Skip to main content

MolecularSequence

Raw data describing a biological sequence.

Elements

NameRequiredTypeDescription
identifierIdentifier[]

Unique ID for this particular sequence. This is a FHIR-defined id

Details

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

typecode

aa | dna | rna

Details

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

coordinateSysteminteger

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)

Details

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).

patientReference<Patient>

Who and/or what this is about

Details

The patient whose sequencing results are described by this resource.

specimenReference<Specimen>

Specimen used for sequencing

Details

Specimen used for sequencing.

deviceReference<Device>

The method for sequencing

Details

The method for sequencing, for example, chip information.

performerReference<Organization>

Who should be responsible for test result

Details

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

quantityQuantity

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

Details

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

referenceSeqMolecularSequencereferenceSeq

A sequence used as reference

Details

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

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

chromosomeCodeableConcept

Chromosome containing genetic finding

Details

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)).

genomeBuildstring

The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'

Details

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.

orientationcode

sense | antisense

Details

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.

referenceSeqIdCodeableConcept

Reference identifier

Details

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.

referenceSeqPointerReference<MolecularSequence>

A pointer to another MolecularSequence entity as reference sequence

Details

A pointer to another MolecularSequence entity as reference sequence.

referenceSeqStringstring

A string to represent reference sequence

Details

A string like "ACGT".

strandcode

watson | crick

Details

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.

windowStartinteger

Start position of the window on the reference sequence

Details

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.

windowEndinteger

End position of the window on the reference sequence

Details

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.

variantMolecularSequencevariant[]

Variant in sequence

Details

The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

startinteger

Start position of the variant on the reference sequence

Details

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.

endinteger

End position of the variant on the reference sequence

Details

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.

observedAllelestring

Allele that was observed

Details

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)). 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.

referenceAllelestring

Allele in the reference sequence

Details

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)). 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.

cigarstring

Extended CIGAR string for aligning the sequence with reference bases

Details

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).

variantPointerReference<Observation>

Pointer to observed variant information

Details

A pointer to an Observation containing variant information.

observedSeqstring

Sequence that was observed

Details

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.

qualityMolecularSequencequality[]

An set of value as quality of sequence

Details

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)).

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

typecode

indel | snp | unknown

Details

INDEL / SNP / Undefined variant.

standardSequenceCodeableConcept

Standard sequence for comparison

Details

Gold standard sequence used for comparing against.

startinteger

Start position of the sequence

Details

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

endinteger

End position of the sequence

Details

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.

scoreQuantity

Quality score for the comparison

Details

The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).

methodCodeableConcept

Method to get quality

Details

Which method is used to get sequence quality.

truthTPdecimal

True positives from the perspective of the truth data

Details

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.

queryTPdecimal

True positives from the perspective of the query data

Details

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.

truthFNdecimal

False negatives

Details

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.

queryFPdecimal

False positives

Details

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.

gtFPdecimal

False positives where the non-REF alleles in the Truth and Query Call Sets match

Details

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).

precisiondecimal

Precision of comparison

Details

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

recalldecimal

Recall of comparison

Details

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

fScoredecimal

F-score

Details

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

rocMolecularSequencequalityroc

Receiver Operator Characteristic (ROC) Curve

Details

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

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

scoreinteger[]

Genotype quality score

Details

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

numTPinteger[]

Roc score true positive numbers

Details

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

numFPinteger[]

Roc score false positive numbers

Details

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

numFNinteger[]

Roc score false negative numbers

Details

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

precisiondecimal[]

Precision of the GQ score

Details

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

sensitivitydecimal[]

Sensitivity of the GQ score

Details

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

fMeasuredecimal[]

FScore of the GQ score

Details

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

readCoverageinteger

Average number of reads representing a given nucleotide in the reconstructed sequence

Details

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

repositoryMolecularSequencerepository[]

External repository which contains detailed report related with observedSeq in this resource

Details

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

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

typecode

directlink | openapi | login | oauth | other

Details

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

urluri

URI of the repository

Details

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

namestring

Repository's name

Details

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

datasetIdstring

Id of the dataset that used to call for dataset in repository

Details

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.

variantsetIdstring

Id of the variantset that used to call for variantset in repository

Details

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.

readsetIdstring

Id of the read

Details

Id of the read in this external repository.

pointerReference<MolecularSequence>[]

Pointer to next atomic sequence

Details

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

structureVariantMolecularSequencestructureVariant[]

Structural variant

Details

Information about chromosome structure variation.

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

variantTypeCodeableConcept

Structural variant change type

Details

Information about chromosome structure variation DNA change type.

exactboolean

Does the structural variant have base pair resolution breakpoints?

Details

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

lengthinteger

Structural variant length

Details

Length of the variant chromosome.

outerMolecularSequencestructureVariantouter

Structural variant outer

Details

Structural variant outer.

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

startinteger

Structural variant outer start

Details

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

endinteger

Structural variant outer end

Details

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.

innerMolecularSequencestructureVariantinner

Structural variant inner

Details

Structural variant inner.

idstring

Unique id for inter-element referencing

Details

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

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored even if unrecognized

Details

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).

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.

startinteger

Structural variant inner start

Details

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

endinteger

Structural variant inner end

Details

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.

Search Parameters

NameTypeDescriptionExpression
chromosometokenChromosome number of the reference sequenceMolecularSequence.referenceSeq.chromosome
identifiertokenThe unique identity for a particular sequenceMolecularSequence.identifier
patientreferenceThe subject that the observation is aboutMolecularSequence.patient
referenceseqidtokenReference Sequence of the sequenceMolecularSequence.referenceSeq.referenceSeqId
typetokenAmino Acid Sequence/ DNA Sequence / RNA SequenceMolecularSequence.type
variant-endnumberEnd 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-startnumberStart 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-endnumberEnd 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-startnumberStart 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
chromosome-variant-coordinatecompositeSearch 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.MolecularSequence.variant
chromosome-window-coordinatecompositeSearch 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.MolecularSequence.referenceSeq
referenceseqid-variant-coordinatecompositeSearch 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.MolecularSequence.variant
referenceseqid-window-coordinatecompositeSearch 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 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 about 0-based v.s. 1-based above.MolecularSequence.referenceSeq

Inherited Elements

NameRequiredTypeDescription
idstring

Logical id of this artifact

Details

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

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

metaMeta

Metadata about the resource

Details

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.

implicitRulesuri

A set of rules under which this content was created

Details

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.

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.

languagecode

Language of the resource content

Details

The base language in which the resource is written.

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).

textNarrative

Text summary of the resource, for human interpretation

Details

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.

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.

containedResource[]

Contained, inline Resources

Details

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.

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.

extensionExtension[]

Additional content defined by implementations

Details

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.

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.

modifierExtensionExtension[]

Extensions that cannot be ignored

Details

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).

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.