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10.8.7 Resource MolecularDefinition - Examples

Clinical Genomics icon Work GroupMaturity Level: N/AStandards Status: InformativeSecurity Category: N/A Compartments: No defined compartments


10.8.7.1 Sequence and Sequence Representation

The following examples illustrate instances of a sequence, each designed to demonstrate different uses of the representation element.

10.8.7.1.1 Literal (String)

The following MolecularDefinitions show examples of a sequence represented as a literal. The moleculeType and encoding attributes enable unambiguous interpretation of the sequence value.

10.8.7.1.2 Code (Accession Number)

The following MolecularDefinitions show examples of a sequence represented as a code using an accession number.

  • (example file TBD)

10.8.7.1.3 Resolvable (URL)

The following MolecularDefinitions show examples of a sequence represented as a resolvable URL. Note: this example is currently missing the corresponding instance of DocumentReference.

10.8.7.1.4 Resolvable (File)

The following MolecularDefinitions show examples of a sequence represented as an attached file. Note: this example is currently missing the corresponding instance of DocumentReference.

10.8.7.1.5 Extracted (Subsequence)

The following MolecularDefinitions show examples of a sequence represented as a subsequence extracted from a “parent” sequence. In these examples, a sequence representing the CYP2C19 genetic locus is used as the “parent”, from which three subsequences are extracted (corresponding to the upstream region, gene region, and downstream region).

10.8.7.1.6 Concatenated (Assembly)

The following MolecularDefinitions show examples of a sequence represented as a concatenation of sequence instances. In this example, the three subsequences from the Extracted example are reassembled into the full genetic locus.

10.8.7.1.7 Repeated (Motif)

The following MolecularDefinitions show examples of a sequence represented as a repeated sequence motif. In this use case, the CGG trinucleotide repeat from the FMR1 gene is represented in a compressed form that emphasizes the copyCount (convenient for use cases where the number of repeats is important).

10.8.7.1.8 Relative (Edit)

The following MolecularDefinitions show examples of a sequence represented as a relative sequence, which applies an edit to a starting sequence to create the sequence of interest. In this example, the starting sequence is a perfect CGG trinucleotide that was repeated 20 times (see the repeated motif example). The desired sequence is not a perfect repeat, however, and a single nucleotide must be edited to yield the sequence of interest. The result of this edit operation represents an actual CGG repeat region that is found in the FMR1 gene.

10.8.7.2 Contained Resource

Many instances of MolecularDefinition reference other instances of MolecularDefinition. When references within a message are not desired, contained resources can be used. This example shows how contained resources can be used to create a standalone message. It is the same content that was used in the relative (edit) example, but the references have been changed to contained resources.

10.8.7.3 Allele

The following examples illustrate instances of allele. In this example, the asserted state of the allele is different from the state of the context sequence at the given location. Note: the CG group is still determining how to best represent named alleles; therefore, the reference to the star allele in this example should be considered to be a draft (if not ignored).

10.8.7.4 Variation

The following examples illustrate instances of variation. In this example, the state of the alternate allele is defined as being different from the state of the reference allele, but the same structure could be used to represent a variation where the two alleles are the same. Note that this example uses a 0-based interval coordinate system.

The following example illustrates a tri-allelic polymorphism. In this example, it is necessary to unambiguously specify the reference and alternate alleles, neither of which might match the state of the context sequence at the specified location. The slices on the representation element are needed to support this use case.

  • TBD: tri-allelic example in ABCB1
Example Name id Format
Simple sequence example example XML JSON Turtle
Simple Allele example 1 example-allele1 XML JSON Turtle
Simple Allele example 2 example-allele2 XML JSON Turtle
Simple Allele example 3 example-allele3 XML JSON Turtle
Simple Allele example 4 example-allele4 XML JSON Turtle
Simple Allele example 5 example-allele5 XML JSON Turtle
Simple Allele example 6 example-allele6 XML JSON Turtle
Simple Allele example 7 example-allele7 XML JSON Turtle
Example of Allele including slices example-allelesliced1 XML JSON Turtle
Example of Allele including slices for CYP2C19 position 661 example-allelesliced-cyp2c19-661 XML JSON Turtle
Example of Allele including slices for CYP2C19 position 1016 example-allelesliced-cyp2c19-1016 XML JSON Turtle
Example of Allele including slices for CYP2C19 As Literal example-allelesliced-cyp2c19-literal-only XML JSON Turtle
Example of Allele including slices for HLA00381 example-allelesliced-hla00381 XML JSON Turtle
Simple Genotype example 1 example-genotype1 XML JSON Turtle
Simple Haplotype example 1 example-haplotype1 XML JSON Turtle
Simple Haplotype example 2 example-haplotype2 XML JSON Turtle
Simple Replaced Sequence example example-replaced-sequence XML JSON Turtle
Simple replacement Sequence example example-replacement-sequence XML JSON Turtle
Simple Sequence example 0 to be concatenated example-sequence0-2b-concatenated XML JSON Turtle
Simple Sequence example 1 to be concatenated example-sequence1-2b-concatenated XML JSON Turtle
Simple Sequence example 2 to be concatenated example-sequence2-2b-concatenated XML JSON Turtle
Simple Sequence example 1 example-sequence1 XML JSON Turtle
Simple Sequence example A example-sequence-a XML JSON Turtle
Simple Sequence example Amino Acid A, IUPAC example-sequence-a-aa-iupac XML JSON Turtle
Simple Sequence example DNA A, IUPAC example-sequence-a-dna-iupac XML JSON Turtle
Sequence example for Homo sapiens MHC class I antigen (HLA-B) gene example-sequence-af1961831-url XML JSON Turtle
Simple Sequence example C example-sequence-c XML JSON Turtle
Sequence example of CYP2C19 By Accession Number example-sequence-cyp2c19-accession XML JSON Turtle
Sequence example of CYP2C19 as Attachment example-sequence-cyp2c19-attached XML JSON Turtle
Sequence example of CYP2C19 as URL example-sequence-cyp2c19-url XML JSON Turtle
Example of Sequence of FMR1 Gene example-sequence-fmr1 XML JSON Turtle
Simple Sequence example G example-sequence-g XML JSON Turtle
Simple Sequence example GGC example-sequence-ggc XML JSON Turtle
Simple Sequence example HLA00001-1 example-sequence-hla000011 XML JSON Turtle
Simple Sequence example LRG-584 example-sequence-lrg584 XML JSON Turtle
Example of Sequence of MSH2 Gene example-sequence-msh2 XML JSON Turtle
Example of Sequence of NM_0007694 as URL example-sequence-nm0007694-url XML JSON Turtle
Example of repeated sequence from FMR1 gene example-sequence-repeat XML JSON Turtle
Simple Sequence example T example-sequence-t XML JSON Turtle
Simple Sequence example to be extracted example-starting-sequence-2b-extracted XML JSON Turtle
Simple Sequence example to be relative example-starting-sequence-2b-relative XML JSON Turtle
Example of Variation of MSH2 2503C example-variation1 XML JSON Turtle
Example of Variation of CYP2C19 at Position 661 example-variation-cyp2c19-661 XML JSON Turtle
Example of Variation of CYP2C19 at Position 991 as HGVS example-variation-cyp2c19-991-hgvs XML JSON Turtle
Example of Variation of CYP2C19 at Position 1015 as SPDI example-variation-cyp2c19-1015-spdi XML JSON Turtle
Example of Variation of CYP2C19 at Position 1015 as VRS example-variation-cyp2c19-1015-vrs XML JSON Turtle
Example of Variation of CYP2C19 at Position 1016 as VCF example-variation-cyp2c19-1016-vcf XML JSON Turtle
Example of Sequence of CYP2C19 gene region example-sequence-cyp2c19-gene-region XML JSON Turtle
Example of Sequence of CYP2C19 upstream region example-sequence-cyp2c19-upstream-region XML JSON Turtle
Example of Sequence of CYP2C19 downstream region example-sequence-cyp2c19-downstream-region XML JSON Turtle
Example of Sequence of CYP2C19 of concatenated upstream, gene, and downstream regions example-sequence-cyp2c19-Concatenated-regions XML JSON Turtle
Example of Sequence of FMR1 CGG motif repeated 20 times example-sequence-fmr1-cgg-20x-repeat XML JSON Turtle
Example of Sequence of FMR1 using CGG motifs edited by external referenced sequence resources example-sequence-fmr1-cgg-20x-edited-referenced XML JSON Turtle
Example of Sequence of FMR1 using CGG motifs edited by contained referenced sequence resources example-sequence-fmr1-cgg-20x-edited-contained XML JSON Turtle
Example of Sequence of Homo sapiens chromosome 10, GRCh37.p13 Primary Assembly, NC_000010.10 example-sequence-nc00001010-url XML JSON Turtle
Simple Allele example Pgx-var-1011 example-allelesliced-pgx-var-1011 XML JSON Turtle
Example of Variation of Pgx-var-1011 example-variation-pgx-var-1011 XML JSON Turtle
Example of Variation of Pgx-var-1012 example-variation-pgx-var-1012 XML JSON Turtle
Example of Variation of Pgx-var-1013 example-variation-pgx-var-1013 XML JSON Turtle
Example of Variation of Pgx-var-1014 example-variation-pgx-var-1014 XML JSON Turtle
Example of Variation of Pgx-var-1015 example-variation-pgx-var-1015 XML JSON Turtle
Example of Variation of Pgx-var-1016 example-variation-pgx-var-1016 XML JSON Turtle
Example of Variation of Pgx-var-1017 example-variation-pgx-var-1017 XML JSON Turtle
Example of Variation of Pgx-var-1018 example-variation-pgx-var-1018 XML JSON Turtle
Example of Variation of Pgx-var-1019 example-variation-pgx-var-1019 XML JSON Turtle
Example of Variation of Pgx-var-1020 example-variation-pgx-var-1020 XML JSON Turtle
Example of Variation of Pgx-var-1021 example-variation-pgx-var-1021 XML JSON Turtle
 

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.