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If you are reading this page then you know that LexEVS is an enterprise wide terminology server. When first installed it comes with no terminologies loaded into it. This documentation will cover the means for loading most content types that can be loaded. LexEVS was built to accommodate a wide variety of input and meld it into a common form unifying many common formats. This necessitates a variety of loaders, each used on a specific incoming format.
LexEVS provides both a LexEVS administrative GUI and LexEVS loader commands to load terminologies. While the LexEVS administrative GUI is very functional, a system administrator may prefer the command line interface because command scripts can be adjusted to increase memory and tune other java virtual machine settings to insure that loads of larger terminologies have adequate resources. For example, a user may select a loading script, open it in an editor, increase the java heap size and PermGen memory, depending on the machine’s resources, and save the script before running with the appropriate options written into the command line. Still, the GUI can be convenient for loading smaller terminologies and, in many cases, works fine for loading moderately large terminologies like the NCI Thesaurus. Loading terminologies requires some knowledge of the source of the terminology.
Generic loading
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 sources you can use a variation of the following LexEVS command:
Linux
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:title} If you are reading this page then you know that LexEVS is an enterprise wide terminology server. When first installed it comes with no terminologies loaded into it. This documentation will cover the means for loading most content types that can be loaded. LexEVS was built to accommodate a wide variety of input and meld it into a common form unifying many common formats. This necessitates a variety of loaders, each used on a specific incoming format. LexEVS provides both a LexEVS administrative GUI and LexEVS loader commands to load terminologies. While the LexEVS administrative GUI is very functional, a system administrator may prefer the command line interface because command scripts can be adjusted to increase memory and tune other java virtual machine settings to insure that loads of larger terminologies have adequate resources. For example, a user may select a loading script, open it in an editor, increase the java heap size and PermGen memory, depending on the machine’s resources, and save the script before running with the appropriate options written into the command line. Still, the GUI can be convenient for loading smaller terminologies and, in many cases, works fine for loading moderately large terminologies like the NCI Thesaurus. Loading terminologies requires some knowledge of the source of the terminology. h4. Generic loading 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|https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/LexEVS_6.0_Administration_Using_the_GUI_Tool#Load_Terminology_Menu] or the [LexEVS loader commands|https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/Administering_LexEVS_6.0_with_the_Command_Line#Command_Line_Scripts_and_Wrappers_Overview]. For many sources you can use a variation of the following LexEVS command: Linux {code} ./LoadOWL.sh -in "file:///ontologies/owl/amino-acid.owl" {code} Windows {code} |
Windows
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LoadOWL.bat -in "file:///ontologies/owl/amino-acid.owl"
{code}
|
This
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LexEVS
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loader
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command
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loads
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input
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in
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OWL
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format.
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Substituting
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the
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matching
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LexEVS
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loader
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command
...
for
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the
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format
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being
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used
...
and
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point
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the
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loader
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to
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a
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local
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source
...
file.
...
In
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the
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LexEVS
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administrative
...
GUI,
...
loading
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is
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accomplished
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using
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the
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"Load
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Terminology"
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menu.
...
The
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administrative
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options
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must
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be
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enabled
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first
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in
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the
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Command
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menu.
...
Large Terminologies
Loading any larger terminologies can be very time consuming and resource intensive and this can be helped by the following recommendations for database optimization. The primary LexEVS configuration file, <LEXEVS_HOME>/resources/config/lbconfig.props,
...
should
...
be
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changed
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depending
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on
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how
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the
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primary
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key
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for
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the
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database
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should
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be
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generated.
...
The
...
default
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setting
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for
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the
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value
...
of
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the
...
database
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primary
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key
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is
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the
...
following:
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}# DB_PRIMARY_KEY_STRATEGY indicates which strategy will be used # for the primary key of the database tables. # WARNING - This cannot be changed after the initial # schema installation. # # Allowable values include: # # "GUID" # - Primary Keys are implemented as random GUIDs. # "SEQUENTIAL_INTEGER" # - Primary Keys will be sequentially incremented # - as Ingeter values. DB_PRIMARY_KEY_STRATEGY=GUID{code} |
Because
...
this
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default
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is
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very
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taxing
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on
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the
...
index
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processing
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at
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the
...
end
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of
...
the
...
load,
...
we
...
recommend
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changing
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it
...
to
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SEQUENTIAL_INTEGER
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unless
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you
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have
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a
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priority
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need
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for
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Global
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Unique
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Identifiers.
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Special
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Case
...
Loading
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Some
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terminologies
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are
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special
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cases
...
and
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need
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special
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handling.
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Included
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in
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this
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category
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are
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the
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NCI
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Thesaurus
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in
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OWL
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format
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and
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any
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files
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loaded
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from
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UMLS
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RRF
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formatted
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sources.
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The
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NCI
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MetaThesaurus
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is
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the
...
largest
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terminology
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we
...
load
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and
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as
...
such
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it
...
also
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requires
...
special
...
handling.
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OWL
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terminologies
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do
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not
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normally
...
require
...
special
...
handling,
...
but
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LexEVS
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offers
...
some
...
advanced
...
loading
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options
...
users
...
may
...
take
...
advantage
...
of.
...
Each of these has its own documentation:
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