Versions Compared

Old Version 11

changes.mady.by.user Rachel Eastwood

Saved on

compared with

New Version 12

changes.mady.by.user Philip Trevvett

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Adaptermappings for i2b2 Demo Data:

https://open.med.harvard.edu/svn/shrine/trunk/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.csv

https://open.med.harvard.edu/svn/shrine/trunk/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.xml

Mapping Ontology to Local Site:

  • Mappings can be loaded as xml file or csv file (see mapping files for Demo Data)
  • Mappings should be from SHRINE term to local site term, mapping C_FULLNAME fields with 'SHRINE' prefix for SHRINE terms and prefix from TABLE_ACCESS.C_TABLE_CD for Site terms.
    • Example: "\\SHRINE\SHRINE\Demographics\Age\0-9 years old\0 years old\","\\i2b2_DEMO\i2b2\Demographics\Age\0-9 years old\0 years old\"

Mapping details for specific data elements:

  • Modifier Terms should be mapped in the same format as other terms.  Mappings are not necessary for various M_APPLIED_PATH values, only for C_FULLNAME.  The Demo Ontology includes diagnosis modifiers for Admit, Primary, and Secondary Diagnosis.  While each modifier is represented in multiple rows for each M_APPLIED_PATH value, each Modifier only requires a mapping from SHRINE C_FULLNAME to i2b2 C_FULLNAME:

    • "\\SHRINE\Admit Diagnosis\","\\i2b2_DIAG\Admit Diagnosis\"

  • Query By Values: For SHRINE terms where value based queries are enabled, the mapping should again follow the same format as a standard mapping, however it is also necessary to check the SHRINE.C_METADATAXML against the local i2b2 C_METADATAXML

  • In order for value based queries to work correctly, the <NormalUnits> represented in the SHRINE.C_METADATAXML must be represented in the local i2b2 C_METADATAXML in one of the follow ways:

    • Match local <NormalUnits> to SHRINE <NormalUnits>

    • Include SHRINE <NormalUnits> as local <EqualUnits>

    • If units are not equivalent, include Shrine <NormalUnits> using <ConvertingUnits><Units></Units><MultiplyingFactor></MultiplyingFactor></ConvertingUnits>, listing Shrine units in <units> and the multiplier needed to convert to local i2b2's <NormalUnits> as <MultiplyingFactor>.

Ontology Load Checklist:

  • Ontology navigation for each data element in webclient
  • Ontology search by code in webclient works for each data element
  • Ontology search by name in webclient works for each data element

...