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standardhealth / fsh-mcode

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Cannot bind to code systems #37

Closed markkramerus closed 4 years ago

markkramerus commented 4 years ago

There were several places where we were attempting to bind to a code system, instead of a value set, for example, this line: component[GenomicDNAChange].valueCodeableConcept from HGVS and this: * component[GeneStudied].valueCodeableConcept from HGNC

Be careful because neither of these are value sets. They are both code systems.

markkramerus commented 4 years ago

Fixed. Created new value sets as follows:

ValueSet:    ClinVarVS
Title: "ClinVar Value Set"
Description: "Value set of human genetic variants, drawn from [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/). The codes in this value set refer to the ClinVar Variation ID, or the identifier for the variant or set of variants that were interpreted. [Source: NCBI ClinVar Data Dictionary](https://www.ncbi.nlm.nih.gov/projects/clinvar/ClinVarDataDictionary.pdf)"
* codes from system CLINVAR

ValueSet:  HGNCVS
Title: "HUGO Gene Nomenclature Committee Gene Names Value Set"
Description: "HUGO Gene Nomenclature Committee Gene Names Value Set"
* codes from system HGNC

ValueSet: HGVSVS
Title: "Human Genome Variation Society Sequence Variant Nomenclature Value Set"
Description: "HGVS nomenclature is used to report and exchange information regarding variants found in DNA, RNA, and protein sequences."
* codes from system HGVS