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* release/31.x:
  #4560 - Describe how to use ELK to process Snomed before import

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%	inception/inception-kb/src/main/resources/de/tudarmstadt/ukp/inception/kb/yaml/knowledgebase-profiles.yaml
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reckart committed Feb 26, 2024
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Expand Up @@ -373,6 +373,16 @@ snomed-ct:
- Download SNOMED CT RD2 data files, e.g. from the [National Library of Medicine](https://www.nlm.nih.gov/healthit/snomedct/international.html)
- The RD2 package contains a data file in _OWL Functional Syntax_ wiht the ending `.owl` - rename the file to end in `.ofn`
- Import the renamed 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.ofn -c -o snomed-classified-file.ofn`
- Import that converted classified file 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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