NCI Thesaurus vocabulary===
This section describes the steps to download and install a full version of the NCI Thesaurus for the LexEVS Service.
Step |
Action |
|---|
!style="background:#CCCCCC;"| Step
!style="background:#CCCCCC;"| Action
|
<center>1</center> |
Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ |
[[Image:Ftp\_Directory.jpg]]
|
<center>2</center> |
Select the version of NCI Thesaurus OWL you wish to download. Save the file to a directory on your machine. |
|
<center>3</center> |
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 |
|
<center>4</center> |
Using the LexEVS utilities load the NCI Thesaurus |
<tt>'''''cd
/admin'''''</tt>
For Windows installation use the following command
<tt>'''''LoadOWL.bat –in "file:///
/Thesaurus_10.10d.owl"'''''</tt>
For Linux installation use the following command
<tt>'''''LoadOWL.sh –in "file:///
/Thesaurus_10.10d.owl"'''''</tt>
} |
''Table 7 – Example output from load of NCI Thesaurus 05.12f''
…
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
===NCI Metathesaurus vocabulary===
=====Loading the Metathesaurus=====
This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service.
{| style="width:800px;" border="0"
!style="background:#CCCCCC;"| Step
!style="background:#CCCCCC;"| Action
|
<center>1</center> |
Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ |
[[Image:Ftp\_Client.jpg]]
|
<center>2</center> |
Select the version of NCI Metathesaurus RRF you wish to download. Save the file to a directory on your machine. |
|
<center>3</center> |
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. Note: RELASE_INFO.RRF is required to be present for the load utility to work. |
|
<center>4</center> |
Using the LexEVS utilities load the NCI Thesaurus |
<tt>'''''cd
/admin'''''</tt>
For Windows installation use the following command
<tt>'''''LoadMetaBatch.bat –in "file:///
/" '''''</tt>
For Linux installation use the following command
<tt>'''''LoadMetaBatch.sh –in "file:///
/"'''''</tt>
} |
===== Resuming Loads =====
Since this loader is resource hungry we provide the option to restart should you find your resource settings to be inadequate. Resuming loads which have crashed or been interrupted by server problems is possible using the ResumeBatchLoad script set.
{| style="width:800px;" border="0"
!style="background:#CCCCCC;"| Step
!style="background:#CCCCCC;"| Action
|
<center>1</center> |
Using the LexEVS utilities load the NCI Thesaurus |
<tt>'''''cd
/admin'''''</tt>
For Windows installation use the following command
<tt>'''''ResumeMetaBatch.bat –in "file:///
/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"'''''</tt>
For Linux installation use the following command
<tt>'''''ResumeMetaBatch.sh –in "file:///
/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"'''''</tt>
} |
===NCI History===
This section describes the steps to download and install a history file for NCI Thesaurus.
{| style="width:800px;" border="0"
!style="background:#CCCCCC;"| Step
!style="background:#CCCCCC;"| Action
|
<center>1</center> |
Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/ |
|
<center>2</center> |
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. |
|
<center>3</center> |
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 |
|
<center>4</center> |
Using the LexEVS utilities load the NCI Thesaurus |
<tt>'''''cd
/admin'''''</tt>
For Windows installation use the following command
<tt>'''''LoadNCIHistory.bat –nf –in "file:///
" –vf “file:///NCI_HISTORY_DIRECTORY}/VersionFile”'''''</tt>
For Linux installation use the following command
<tt>'''''LoadNCIHistory.sh –nf –in "file:///
" –vf “file:///NCI_HISTORY_DIRECTORY}/VersionFile” '''''</tt>
} |