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Step

Action

1

Using a web or ftp client go to the URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/

Image Removed

screenshot of FTP directory

2

Select the version of NCI Thesaurus OWL you wish to download. Save the file to a directory on your machine.

3

Extract the OWL file from the zip download and save in a directory on your machine. This directory will be referred to as NCI_THESAURUS_DIRECTORY

4

Using the LexEVS utilities load the NCI Thesaurus:

Code Block
cd {LexBIGLEXEVS_DIRECTORYHOME}/admin

For Windows installation use the following command:

Code Block
LoadOWL.bat –in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl

For Linux installation use the following command:

Code Block
LoadOWL.sh –in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl
Note
titleNote

The NCI Thesaurus has grown large enough that it can no longer be loaded on many typical desktop machines. We recommend a 64-bit operating system running on a multiprocessor computer with a minimum of 4g of memory. Server class Linux machines are the typical target for these loads. The time to load NCI Thesaurus will vary depending on machine, memory, and disk speed. Expect a couple of hours for a higher end machine.

Example output from load of NCI Thesaurus 05.12f

Code Block
 …
[LexBIG] Processing TOP Node... Retired_Kind
[LexBIG] Clearing target of NCI_Thesaurus...
[LexBIG] Writing NCI_Thesaurus to target...
[LexBIG] Finished loading DB - loading transitive expansion table
[LexBIG] ComputeTransitive - Processing Anatomic_Structure_Has_Location
[LexBIG] ComputeTransitive - Processing Anatomic_Structure_is_Physical_Part_of
[LexBIG] ComputeTransitive - Processing Biological_Process_Has_Initiator_Process
[LexBIG] ComputeTransitive - Processing Biological_Process_Has_Result_Biological_Process
[LexBIG] ComputeTransitive - Processing Biological_Process_Is_Part_of_Process
[LexBIG] ComputeTransitive - Processing Conceptual_Part_Of
[LexBIG] ComputeTransitive - Processing Disease_Excludes_Finding
[LexBIG] ComputeTransitive - Processing Disease_Has_Associated_Disease
[LexBIG] ComputeTransitive - Processing Disease_Has_Finding
[LexBIG] ComputeTransitive - Processing Disease_May_Have_Associated_Disease
[LexBIG] ComputeTransitive - Processing Disease_May_Have_Finding
[LexBIG] ComputeTransitive - Processing Gene_Product_Has_Biochemical_Function
[LexBIG] ComputeTransitive - Processing Gene_Product_Has_Chemical_Classification
[LexBIG] ComputeTransitive - Processing Gene_Product_is_Physical_Part_of
[LexBIG] ComputeTransitive - Processing hasSubtype
[LexBIG] Finished building transitive expansion - building index
[LexBIG] Getting a results from sql (a page if using mysql)
[LexBIG] Indexed 0 concepts.
[LexBIG] Indexed 5000 concepts.
[LexBIG] Indexed 10000 concepts.
[LexBIG] Indexed 15000 concepts.
[LexBIG] Indexed 20000 concepts.
[LexBIG] Indexed 25000 concepts.
[LexBIG] Indexed 30000 concepts.
[LexBIG] Indexed 35000 concepts.
[LexBIG] Indexed 40000 concepts.
[LexBIG] Indexed 45000 concepts.
[LexBIG] Indexed 46000 concepts.
[LexBIG] Getting a results from sql (a page if using mysql)
[LexBIG] Closing Indexes Mon, 27 Feb 2006 01:44:22
[LexBIG] Finished indexing

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Step

Action

1

Using a web or ftp client go to the URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/

Image Removed

screenshot of FTP directory

2

Select the version of NCI Metathesaurus RRF you wish to download. Save the file to a directory on your machine.

3

Extract the RRF files from the zip download and save in a directory on your machine. This directory will be referred to as NCI_METATHESAURUS_DIRECTORY.

Info
titleNote

RELASE_INFO.RRF is required to be present for the load utility to work.

4

Using the LexEVS utilities load the NCI Thesaurus:

Code Block
{LexBIGLEXEVS_DIRECTORYHOME}/admin

For Windows installation use the following command:

Code Block
LoadMetaBatch.bat –in "file:///{NCI_METATHESAURUS_DIRECTORY}/"

For Linux installation use the following command:

Code Block
LoadMetaBatch.sh –in "file:///{NCI_THESAURUS_DIRECTORY}/"

...

Step

Action

1

Using the LexEVS utilities load the NCI Thesaurus:

Code Block
{LexBIGLEXEVS_DIRECTORYHOME}/admin

For Windows installation use the following command:

Code Block
ResumeMetaBatch.bat –in "file:///{NCI_METATHESAURUS_DIRECTORY}/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"

For Linux installation use the following command:

Code Block
ResumeMetaBatch.sh –in "file:///{NCI_THESAURUS_DIRECTORY}/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"

...

Step

Action

1

Using a web or ftp client go to the URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/

Image Removed

2

Select the version of NCI History you wish to download. Save the file to a directory on your machine. Select the VersionFile download to the same directory as the history file.

3

Extract the History files from the zip download and save in a directory on your machine. This directory will be referred to as NCI_HISTORY_DIRECTORY

4

Using the LexEVS utilities load the NCI Thesaurus:

Code Block
cd {LexBIGLEXEVS_DIRECTORYHOME}/admin

For Windows installation use the following command:

Code Block
LoadNCIHistory.bat –nf –in "file:///{NCI_HISTORY_DIRECTORY}" –vf “file:///NCI_HISTORY_DIRECTORY}/VersionFile”

For Linux installation use the following command:

Code Block
LoadNCIHistory.sh –nf –in "file:///{NCI_HISTORY_DIRECTORY}" –vf “file:///NCI_HISTORY_DIRECTORY}/VersionFile”

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