i2b2 Ontology and CRC Discussion: 1

Questions asked and points to ponder. Access to the demo database is useful here...

Ontology Cell tables compared to CRC concept_dimension table

There are three ontology tables within the demo Ontology cell: birn, i2b2 and custom_meta.

When I do a select count(*) from <table_name> where c_visualattributes like '%LA%' I get the following figures:

• birn: 37
• custom_meta: 0
• i2b2: 93807

When I do a "select count(*) from concept_dimension" within the CRC cell I get a count of 73590.

The totals are 93844 as opposed to 73590. Why is there a difference and what does it mean?

In an Ontology table, what does c_columndatatype really mean?

The docs state: "either ‘T’ for text or ‘N’ for numeric and describes the datatype of the concept". Yet the length of the column is varchar 50.

Within the demo project:

• select count(*) from i2b2 where c_columndatatype like '%N%' ===> returns 0
• select count(*) from i2b2 where c_columndatatype like '%T%' ===> returns 134762
• select count(*) from i2b2 ===> returns 134762

Yet within the query tool (from the Workbench) I can select terms from a Labtest and constrain by value. This is undoubtedly possible because of the optional metadataxml column. But even so, what does c_columndatatype really mean?

Facts constrained by enumerated concepts

Facts can be constrained by simply pointing at a concept row within the concept_dimension table with very little else alongside it. For example, a numeric value like AGE can be divided into an enumeration of concepts, say one for each age from 0 to 114, as is the demo system. Here is a selection based upon this:

select * from observation_fact where concept_cd like 'DEM|AGE:50' ;

This retrieved 3 rows from the fact table: ENCOUNTER_NUM PATIENT_NUM CONCEPT_CD PROVIDER_ID START_DATE MODIFIER_CD VALTYPE_CD TVAL_CHAR NVAL_NUM VALUEFLAG_CD QUANTITY_NUM INSTANCE_NUM UNITS_CD END_DATE LOCATION_CD CONFIDENCE_NUM OBSERVATION_BLOB UPDATE_DATE DOWNLOAD_DATE IMPORT_DATE SOURCESYSTEM_CD UPLOAD_ID 2005000014 1000000014 DEM|AGE:50 @ 22-MAY-06 @ @ - - - - - @ 25-APR-07 @ - - 25-APR-07 25-APR-07 25-APR-07 DEMOGRAPH|DEMO - 2005000082 1000000082 DEM|AGE:50 @ 25-MAY-06 @ @ - - - - - @ 25-APR-07 @ - - 25-APR-07 25-APR-07 25-APR-07 DEMOGRAPH|DEMO - 2005000095 1000000095 DEM|AGE:50 @ 05-MAY-07 @ @ - - - - - @ 25-APR-07 @ - - 25-APR-07 25-APR-07 25-APR-07 DEMOGRAPH|DEMO -