Demo Downloads
Shrine Core Ontology:
https://open.med.harvard.edu/svn/shrine/trunk/ontology/SHRINE_Demo_Downloads/ShrineDemo.sql
Adaptermappings for i2b2 Demo Data:
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
Test | Action |
---|---|
Ontology navigation for each data element in webclient | Open Webclient, navigate ontology hierarchy for each data-type |
Ontology search by code in webclient works for each data element | Search in webclient for each datatype by code of term. Expected term should return. |
Ontology search by name in webclient works for each data element | Search in webclient for each datatype by name of term. Expected term should return. |
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’
Test | Action |
---|---|
Confirm query returns via small sample test prior to programmatic test | Run sample of basic queries to confirm response |
All mapped terms should complete query for each mapped site | Run Scan tool to programmatically test all ontology terms. Compare pre-generated list of mapped local terms to Scan tool results. |
Unmapped terms return ‘no mappable local items’ | Compare pre-generated list of unmapped local terms to Scan tool results |
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
Test | Action |
---|---|
Data/Counts should return for new dates added | Execute single term queries with new dates specified. |
Counts for old dates should remain consistent | Execute single term queries with previously loaded dates specified. Compare results with previously returned counts (prior to data update). |
Total counts for all dates should increase | Execute single term queries with previously loaded dates specified. Compare results with previously returned counts for all dates (prior to data update). |