Page History

...

shrine { 
...
  adapter {
...
    adapterMappingsFileName = "RenamedAdapterMappings.csv"
...
  }
...
} 

How and When to edit or change an

...

AdapterMappings file.

It is critical that your SHRINE host is using an ontology mappings AdapterMappings file that is specific to the network and local i2b2 that you are working with. If your network ontology and local i2b2 ontology are the same, then you can use a one-to-one mapping file following the below steps, or create one if one does not already exist. (A one-to-one mapping file should generally be provided by whoever is setting up the network/releasing the network ontology.)

...

The end product will be a 2 column csv file, with the same base strings in both columns (a 1-to-1 mapping), differing only in the prepended C_TABLE_CD if necessary.

Column 1 represents concepts in the SHRINE (network) ontology, and is created by prepending “\\” AND the appropriate C_TABLE_CD value from the network ontology’s TABLE_ACCESS table to the C_FULLNAME field from the metadata tables. (These values can be accessed by refering referring to the SHRINE ontology source files used to generate SHRINE indices.)

...

• As with a 1-to-1 mapping file, C_FULLNAME values will need to be prepended with “\\” AND the appropriate C_TABLE_CD value from each TABLE_ACCESS. (Column 1 values will be prepended with the appropriate C_TABLE_CD from the SHRINE Network ontology’s TABLE_ACCESS Table, and Column 2 will be prepended with the appropriate C_TABLE_CD from the local i2b2 TABLE_ACCESS Table.
• 1-to-Many mappings may be necessary when managing a customer custom mapping file
• When hierarchical folders do not align between ontologies, the hierarchical folders in the network ontology will need to be mapped to the appropriate set of specific concepts. (When a corresponding folder does not exist in the local ontology).
• Concepts that have the following C_VISUALATTRIBUTE values do not need to be mapped: FH, FI, LH, LI.
• These concepts cannot actually be included in a SHRINE query, so do not need to be mapped.

...