HLA Reporting Implementation Guide
0.0.1 - Draft

This page is part of the HLA Reporting Implementation Guide (v0.0.1: Trial Use: 1) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

StructureDefinition: HLAMolecularSequence - Detailed Descriptions

Definitions for the hla-molecularsequence Profile.

1. MolecularSequence
Definition

Raw data describing a biological sequence.

Control0..*
InvariantsDefined on this element
dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (: contained.contained.empty())
dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource (: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty())
dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated (: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty())
dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (: contained.meta.security.empty())
dom-6: A resource should have narrative for robust management (: text.`div`.exists())
msq-3: Only 0 and 1 are valid for coordinateSystem (: coordinateSystem = 1 or coordinateSystem = 0)
2. MolecularSequence.id
Definition

The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

Control0..1
Typestring
Comments

The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

3. MolecularSequence.meta
Definition

The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.

Control0..1
TypeMeta
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
4. MolecularSequence.implicitRules
Definition

A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

Control0..1
Typeuri
Is Modifiertrue
Comments

Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
5. MolecularSequence.language
Definition

The base language in which the resource is written.

Control0..1
BindingA human language.
The codes SHOULD be taken from CommonLanguages
Max Binding: AllLanguages
Typecode
Comments

Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
6. MolecularSequence.text
Definition

A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.

Control0..1
TypeNarrative
Alternate Namesnarrative, html, xhtml, display
Comments

Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
7. MolecularSequence.contained
Definition

These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

Control0..*
TypeResource
Alternate Namesinline resources, anonymous resources, contained resources
Comments

This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.

8. MolecularSequence.extension
Definition

May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
9. MolecularSequence.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
10. MolecularSequence.identifier
Definition

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

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

Allows sequences to be distinguished and referenced.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
11. MolecularSequence.type
Definition

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Control0..1
BindingType if a sequence -- DNA, RNA, or amino acid sequence.
The codes SHALL be taken from sequenceType
Typecode
Pattern Valuedna
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
12. MolecularSequence.coordinateSystem
Definition

Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).

Control1..1
Typeinteger
Pattern Value0
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
13. MolecularSequence.patient
Definition

The patient whose sequencing results are described by this resource.

Control0..1
TypeReference(Patient)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
14. MolecularSequence.specimen
Definition

Specimen used for sequencing.

Control0..1
TypeReference(Specimen)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
15. MolecularSequence.device
Definition

The method for sequencing, for example, chip information.

Control0..1
TypeReference(Device)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
16. MolecularSequence.performer
Definition

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

Control0..1
TypeReference(Organization)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
17. MolecularSequence.quantity
Definition

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

Control0..1
TypeQuantity
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
18. MolecularSequence.referenceSeq
Definition

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

Control1..1
TypeBackboneElement
Must Supporttrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
msq-5: GenomeBuild and chromosome must be both contained if either one of them is contained (: (chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists()))
msq-6: Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString; (: (genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1)
19. MolecularSequence.referenceSeq.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
20. MolecularSequence.referenceSeq.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
21. MolecularSequence.referenceSeq.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
22. MolecularSequence.referenceSeq.chromosome
Definition

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340).

Control0..1
BindingChromosome number for human.
For example codes, see chromosome-human
TypeCodeableConcept
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
23. MolecularSequence.referenceSeq.genomeBuild
Definition

The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
24. MolecularSequence.referenceSeq.orientation
Definition

A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

Control0..1
BindingType for orientation.
The codes SHALL be taken from orientationType
Typecode
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
25. MolecularSequence.referenceSeq.referenceSeqId
Definition

Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences.

Control1..1
BindingReference identifier.
For example codes, see ENSEMBL
TypeCodeableConcept
Pattern Value<valueCodeableConcept xmlns="http://hl7.org/fhir">
  <coding>
    <system value="http://www.ebi.ac.uk/ipd/imgt/hla"/>
  </coding>
</valueCodeableConcept>
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
26. MolecularSequence.referenceSeq.referenceSeqPointer
Definition

A pointer to another MolecularSequence entity as reference sequence.

Control0..1
TypeReference(MolecularSequence)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
27. MolecularSequence.referenceSeq.referenceSeqString
Definition

A string like "ACGT".

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
28. MolecularSequence.referenceSeq.strand
Definition

An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

Control0..1
BindingType for strand.
The codes SHALL be taken from strandType
Typecode
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
29. MolecularSequence.referenceSeq.windowStart
Definition

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

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
30. MolecularSequence.referenceSeq.windowEnd
Definition

End position of the window on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
31. MolecularSequence.variant
Definition

The definition of variant here originates from Sequence ontology (variant_of). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
32. MolecularSequence.variant.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
33. MolecularSequence.variant.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
34. MolecularSequence.variant.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
35. MolecularSequence.variant.start
Definition

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

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
36. MolecularSequence.variant.end
Definition

End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
37. MolecularSequence.variant.observedAllele
Definition

An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
38. MolecularSequence.variant.referenceAllele
Definition

An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
39. MolecularSequence.variant.cigar
Definition

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

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
40. MolecularSequence.variant.variantPointer
Definition

A pointer to an Observation containing variant information.

Control0..1
TypeReference(Observation)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
41. MolecularSequence.observedSeq
Definition

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

Control1..1
Typestring
Must Supporttrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
42. MolecularSequence.quality
Definition

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

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
43. MolecularSequence.quality.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
44. MolecularSequence.quality.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
45. MolecularSequence.quality.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
46. MolecularSequence.quality.type
Definition

INDEL / SNP / Undefined variant.

Control1..1
BindingType for quality report.
The codes SHALL be taken from qualityType
Typecode
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
47. MolecularSequence.quality.standardSequence
Definition

Gold standard sequence used for comparing against.

Control0..1
BindingReference identifier of the sequence that used to mark the quality of tested samples.
For example codes, see FDA-StandardSequence
TypeCodeableConcept
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
48. MolecularSequence.quality.start
Definition

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

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
49. MolecularSequence.quality.end
Definition

End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
50. MolecularSequence.quality.score
Definition

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

Control0..1
TypeQuantity
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
51. MolecularSequence.quality.method
Definition

Which method is used to get sequence quality.

Control0..1
BindingThe method used to evaluate the numerical quality of the observed sequence.
For example codes, see FDA-Method
TypeCodeableConcept
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
52. MolecularSequence.quality.truthTP
Definition

True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
53. MolecularSequence.quality.queryTP
Definition

True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
54. MolecularSequence.quality.truthFN
Definition

False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
55. MolecularSequence.quality.queryFP
Definition

False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
56. MolecularSequence.quality.gtFP
Definition

The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
57. MolecularSequence.quality.precision
Definition

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

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
58. MolecularSequence.quality.recall
Definition

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

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
59. MolecularSequence.quality.fScore
Definition

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

Control0..1
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
60. MolecularSequence.quality.roc
Definition

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

Control0..1
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
61. MolecularSequence.quality.roc.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
62. MolecularSequence.quality.roc.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
63. MolecularSequence.quality.roc.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
64. MolecularSequence.quality.roc.score
Definition

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

Control0..*
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
65. MolecularSequence.quality.roc.numTP
Definition

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

Control0..*
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
66. MolecularSequence.quality.roc.numFP
Definition

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

Control0..*
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
67. MolecularSequence.quality.roc.numFN
Definition

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

Control0..*
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
68. MolecularSequence.quality.roc.precision
Definition

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

Control0..*
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
69. MolecularSequence.quality.roc.sensitivity
Definition

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

Control0..*
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
70. MolecularSequence.quality.roc.fMeasure
Definition

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

Control0..*
Typedecimal
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
71. MolecularSequence.readCoverage
Definition

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

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
72. MolecularSequence.repository
Definition

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

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
73. MolecularSequence.repository.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
74. MolecularSequence.repository.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
75. MolecularSequence.repository.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
76. MolecularSequence.repository.type
Definition

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

Control1..1
BindingType for access of external URI.
The codes SHALL be taken from repositoryType
Typecode
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
77. MolecularSequence.repository.url
Definition

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

Control0..1
Typeuri
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
78. MolecularSequence.repository.name
Definition

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

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
79. MolecularSequence.repository.datasetId
Definition

Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
80. MolecularSequence.repository.variantsetId
Definition

Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
81. MolecularSequence.repository.readsetId
Definition

Id of the read in this external repository.

Control0..1
Typestring
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
82. MolecularSequence.pointer
Definition

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

Control0..*
TypeReference(MolecularSequence)
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
83. MolecularSequence.structureVariant
Definition

Information about chromosome structure variation.

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
84. MolecularSequence.structureVariant.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
85. MolecularSequence.structureVariant.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
86. MolecularSequence.structureVariant.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
87. MolecularSequence.structureVariant.variantType
Definition

Information about chromosome structure variation DNA change type.

Control0..1
BindingDNA change type.
The codes SHALL be taken from LOINC Answer List LL379-9|4.0.1
TypeCodeableConcept
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
88. MolecularSequence.structureVariant.exact
Definition

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

Control0..1
Typeboolean
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
89. MolecularSequence.structureVariant.length
Definition

Length of the variant chromosome.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
90. MolecularSequence.structureVariant.outer
Definition

Structural variant outer.

Control0..1
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
91. MolecularSequence.structureVariant.outer.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
92. MolecularSequence.structureVariant.outer.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
93. MolecularSequence.structureVariant.outer.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
94. MolecularSequence.structureVariant.outer.start
Definition

Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
95. MolecularSequence.structureVariant.outer.end
Definition

Structural variant outer end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
96. MolecularSequence.structureVariant.inner
Definition

Structural variant inner.

Control0..1
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
97. MolecularSequence.structureVariant.inner.id
Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
98. MolecularSequence.structureVariant.inner.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
99. MolecularSequence.structureVariant.inner.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Control0..*
TypeExtension
Is Modifiertrue
Requirements

Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (: extension.exists() != value.exists())
100. MolecularSequence.structureVariant.inner.start
Definition

Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
101. MolecularSequence.structureVariant.inner.end
Definition

Structural variant inner end. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Control0..1
Typeinteger
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))