1 BackboneElement Variant in A sequence used as starting sequence
start Σ 0..1 integer Start position + Rule: Both genomeAssembly and chromosome must be both contained if either one of the variant on the reference sequence end Σ 0..1 integer them is contained
End position + Rule: Have and only have one of the variant on the reference following elements in startingSequence: 1. genomeAssembly; 2 sequence observedAllele Σ 0..1 string
Allele that was observed
. referenceAllele Σ 0..1 string Allele in the reference sequence . . . cigar . genomeAssembly Σ 0..1 string CodeableConcept Extended CIGAR string The genome assembly used for aligning the sequence with reference bases variantPointer Σ 0..1 starting sequence, e.g. GRCh38
LL1040-6 icon Reference ( Observation Extensible ) Pointer to observed variant information observedSeq Σ 0..1 string Sequence that was observed quality Σ 0..* BackboneElement An set of value as quality of sequence
. type Σ 1..1 code indel | snp | unknown qualityType ( Required ) . . . . standardSequence chromosome Σ 0..1 CodeableConcept Standard sequence for comparison Chromosome Identifier
FDA-StandardSequence LL2938-0 icon ( Example Required ) start Σ 0..1 integer
Start position of the sequence
. end Σ 0..1 integer End position of the sequence . . . score . sequence[x] Σ 0..1 Quantity Quality score for The reference sequence that represents the comparison method Σ 0..1 CodeableConcept Method to get quality starting sequence
FDA-Method Multiple bindings acceptable (NCBI or LRG) ( Example ) truthTP Σ 0..1 decimal
True positives from the perspective of the truth data
. queryTP Σ 0..1 decimal True positives from the perspective of the query data . . truthFN Σ 0..1 decimal False negatives . . queryFP . sequenceCodeableConcept Σ 0..1 decimal False positives gtFP Σ CodeableConcept
. precision Σ 0..1 decimal Precision of comparison . . . . . recall Σ sequenceString 0..1 decimal Recall of comparison fScore Σ 0..1 decimal F-score roc Σ string 0..1 BackboneElement
. . . score . . . sequenceReference Σ 0..* integer Genotype quality score numTP Σ Reference 0..* integer ( MolecularSequence )
. . numFP Σ 0..* integer Roc score false positive numbers . . . numFN windowStart Σ 0..* 0..1 integer Roc score false negative numbers precision Σ 0..* decimal Precision Start position of the GQ score window on the starting sequence
. . sensitivity Σ 0..* decimal Sensitivity of the GQ score . . . fMeasure windowEnd Σ 0..* decimal FScore of the GQ score readCoverage Σ 0..1 integer 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 1..1 0..1 code directlink | openapi | login | oauth sense | other antisense
repositoryType orientationType ( Required ) url Σ 0..1 uri URI of the repository name Σ 0..1 string
Repository's name
. variantsetId Σ 0..1 string Id of the variantset that used to call for variantset in repository . . . . readsetId strand Σ 0..1 string code Id of the read pointer Σ 0..* watson | crick
Reference strandType ( MolecularSequence Required ) Pointer to next atomic sequence
. . . variantType . edit Σ 0..1 0..* CodeableConcept BackboneElement Structural variant change type Changes in sequence from the starting sequence
LOINC LL379-9 answerlist
( Required )
. . . . . exact start Σ 0..1 boolean Does the structural variant have base pair resolution breakpoints? length Σ 0..1 integer BackboneElement Start position of the edit on the starting sequence
. . . . . start end Σ 0..1 integer Structural variant outer start end Σ 0..1 integer Structural variant outer end inner Σ 0..1 BackboneElement End position of the edit on the starting sequence
Structural variant inner
. . . . . start replacementSequence Σ 0..1 integer string Structural variant inner start Allele that was observed
. . . . . end replacedSequence Σ 0..1 integer string Structural variant inner end Allele in the starting sequence

doco Documentation for this format

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] « null (Strength=Required) 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) coordinateSystem : integer [1..1] The patient whose sequencing results are described by this resource associated too patient subject : Reference [0..1] « Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct » 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] ReferenceSeq StartingSequence The genome assembly used for starting sequence, e.g. GRCh38 genomeAssembly : CodeableConcept [0..1] « null (Strength=Extensible) LL1040-6 + » 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] « null (Strength=Example) (Strength=Required) chromosome-human ?? LL2938-0 ! » 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 ...?? » 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] « null (Strength=Required) 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] « null (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] « null (Strength=Required) 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] « null (Strength=Required) qualityType ! » Gold standard sequence used for comparing against standardSequence : CodeableConcept [0..1] « null (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] « null (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] « null (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] « null (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|Device|Group|Location|
   Medication|NutritionProduct|Organization|Patient|Practitioner|Procedure|
   Substance) Subject this sequence is associated too --></subject>
 <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>
  <
  <
  <
  <
  <
  <
  <
  <
  <
   <
   <
   <
   <
   <
   <
   <
  </roc>
 </quality>
 <
 <
  <
  <
  <
  <
  <
  <
 </repository>
 <</pointer>
 <
  <</variantType>
  <
  <
  <
   <
   <
  </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><!-- 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38 icon --></genomeAssembly>
   <chromosome><!-- 0..1 CodeableConcept Chromosome Identifier icon --></chromosome>
   <sequence[x]><!-- 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|Device|Group|Location|
   Medication|NutritionProduct|Organization|Patient|Practitioner|Procedure|
   Substance) }, // Subject this sequence is associated too
  "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 }, // The genome assembly used for starting sequence, e.g. GRCh38 icon
      "chromosome" : { CodeableConcept }, // 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:

  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence

  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:
  fhir:

  fhir:MolecularSequence.subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|Medication|NutritionProduct|
  Organization|Patient|Practitioner|Procedure|Substance) ]; # 0..1 Subject this sequence is associated too
  fhir:MolecularSequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:MolecularSequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:MolecularSequence.performer [ Reference(Organization) ]; # 0..1 Who should be responsible for test result
  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:MolecularSequence.literal [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.formatted [ Attachment ], ... ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:MolecularSequence.relative [ # 0..* A sequence defined relative to another sequence
    fhir:MolecularSequence.relative.coordinateSystem [ CodeableConcept ]; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:MolecularSequence.relative.ordinalPosition [ integer ]; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:MolecularSequence.relative.sequenceRange [ Range ]; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:MolecularSequence.relative.startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:MolecularSequence.relative.startingSequence.genomeAssembly [ CodeableConcept ]; # 0..1 The genome assembly used for starting sequence, e.g. GRCh38
      fhir:MolecularSequence.relative.startingSequence.chromosome [ CodeableConcept ]; # 0..1 Chromosome Identifier
      # MolecularSequence.relative.startingSequence.sequence[x] : 0..1 The reference sequence that represents the starting sequence. One of these 3
        fhir:MolecularSequence.relative.startingSequence.sequenceCodeableConcept [ CodeableConcept ]
        fhir:MolecularSequence.relative.startingSequence.sequenceString [ string ]
        fhir:MolecularSequence.relative.startingSequence.sequenceReference [ Reference(MolecularSequence) ]
      fhir:MolecularSequence.relative.startingSequence.windowStart [ integer ]; # 0..1 Start position of the window on the starting sequence
      fhir:MolecularSequence.relative.startingSequence.windowEnd [ integer ]; # 0..1 End position of the window on the starting sequence
      fhir:MolecularSequence.relative.startingSequence.orientation [ code ]; # 0..1 sense | antisense
      fhir:MolecularSequence.relative.startingSequence.strand [ code ]; # 0..1 watson | crick

    ];
    fhir:MolecularSequence.relative.edit [ # 0..* Changes in sequence from the starting sequence
      fhir:MolecularSequence.relative.edit.start [ integer ]; # 0..1 Start position of the edit on the starting sequence
      fhir:MolecularSequence.relative.edit.end [ integer ]; # 0..1 End position of the edit on the starting sequence
      fhir:MolecularSequence.relative.edit.replacementSequence [ string ]; # 0..1 Allele that was observed
      fhir:MolecularSequence.relative.edit.replacedSequence [ string ]; # 0..1 Allele in the starting sequence
    ], ...;

  ], ...;
]

Changes since Release 4

MolecularSequence
MolecularSequence.subject
  • No Changes Added Element
MolecularSequence.literal
  • Added Element
MolecularSequence.formatted
  • Added Element
MolecularSequence.relative
  • Added Element
MolecularSequence.relative.coordinateSystem
  • Added Mandatory Element
MolecularSequence.relative.ordinalPosition
  • Added Element
MolecularSequence.relative.sequenceRange
  • Added Element
MolecularSequence.relative.startingSequence
  • Added Element
MolecularSequence.relative.startingSequence.genomeAssembly
  • Added Element
MolecularSequence.relative.startingSequence.chromosome
  • Added Element
MolecularSequence.relative.startingSequence.sequence[x]
  • Added Element
MolecularSequence.relative.startingSequence.windowStart
  • Added Element
MolecularSequence.relative.startingSequence.windowEnd
  • Added Element
MolecularSequence.relative.startingSequence.orientation
  • Added Element
MolecularSequence.relative.startingSequence.strand
  • Added Element
MolecularSequence.relative.edit
  • Added Element
MolecularSequence.relative.edit.start
  • Added Element
MolecularSequence.relative.edit.end
  • Added Element
MolecularSequence.relative.edit.replacementSequence
  • Added Element
MolecularSequence.relative.edit.replacedSequence
  • Added Element
MolecularSequence.coordinateSystem
  • deleted
MolecularSequence.patient
  • deleted
MolecularSequence.quantity
  • deleted
MolecularSequence.referenceSeq
  • deleted
MolecularSequence.variant
  • deleted
MolecularSequence.observedSeq
  • deleted
MolecularSequence.quality
  • deleted
MolecularSequence.readCoverage
  • deleted
MolecularSequence.repository
  • deleted
MolecularSequence.pointer
  • deleted
MolecularSequence.structureVariant
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON .

Conversions between R3 and R4

 

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

10.6.4.1 10.7.4.1 Terminology Bindings

MolecularSequence.referenceSeq.chromosome MolecularSequence.referenceSeq.referenceSeqId MolecularSequence.quality.type MolecularSequence.quality.method MolecularSequence.repository.type MolecularSequence.structureVariant.variantType
Path Definition Type Reference
MolecularSequence.type

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

Required sequenceType
MolecularSequence.relative.coordinateSystem Example chromosome-human Extensible MolecularSequence.referenceSeq.orientation Required http://loinc.org/LL5323-2/ icon orientationType
MolecularSequence.relative.startingSequence.genomeAssembly Example ENSEMBL Extensible MolecularSequence.referenceSeq.strand Required http://loinc.org/LL1040-6/ icon strandType
MolecularSequence.relative.startingSequence.chromosome Required qualityType MolecularSequence.quality.standardSequence Example http://loinc.org/LL2938-0/ icon FDA-StandardSequence
MolecularSequence.relative.startingSequence.sequence[x] Example FDA-Method ??
MolecularSequence.relative.startingSequence.orientation

Type for orientation.

Required repositoryType orientationType
MolecularSequence.relative.startingSequence.strand

Type for strand.

Required http://loinc.org/vs/LL379-9 strandType

10.6.4.2 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()) genomeAssembly.empty()) or (chromosome.exists() and genomeBuild.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()) (genomeAssembly.count()+sequenceCodeableConcept.count()+ sequenceReference.count()+ sequenceString.count()) = 1

10.6.5 10.7.5 Notes: Notes

10.6.5.1 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 MolecularSequence.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

MolecularSequence.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 an 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 MolecularSequence.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

MolecularSequence.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

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

MolecularSequence.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 representing 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

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

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

The MolecularSequence.relative.startingSequence.windowStart and MolecularSequence.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.

MolecularSequence.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

10.6.5.2 10.7.5.1.3.4 Choice of Strand

There are lots of definition concerning with the Directionality directionality of DNA or RNA. Here we are using referenceSeq.orientation MolecularSequence.relative.startingSequence.orientation and MolecularSequence.relative.startingSequence.strand . referenceSeq.strand . orientation Orientation represents the sense of the sequence, which has different meanings depending on the 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').

10.6.5.3 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 word in different omics scenario, below are simple example 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.

10.6.6 10.7.6 Search Parameters

Search parameters for this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

variant-end number End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant. MolecularSequence.variant.end variant-start number Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant. MolecularSequence.variant.start window-end number End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence. MolecularSequence.referenceSeq.windowEnd window-start number Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence. MolecularSequence.referenceSeq.windowStart
Name Type Description Expression In Common
chromosome token Chromosome number of the reference sequence MolecularSequence.referenceSeq.chromosome chromosome-variant-coordinate composite Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as chromosome-variant-coordinate=1$lt345$gt123 , this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above. 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 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. On MolecularSequence.referenceSeq:   chromosome: chromosome   window-start: windowStart   window-end: windowEnd identifier token The unique identity for a particular sequence MolecularSequence.identifier
patient reference The subject that the observation sequence is about MolecularSequence.patient MolecularSequence.subject
( Practitioner , Group , Organization , BiologicallyDerivedProduct , NutritionProduct , Device , Medication , Patient , Procedure , Substance , Location )
referenceseqid token Reference Sequence of the sequence MolecularSequence.referenceSeq.referenceSeqId 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 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 ( Practitioner , Group , Organization , BiologicallyDerivedProduct , NutritionProduct , Device , Medication , Patient , Procedure , Substance , Location )
type token Amino Acid Sequence/ DNA Sequence / RNA Sequence MolecularSequence.type