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#4560 - Describe how to use ELK to process Snomed before import
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- Add recommendation to use ELK to generate missing statements and to enable the read-only mode
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reckart committed Feb 25, 2024
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Expand Up @@ -386,6 +386,17 @@ snomed-ct:
- Convert the _RD2_ data to _OWL Functional Syntax_ using the [snomed-owl-toolkil](https://github.com/IHTSDO/snomed-owl-toolkit)
- Convert the _OWL Functional Syntax_ data to _RDF/XML_ e.g. using [Protégé](https://protege.stanford.edu)
- Import the _RDF/XML_ file into the knowledge base created from this profile (this may take a while)
At this point, you will be able to link against SNOMED concepts, but the tree browser will not be able to find
certain concepts. To fix this, an additional step has to be performed:
- Obtain a copy for the [ELK Reasoner standalone executable](https://github.com/liveontologies/elk-reasoner/releases)
- Use ELK to classify the SNOMED _OWL Functional Syntax_ data: <br>
`java -jar elk-standalone.jar -i snomed-file.owl -c -o snomed-classified-file.owl`
- Convert the classified file produced by ELK from _OWL Functional Syntax_ data to _RDF/XML_ e.g. using [Protégé](https://protege.stanford.edu)
- Import that convered classified _RDF/XML_ into same knowledge base that already contains the other SNOMED data
After all imports are complete, enable the _read only_ checkbox - this enables an internal cache and improves performance.
host-institution-name: SNOMED International
website-url: https://www.snomed.org
license-url: https://www.snomed.org/get-snomed

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