Skip to main content

MolecularSequenceReferenceSeq

Raw data describing a biological sequence.

type MolecularSequenceReferenceSeq implements Element {
  chromosome: CodeableConcept
  genomeBuild: String
  orientation: String
  referenceSeqId: CodeableConcept
  referenceSeqPointer: Reference
  referenceSeqString: String
  strand: String
  windowStart: Int
  windowEnd: Int
  modifierExtension: [Extension]
  extension: [Extension]
  id: String
}

Fields​

MolecularSequenceReferenceSeq.chromosome ● CodeableConcept object​

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).

MolecularSequenceReferenceSeq.genomeBuild ● String scalar​

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.

MolecularSequenceReferenceSeq.orientation ● String scalar​

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.

MolecularSequenceReferenceSeq.referenceSeqId ● CodeableConcept object​

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.

MolecularSequenceReferenceSeq.referenceSeqPointer ● Reference object​

A pointer to another MolecularSequence entity as reference sequence.

MolecularSequenceReferenceSeq.referenceSeqString ● String scalar​

A string like ACGT .

MolecularSequenceReferenceSeq.strand ● String scalar​

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.

MolecularSequenceReferenceSeq.windowStart ● Int scalar​

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.

MolecularSequenceReferenceSeq.windowEnd ● Int scalar​

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.

MolecularSequenceReferenceSeq.modifierExtension ● [Extension] list object​

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).

MolecularSequenceReferenceSeq.extension ● [Extension] list object​

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.

MolecularSequenceReferenceSeq.id ● String scalar​

Interfaces​

Element interface​

Base definition for all elements in a resource. If the element is present, it must have a value for at least one of the defined elements, an @id referenced from the Narrative, or extensions

Member Of​

MolecularSequence object