ARCHETYPE Phenopacket SpdiAllele (openEHR-EHR-CLUSTER.pp_spdiallele.v0)

ARCHETYPE IDopenEHR-EHR-CLUSTER.pp_spdiallele.v0
ConceptPhenopacket SpdiAllele
DescriptionSpdiAllele
UseTools for interconversion between SPDI, HGVS and VCF exist at the NCBI. SPDI stands for S = SequenceId P = Position , a 0-based coordinate for where the Deleted Sequence starts D = DeletedSequence , sequence for the deletion, can be empty I = InsertedSequence , sequence for the insertion, can be empty For instance, Seq1:4:A:G refers to a single nucleotide variant at the fifth nucleotide ( nucleotide 4 according to zero-based numbering) from an A to a G. See the SPDI webpage for more examples. The SPDI notation represents variation as deletion of a sequence (D) at a given position (P) in reference sequence (S) followed by insertion of a replacement sequence (I) at that same position. Position 0 indicates a deletion that starts immediately before the first nucleotide, and position 1 represents a deletion interval that starts between the first and second residues, and so on. Either the deleted or the inserted interval can be empty, resulting a pure insertion or deletion. Note that the deleted and inserted sequences in SPDI are all written on the positive strand for two-stranded molecules.
PurposeThis option can be used as an alternative to the VcfAllele, and describes variants using the Sequence Position Deletion Insertion (SPDI) notation. We recommend that users familiarize themselves with this relatively new notation, which differs in important ways from other standards such as VCF and HGVS.
References
Copyright© openEHR Foundation
AuthorsAuthor name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
Other Details LanguageAuthor name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
OtherDetails Language Independent{licence=This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/., custodian_organisation=openEHR Foundation, original_namespace=org.openehr, original_publisher=openEHR Foundation, custodian_namespace=org.openehr, MD5-CAM-1.0.1=9F513AD41E5D638C8CCC85E35FB18EAD, build_uid=a6dbe31a-5136-43e5-b225-c4c6d8e5fb39, revision=0.0.1-alpha}
Keywords
Lifecyclein_development
UID02834644-cadd-4a05-8f8f-b78eabe149c5
Language useden
Citeable Identifier1013.1.4149
Revision Number0.0.1-alpha
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