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Coding Systems to Add:81259-4 Probable Associated PhenotypeDisease OntologyWebsite: Downloads: The?Disease Ontology?has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. OMIM (Online Mendelian Inheritance in Man)Website: Downloads: OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes, containing information on all known Mendelian disorders and over 15,000 genes. OrphanetWebsite: Downloads: Orphanet is resource aiming to provide information on rare diseases, each of which is assigned a unique and stable identifier, the ORPHA number. Orphanet provides information on every gene related to a rare disorder, including genetic international nomenclature, the gene typology (gene with protein product, locus, non-coding RNA), the chromosomal location, the cross-mappings with international genetic databases.MeSH Website: Downloads: MeSH provides a hierarchically-organized terminology for indexing and cataloging of biomedical information such as MEDLINE/PUBmed and other NLM databases. We would use Category C, which lists diseases. 81252-9 Discrete genetic variant 81260-2 Complex genetic variantCanonical Allele Identifier – Clingen Website: Downloads: (API)The Canonical Allele Identifier is a unique identifier, within a system, that can be associated with equivalent alleles. It represents an aggregation of the many representations of the Allele entity into a single object with a stable identifier. One feature of canonicalization that differs from common usage is that alleles on amino acid sequences are canonicalized separately from alleles on nucleic acid sequencesContextual Allele ID – ClingenWebsite: Downloads: (API)ContextualAllele is a resource representing one of the multiple variant sequences at a contiguous region in a particular ReferenceSequence. A ContextualAllele should either represent a contiguous section of the ReferenceSequence, or the replacement of such a section with a new contiguous section (including an empty section for a deletion). Each ContextualAllele is the representation of an allele within a single sequence. For example, if a variant occurs within the coding region of a transcript, three different ContextualAlleles will be used to represent the same variant: one representing the allele in the context of the ReferenceSequence for the genome, a second representing the allele in the context of the ReferenceSequence for the transcript, and a third in the context of the ReferenceSequence for the amino acid chain.ClinVar RCVWebsite: 'RCV' refers to the first 3 letters of the accession calculated by ClinVar to aggregate information from all submissions interpreting the same phenotype relative to the same variant or set of variants.?Notes on adding coding systems in V2:Need to register OID OID TypePreferred RealmDesired Symbolic NameFull NameDescriptionSubmitterResponsible BodyAdd coding system to Table 396 (contact Ted Klein) Need to make symbol name, description of system, source ................
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