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There are two value metadata types that accompany the two variant concepts, SNP and indel. The SNP variant concept has the datatype = GENETIC_VARIANT_SNP and indel variant concept has the datatype = GENETIC_VARIANT_INDEL. The concept code of each type is contained in the TestID tag.SNP:
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<?xml version="1.0"?> |
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<ValueMetadata>...
<ValueMetadata> <Version>3.03</Version> |
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<CreationDateTime>01/28/2016</CreationDateTime> |
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<TestID>SO:0001483</TestID> |
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<TestName>SNP</TestName> |
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<DataType>GENETIC_VARIANT_SNP</DataType> |
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<Oktousevalues /> |
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<MaxStringLength>30</MaxStringLength> |
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<EnumValues /> |
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<UnitValues> <NormalUnits/>...
<UnitValues> <NormalUnits/> </UnitValues> |
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</ValueMetadata> |
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<?xml version="1.0"?> |
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<ValueMetadata>...
<ValueMetadata> <Version>3.03</Version> |
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<CreationDateTime>01/28/2016</CreationDateTime> |
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<TestID>SO:1000032</TestID> |
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<TestName>indel</TestName> |
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<DataType>GENETIC_VARIANT_INDEL</DataType> |
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<Oktousevalues /> |
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<MaxStringLength>30</MaxStringLength> |
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<EnumValues /> |
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<UnitValues> <NormalUnits/>...
<UnitValues> <NormalUnits/> </UnitValues> |
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</ValueMetadata> |
Sample scripts to create and insert Genomics data in metadata_genomics table can be found inside the package in “Scripts for Sample Data” folder.
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- In the background the CRC will convert the request XML to a proper SQL Server contains statement (in this example below):
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with t as ( |
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select f.patient_ |
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num from dbo.observation_fact f |
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where...
where f.concept_cd IN |
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(...
( select concept_cd |
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from dbo.concept_ |
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dimension where concept_cd IN ('SO:0001483','SO:1000032') |
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) ...
) AND (modifier_cd = '@' |
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AND |
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valtype_cd = 'B' |
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AND CONTAINS(observation_blob,'rs377573539 AND T_to_C AND (Heterozygous OR Homozygous OR missing_zygosity)') |
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) |
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After the query is executed all patients matching the input genomic variants will be returned to the i2b2 web client.
