Page History
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- Create Concepts in Concept_Dimension table
- Create entries in metadata table (metadata_genomics in our example)
- Create an entry in the Table_Access table
Concepts Entries:
Variants are differences between two genomes. We have considered the following 2 important types of variants:
...
Variant/Concept Name | Concept Code |
SNP | SO:0001483 |
indel | SO:1000032 |
Metadata Entries:
The metadata table entries determine the Ontology hierarchical structure of concepts as presented by i2b2 web-client. They also determine the names and data type of concepts and operators to apply on them as part of ValueMetadata in the “C_METADATAXML” field in metadata table (metadata_genomics in our example)
...
Sample scripts to create and insert Genomics data in metadata_genomics table can be found inside the package in “Scripts for Sample Data” folder.
Table_Access Entries:
Table_Access table entry determines which metadata table should i2b2 consider to generate the correct Ontology structure.
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- In the background the CRC will convert the request XML to a proper SQL Server contains statement (in case of SQL Server DB)this example below):
with t as (
select f.patient_num
from dbo.observation_fact f
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.
