Unattributed Code Systems

Copyright Fragment

This fragment is available on en/index.html

This publication includes IP covered under the following statements.

Copyright and Registered Trademark Uses

External References

Type Reference Content
web example.org http://example.org/identifiers/files/11114
web example.org http://example.org/identifiers/files/11111
web example.org http://example.org/identifiers/files/11112
web example.org http://example.org/identifiers/files/11113
web example.org http://example.org/identifiers/files/11115
web example.org http://example.org/files/pgx-variants.vcf
web example.org http://example.org/files/somatic-called-regions.bed
web example.org http://example.org/files/somatic-fusions.vcf
web example.org http://example.org/files/rna-studied-regions.bed
web example.org http://example.org/files/somatic-dna-variants.vcf
web www.genenames.org Include all codes defined in http://www.genenames.org version Not Stated (use latest from terminology server)
web www.ebi.ac.uk https://www.ebi.ac.uk/ena/browser/api/fasta/AF196183.1
web www.ebi.ac.uk https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=imgthla;id=HLA00001;format=fasta;style=raw
web www.lrg-sequence.org Include all codes defined in http://www.lrg-sequence.org version Not Stated (use latest from terminology server)
web github.com Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
web software.broadinstitute.org The data format relevant to genomics. These formats and relevant codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute.
web software.broadinstitute.org The input and output type example codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute.
web www.sequenceontology.org The changeType element has a preferred binding. The codes were based on discussions by Clinical Genomics Workgroup and draw from Sequence Ontology (SO) terms such as SO:0001483 (SNV), SO:0002007 (MNV), SO:1000032 (delins), SO:0001019 (copy_number_variation), SO:0001565 (gene_fusion), and SO:0001576 (transcript_variant). Implementers should use the bound codes where applicable.
web www.bioinformatics.org IUPAC symbols for nucleotide sequences
web iupac.qmul.ac.uk IUPAC symbols for amino acid sequences (1-letter code)
web iubmb.qmul.ac.uk IUPAC symbols for nucleotide sequences (IUBMB)
web iupac.qmul.ac.uk IUPAC symbols for amino acid sequences (3-letter code)
web www.sequenceontology.org Sequence Ontology (SO)
web www.sequenceontology.org The changeType ValueSet enumerates variant consequence types drawn from Sequence Ontology . The binding was upgraded from example to preferred for the same rationale as methodType .
web www.genenames.org HGNC (HUGO Gene Nomenclature Committee) is the authoritative source of approved human gene symbols and identifiers. Using HGNC gene identifiers (e.g., HGNC:76 for ABL1) is clearly preferable to using gene symbols alone (which are subject to change) or NCBI Gene IDs (which are database-internal identifiers). HGNC identifiers are stable, publicly available, and already used throughout the genomics-reporting IG for gene-quantified observations.
web software.broadinstitute.org File format codes (BAM, CRAM, FASTQ, VCF, MAF, BED, etc.) are drawn from the Integrative Genomics Viewer (IGV) documentation by Broad Institute. The binding is example because:

Internal Images

../assets/images/001.svg
../assets/images/001.svg
help.png
help.png
tree-filter.png
tree-filter.png