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1

Download and install the UMLS Metathesaurus:
Loading to LexEVS from these source files requires that they reside locally so it can be accessed quickly from LexEVS.  This is not just a download. The UMLS Metathesaurus also has install steps that are documented by NLM on the UMLS website.

2

Subset the desired terminology (recommended):
Once the UMLS Metathesaurus is installed, users can either load the entire set of files to LexEVS by pointing to the containing file directory or they can use the UMLS MetamorphoSys tool to subset a terminology.  Subsetting the terminology is the same as creating a smaller set with only your desired concepts. For example, you can select to subset out one of the source terminologies that make up the UMLS. This provides improved performance during loads and is typical when you want only one of the original source coding schemes. Again, the documentation to use MetamorphoSys to subset out a terminology is on the UMLS website.

3

Set command line options in the loading script:
If you are loading a subset you may or may not need to change the memory options. If you load the entire UMLS Metathesaurus, we usually recommend use of the command line options. 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 <LEXEVS_HOME>/admin. If a user is working on a Linux environment with a 64 bit architecture, then they can use the LoadUmlsBatch.sh file.  On a server class computer with say 16 gigabytes of memory and 8 four core processors users can access fairly substantial resources to load content. Open the .sh file with a text editor and edit the values for -Xmx and -XX:MaxPermSize as follows "-Xmx6000M -XX:MaxPermSize=256M" or more if you have adequate resources available.

If you have not set the DB_PRIMARY_KEY value to SEQUENTIAL_INTEGER as described under best practices it could take 33 hours to load a terminology as large as SNOMED which otherwise could complete in 4 hours.

4

Find the SAB (RSAB) in the MRSAB.RRF file:
Both the LexEVS Administrative GUI and the LexEVS Administrative commands require the user to enter a SAB or source abbreviation when loading RRF files. This requires that you either know this source abbreviation, or find it in the MRSAB.RRF file contained in the folder of the UMLS installation or the subset you made for the terminology you wish to load. We recommend you open this file in a text editor and search on the terminology name, for instance SNOMED and you should find a line with that name in a row of text separated by a “pipe” character or “ | ”.

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The current format of UMLS has the RSAB in column four, which in the case of SNOMED is "SNOMEDCT".  Notice that this is a licensed terminology and all use must be in accordance with the licensing agreements.

5

Load the Terminology from the command line referencing the SAB.
 

./LoadUmlsBatch.sh -in "file:///data/phont/ontologies/2011AA" -s "SNOMEDCT"

Note:

The

file

path

is

pointing

to

the

directory

directly

above

the

.RRF

files.

6

Monitor output (optional):

The

output

from

the

UMLS

batch

loader

indicates

steps

of

the

batch

load

and

can

be

monitored

from

the

logs

at

<LexEVS

Install

Root>/logs/LexBIG_load_log.text.

If

you

are

on

Linux

this

can

be

done

using:

Sample

output

of

an

early

load

step

is

as

follows:
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Sample output of a final load step:
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1

Open the lbGUI

2

Find in the table the terminology with the broken or stopped load
This should have a status of pending

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3

Highlight and double click the terminology row in the table

4

On the resulting window note for the following command line execution:
The URI and the version.
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5

Using the LexEVS utilities restart the load of the RRF source:

<LEXEVS_HOME>/admin

For Windows installation use the following command:

ResumeUmlsBatch.bat-in [file:///home/LargeStorage/ontologies/rrf/RXNORM/2011AA/] \-s RXNORM \-uri "urn:oid:2.16.840.1.113883.6.88" \-version "10AB_110307F"

For

Linux

installation

use

the

following

command: