Definitional content for a molecular entity, such as a nucleotide or protein sequence.

A unique identifier for a particular instance of this resource.

A description of the molecular entity in a human friendly format.

The type of molecule (e.g., DNA, RNA, amino acid). This is a broad concept that refers to the general physical composition of the molecule, intended to facilitate searching and to provide domain context for profiles and instances. The terminology binding may be expanded to support additional types of molecules in the future (e.g., peptide nucleic acids, oligosaccharides).

Classifications of an instance of the resource into arbitrary types, based on domain semantics. For example, this element could indicate that an instance of moleculeType 'RNA' could have a type of 'mRNA' or 'siRNA'.

The structural topology of the molecular entity. For sequences (e.g., DNA), this could specify 'linear' and 'circular'. More complex entities might be branched or have a quaternary structure.

Reserved for future profiles (e.g., haplotype, genotype).

A defined location on a molecular entity. Location definitions may vary with respect to coordinate space and precision or level of granularity.

A location on a sequence, defined using a nucleotide coordinate system.

A reference to a sequence on which the location is defined.

An interval on a sequence, defined by coordinate-based start and end coordinates.

A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).

The normalization method used for determining a location within the coordinate system. Examples include left shift (e.g., VCF), right shift (e.g., HGVS), or fully justified (e.g., VOCA).

The start location of the interval expressed as a precise coordinate (Quantity) or expressed as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported.

The end location of the interval expressed as a precise coordinate (Quantity) or as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported..

The specific strand at the coordinateInterval, when the interval alone is not sufficient to define a location (e.g., double stranded DNA). Example values include 'forward' and 'reverse'.

A location on a sequence, defined using cytobands.

The reference genome assemble.

Species of the organism.

The build number of this genome assemble.

The accession of this genome assemble.

The description of this genome assembly.

The Cytoband Interval.

The chromosome where this cytoband interval occurs.

The start of this cytoband Interval.

The arm of this start interval.

The region of this start interval.

The band of this start interval.

The sub-band of this start interval.

The end of this cytoband Interval.

The arm of this end interval.

The region of this end interval.

The band of this end interval.

The sub-band of this end interval.

Reserved and possibly deprecated.

A representation of a molecular entity, specifically including sequence. Note this element is intended to define the entity primarily through computable, discrete elements that express domain semantics rather than replicating a particular file format or relational schema.

The domain concept that is the focus of the representation. This element is used to disambiguate the representations of the “reference” and the “alternate” alleles at a given location, for example.

A code (e.g., sequence accession number) used to represent a molecular entity.

A molecular entity defined as a string literal.

The encoding used for the expression of the entity. For a primary sequence, this element represents the alphabet used (e.g., 1 character DNA without ambiguity codes, 3 character amino acid codes).

A string literal representation of the molecular entity, using a specific encoding. For example, this may be the primary sequence of a strand of DNA.

A resolvable representation of a molecular entity, which may be specified as a URI and/or attached document (in a defined format).

A molecular entity that is represented as a portion of a different entity. For example, this element can represent a subsequence (e.g., genetic region) that is part of and conceptually extracted from a longer sequence (e.g., chromosome sequence). The “parent” entity is specified in startingMolecule and the location of the intended molecular entity on the parent entity is defined by coordinateInterval.

A reference to the molecular entity that serves as the conceptual 'parent' from which the intended entity is derived. For example, this could be a chromosome sequence on which a coordinateInterval is defined.

The interval on startingMolecule that defines the portion to be extracted in order to create the intended entity.

The coordinate system used to define the location, which may vary depending on application or context of use.

A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).

The normalization method used for determining a location within the coordinate system. Examples include left shift (e.g., VCF), right shift (e.g., HGVS), or fully justified (e.g., VOCA).

The start location of the interval expressed as a precise coordinate (Quantity) or expressed as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported.

The end location of the interval expressed as a precise coordinate (Quantity) or as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported..

A flag that indicates whether the extracted sequence should be reverse complemented in order to produce the intended entity. This element is only relevant to molecular entities that support the concept of reverse complement (e.g., double stranded DNA).

A representation of a molecular entity that is expressed as a number of copies of a repeated motif.

The motif that is repeated in tandem, which ultimately defines the intended molecular entity.

The number of times the motif is repeated to create the intended molecular entity.

A representation comprised of an ordered concatenation of two or more molecular entities.

One of the concatenated entities within the concatenated representation.

At least two elements are required to represent a concatenated sequence.

A reference to the sequence that defines this specific concatenated element.

The ordinal index of the element within the concatenated representation.

0 or 1 based indices are possible, could potentially skip numbers in the sequence, suggest implementers sort numerically prior to concatenating

A molecular entity represented as an ordered series of edits on a specified starting entity. This representation can be used to define one entity relative to another.

The molecular entity that serves as the starting point, on which edits will be applied.

A defined edit (change) to be applied to the molecular entity.

Edits are applied sequentially. The sequence that results from one edit operation is used as the 'starting' sequence of the next edit operation.

Defines the order of edits when multiple edits are to be applied to the startingMolecule. This is important when edits may overlap (intervals) or when edits change the length of the entity.

The interval on startingMolecule that defines the portion to be extracted in order to create the intended entity.

The coordinate system used to define the location, which may vary depending on application or context of use.

A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).

The normalization method used for determining a location within the coordinate system. Examples include left shift (e.g., VCF), right shift (e.g., HGVS), or fully justified (e.g., VOCA).

The start location of the interval expressed as a precise coordinate (Quantity) or expressed as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported.

The end location of the interval expressed as a precise coordinate (Quantity) or as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported..

The molecular entity that serves as the replacement in the edit operation. After the edit has been applied, the state of the entity at the specified coordinateInterval is defined by the state of the replacementMolecule.

The portion of the molecular entity that is replaced by the replacementMolecule as a result of the edit. The value of this element can be derived as the state of the entity at the specified coordinateInterval, prior to the edit being applied. It is provided for convenience.