[[i2b2 - UHL clinical informatics system integration PATS|Back]]

The PATS mappings are split into text and numeric fields.

== Text Fields

Text fields are mapped to the i2b2 Observation Fact table like this

||i2b2 Field||Source||
||Encounter_Num||i2b2 Patient ID||
||Patient_Num||i2b2 PatientID||
||Concept_Cd||Enum lookup value (see below)||
||Provider_Id||"@"||
||Start_Date||The source table observation date field (see below)||
||Modifier_Cd||"@"||
||ValType_Cd||"T" (text)||
||Units_Cd||"@"||
||Location_Cd||"@"||
||Update_Date||The current date using the GETDATE() Function||
||SourceSystem_Cd||"BRICCS"||
||Upload_Id||"1"||

'''''SOMETIME (RB): Convert Update_Date to use a date parameter.  It's just a little quicker.'''''

'''''SOMETIME (RB): Should the SourceSystem_Cd not be "PATS"? Or maybe "MINAP" or whatever.'''''

'''''SOMETIME (RB): The Upload_Id is presumably always one because everything is reloaded each time.  Might be nice to change this to something more meaningful.'''''

=== Enum Lookup Value

The Concept Code to use is found in the table DATA_DICTIONARY_ENUM_VALUES in the DWBRICCS database on UHLDWH server.  This table contains records for concept code keyed on source table name, column name and column value.  NULL column values may be mapped to the field '(empty)'.

'''''ACTION (RB): Check if all possible values of column value contain a mapping in the ''DATA_DICTIONARY_ENUM_VALUES'' table.'''''

=== Source Table Observation Date Field

For each source table in the there is a single field that is used as the start date for all columns from that field.  The observation date field to use for each table is stored in the ''pats_tables'' table in the DWBRICS on the UHLDWH server.

== Numeric Fields

Numeric fields are mapped to the i2b2 Observation Fact table like this

||i2b2 Field||Source||
||Encounter_Num||i2b2 Patient ID||
||Patient_Num||i2b2 PatientID||
||Concept_Cd||"PTS:{TABLE_NAME}_{COLUMN_ID}"||
||Provider_Id||"@"||
||Start_Date||The source table observation date field (see above)||
||Modifier_Cd||"@"||
||ValType_Cd||"N" (numeric)||
||TVal_Char||"E" (see below)||
||Units_Cd||Value calculated by ufn_get_units function (see below)||
||Location_Cd||"@"||
||Update_Date||The current date using the GETDATE() Function||
||SourceSystem_Cd||"BRICCS"||
||Upload_Id||"1"||

=== TVal_Char

The ''TVal_Char'' describes the meaning of the value contained in the ''NVal_Num'' field.

For all values currently the value of ''TVal_Char'' is set to "E", which means equals.  That is, the value in the ''NVal_Num'' field is the result of the test.  All possible values of ''TVal_Char'' are:

||Value||Meaning||
||E||Equals||
||NE||Not Equal||
||L||Less Than||
||LE||Less Than or Equals||
||G||Greater Than||
||GE||Greater Than or Equals||

From a casual look at the data, I think that a value of less than X, or greater than Y is sometimes used for Pathology data.

=== ufn_get_units Function

The function ufn_get_units in the DWBRICCS database is called with parameters of ''table_name'' and ''field_name'' to determine the units.

'''''ACTION (RB): Work out what this function actually does and then move the logic into a join if possible.  This should be clearer and also quicker.'''''

== Tables

=== CATH_CATHINITIALVW
=== CS2003F_PostProcedure
=== CS2003F_PreProcedure
=== CS2010F_PostProcedure
=== CS2010F_PreProcedure
=== EPS_EPSINIVW
=== GGHMINAP_GGHMINAP
=== GGHMINAPNEW
=== GGHMINAPNEW_GGHMINAPINIVW
=== GGHPACEICD_GGHPACEICDINIALVW
=== GGHPCI_FLWGGHPCIVIEW
=== GGHPCI_INITIALGGHPCIVIEW
=== LRIMINAPNEW
=== LRIMINAPNEW_LRIMINAPNEWINITIALVW
=== VERTED_VERTEDINIALVW