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Most terminology loads can be easily accomplished by pointing either the LexEVS commands or the LexEVS administrative GUI at the terminology source file and running the loader. Generic loading instructions can be found for the LexEVS administrative GUI or the LexEVS loader commands. For many source formats you can use a variation of the following LexEVS command:
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This LexEVS loader command loads input in OWL format. Substituting the matching LexEVS loader command for the source format being used and pointing the loader to a local file will load most terminologies. For example, the OBO source format would be loaded by the LoadOBO command. In the LexEVS administrative GUI, all of the various source format loaders are found under the "Load Terminology" menu. The administrative options must be enabled first in the Command menu.
It is important to note that many terminology providers produce more than one source format that can be downloaded. Things like text only, CSV, tab delimited, and spreadsheets are not acceptable source formats for LexEVS. If you can not find an acceptable source format for a popular terminology there are potentially a couple other ways to download them. This is true of things like LOINC, SNOMED, and MedDRA, etc.
- Get the entire UMLS terminology and subset it with a tool called MetamorphoSys.
- Try to download versions that have been placed on BioPortal.
Best Practices
As you work with terminologies in LexEVS there are some things that you will find are the best way to approach things to make life easy as far as loading goes.
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