...

1. Create Concepts in Concept_Dimension table
2. Create entries in metadata table (metadata_genomics in our example)
3. 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:

...

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.

...

• 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.