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Demo Downloads
Shrine Core Ontology:
https://open.med.harvard.edu/svn/shrine/trunk/-ontology/SHRINE_Demo_Downloads/trunk/ShrineDemo.sql
Adaptermappings for i2b2 Demo Data:
https://open.med.harvard.edu/svn/shrine/trunk/-ontology/SHRINE_Demo_Downloads/trunk/AdapterMappings_i2b2_DemoData.csvhttps://open.med.harvard.edu/svn/shrine/trunk/ontology/SHRINE_Demo_Downloads/AdapterMappings_i2b2_DemoData.xml
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:
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- 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>
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- 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 |
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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 |
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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). |