Page History
...
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:
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
<?xml version="1.0"?> |
...
<ValueMetadata> |
...
<Version>3.03</Version> |
...
<CreationDateTime>01/28/2016</CreationDateTime> |
...
<TestID>SO:0001483</TestID> |
...
<TestName>SNP</TestName> |
...
<DataType>GENETIC_VARIANT_SNP</DataType> |
...
<Oktousevalues /> |
...
<MaxStringLength>30</MaxStringLength> |
...
<EnumValues /> |
...
<UnitValues> <NormalUnits/> </UnitValues><UnitValues> <NormalUnits/> </UnitValues> </ValueMetadata> |
...
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
<?xml version="1.0"?> |
...
<ValueMetadata> |
...
<Version>3.03</Version> |
...
<CreationDateTime>01/28/2016</CreationDateTime> |
...
<TestID>SO:1000032</TestID> |
...
<TestName>indel</TestName> |
...
<DataType>GENETIC_VARIANT_INDEL</DataType> |
...
<Oktousevalues /> |
...
<MaxStringLength>30</MaxStringLength> |
...
<EnumValues /> |
...
<UnitValues> <NormalUnits/> </UnitValues><UnitValues> <NormalUnits/> </UnitValues> </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.
...
- In the background the CRC will convert the request XML to a proper SQL Server contains statement (in this example below):
| Code Block | ||||
|---|---|---|---|---|
| ||||
with t as ( |
...
|
...
select f.patient_ |
...
num from dbo.observation_fact f |
...
where...
where f.concept_cd IN |
...
(...
( select concept_cd |
...
|
...
from dbo.concept_ |
...
dimension where concept_cd IN ('SO:0001483','SO:1000032') |
...
) ...
) AND (modifier_cd = '@' |
...
|
...
AND valtype_cd = 'B' |
...
AND CONTAINS(observation_blob,'rs377573539 AND T_to_C AND (Heterozygous OR Homozygous OR missing_zygosity)') |
...
) |
...
After the query is executed all patients matching the input genomic variants will be returned to the i2b2 web client.
