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Loading from UMLS RRF (Rich Resource Format) files
The National Library of Medicine (NLM) regularly releases the Unified Medical Language System regularly releases (UMLS) as a set of terminologies in a large set of files referred to as the UMLS Metathesaurus. LexEVS can load the entire set or individual files from this file set using the LexEVS RRF loader also known as the LexEVS UMLS Batch loader, due it it's memory optimization capabilities. As well .
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The UMLS Metathesaurus tools are briefly discussed on this page. Since all documentation for these are maintained at the website linked to below, only provide brief pointers are provided. Also, LexEVS has a special purpose RRF loader which loads an NCI version of an entire MetaThesaurus |
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. This is explained in Installing NCI Vocabularies in LexEVS 6.x for the NCI loaders. |
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1 | The UML Metathesaurus is controlled by a license from the NLM. You may obtain a free license of the UMLS Metathesaurus on the NLM license site. |
2 | Download and install the UMLS Metathesaurus: |
3 | Subset the desired terminology (recommended):
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4 | Set command line options in the loading script: |
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. This will allow manipulation of the memory allocated for loads of larger terminologies such as SNOMED. Scripting options can be added to the scripts contained at |
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<LEXEVS_HOME>/admin. If a user is working on a Linux environment with a 64 bit architecture, then they can use the |
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LoadUmlsBatch.sh file. |
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On a server class computer with say |
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16 gigabytes of memory and 8 four core processors users can access fairly substantial resources to load content. |
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Open the .sh file with a text editor and edit the values for -Xmx and -XX:MaxPermSize as follows "-Xmx6000M -XX:MaxPermSize=256M" |
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or more if you have adequate resources available. |
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which otherwise could complete in 4 hours.
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5 | Find the SAB (RSAB) in the MRSAB.RRF file: | ||||
6 | Load the Terminology from the command line referencing the SAB.
The file path is pointing to the directory that contains all of the UMLS RRF files. For UMLS there is not a single source format file. | ||||
7 | Monitor output (optional):
Sample output of an early load step is as follows: |
Restarting an RRF Load
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Killed processes cannot be restarted. The load can recover from an application error, but not from any outside activity that stops the process. |
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1 | Open the LexEVS Administrative GUI. | ||||||
2 | If a terminology was temporarily stopped or broke it should have a status of pending. For example, | ||||||
3 | Double click the terminology row in the table. | ||||||
4 | On the resulting window note for the following command line execution: | ||||||
5 | Using the LexEVS utilities restart the load of the RRF source and pass in the location, the SAB, the URI, and the version:
For Windows installation use the following command:
For Linux installation use the following command:
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Install Metathesaurus to a local folder:
Loading from these sources requires that the UMLS Metathesaurus be installed locally so it can be accessed from LexEVS. This can be done according to documentation available on the UMLS website.
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Subset the desired terminology (optional):
Once the Metathesaurus is downloaded and installed, users can either load from the entire set of files by pointing to the containing file directory or they can use the UMLS tools to subset a terminology (recommended). Subsetting the terminology beforehand provides improved performance during loads.
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