Representation of a molecular sequence.

A unique identifier for this particular sequence instance.

Allows sequences to be distinguished and referenced.

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Indicates the subject this sequence is associated too.

The actual focus of a molecular sequence when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the subject would be the child (proband) and the focus would be the parent.

Specimen used for sequencing.

The method for sequencing, for example, chip information.

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

Sequence that was observed.

Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.

A sequence defined relative to another sequence.

These are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail.

Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together.

Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together.

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

The genome assembly used for starting sequence, e.g. GRCh38.

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 icon).

The reference sequence that represents the starting sequence.

A starting sequence may be represented in one of three ways:

1. CodeableConcept, using NCBI, LRG or other appropriate code systems
2. a simple string of IUPAC codes
3. a reference to another MolecularSequence resource.

Start position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

End position of the window on the starting sequence. This value should honor the rules of the coordinateSystem.

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.

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.

Changes in sequence from the starting sequence.

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

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

Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.