Implementation

Demo Downloads

Shrine Core Ontology:

https://open.med.harvard.edu/svn/shrine-ontology/SHRINE_Demo_Downloads/trunk/ShrineDemo.sql

Adaptermappings for i2b2 Demo Data:

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

Ontology tips, do's and don'ts

No forced formatting through additional text in metadata field C_NAME

• Most importantly, leading spaces should not be used for forced order of terms, and will result in errors when such terms are included in queries.
• 1 exception: "zz " can be used as a prefix in C_NAME and will not be displayed.  A term can be forced to appear last in order of appearance by adding prefix  “zz “ to the C_NAME string. This is useful for terms like ‘unknown’ or ‘other’ which may not otherwise appear last in certain demographics categories.

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>.

Example: Albumin SerPl-mCnc (Albumin in Serum or Plasma) - LOINC:1751-7

• The Mapping included in the mapping file will map shrine C_FULLNAME to local i2b2 C_FULLNAME, as with a standard mapping. For the Shrine demo ontology and i2b2 demo data, such a mappings will look like:
  • "\\SHRINE\SHRINE\Labs\LP31388-9\LP15838-3\LP6118-6\LP43038-6\1751-7\","\\i2b2_LABS\i2b2\Labtests\LAB\(LLB16) Chemistry\(LLB21) General Chemistries\ALB\LOINC:1751-7\"

• The C_METADATAXML for the Shrine term includes the following unit specifications:

  • <UnitValues><NormalUnits>g/dL</NormalUnits><EqualUnits>gm/dL</EqualUnits><ExcludingUnits>No Units</ExcludingUnits><ConvertingUnits><Units>mg/dL</Units><MultiplyingFactor>.001</MultiplyingFactor></ConvertingUnits><ConvertingUnits><Units>g/L</Units><MultiplyingFactor>.1</MultiplyingFactor></ConvertingUnits></UnitValues>

  • In the Shrine C_METADATAXML, <EqualUnits> and <ConvertingUnits> are used to enable display options in the shrine Webclient.  Any value based query will only send the units listed in <NormalUnits>, as part of the query message sites receive.

• Following that, the local C_METADATAXML must be aligned with SHRINE C_METADATAXML for any mapped term in one of the three options listed above and detailed below:

  • If the local site uses unit with the same format, then <NormalUnits> should look the same for the local C_METADATAXML as for SHRINE.

  • If the local site uses a different but equivalent unit, (or the same unit but formatted differently), such as gm/dL, then the unit listed for SHRINE in <NormalUnits>, should be included locally in <Equal Units> (g/dL). So the local units within the C_METADATAXML would look like:

    •     <UnitValues><NormalUnits>gm/dL</NormalUnits><EqualUnits>g/dL</EqualUnits>

  • If the local site uses a non-equivalent, but convertible unit, such as mg/dL, then the local C_METADATAXML should include the SHRINE terms <NormalUnits>, as Converting Units, with the appropriate multiplier.  For the above example the local C_METADATAXML units could look like:

    • <UnitValues><NormalUnits>mg/dL</NormalUnits><ConvertingUnits><Units>g/dL</Units><MultiplyingFactor>1000</MultiplyingFactor></ConvertingUnits><ConvertingUnits><Units>g/L</Units><MultiplyingFactor>100</MultiplyingFactor></ConvertingUnits></UnitValues>

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

AdapterMappings Load Checklist

• Queries should execute with expected mapped/unmapped responses
• All mapped terms should return patient count for each mapped site
• Unmapped terms return ‘no mappable local items’

Data Update Load Checklist:

• Data/Counts should return for new dates added
• Counts for old dates should remain consistent
• Total counts for all dates should increase