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h1. { |
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This page is intended to provide a ready-reference for LexBIG system administrators and candidate material for inclusion in the next release of the LexBIG Administration Guide.
As primary reference, see the Installation and Administration Guide:
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:title} {panel:title=Contents} {toc:minLevel=2} {panel} This page is intended to provide a ready-reference for LexBIG system administrators and candidate material for inclusion in the next release of the LexBIG Administration Guide. As primary reference, see the Installation and Administration Guide: {code}Link provided for historical purposes; contact the page author for access: https://gforge.nci.nih.gov/frs/?group_id=14{code} h2. Building the LexBIG Installer from CVS h3. LexBIG CVS LexBIG source folders have been distributed to the NCI CVS repository: {code} |
Building the LexBIG Installer from CVS
LexBIG CVS
LexBIG source folders have been distributed to the NCI CVS repository:
| Code Block |
|---|
Link provided for historical purposes: cbiocvs2.nci.nih.gov:/share/content/gforge/lexbig{code} |
This
...
location
...
is
...
maintained
...
as
...
a
...
mirror
...
for
...
all
...
source
...
and
...
packaging
...
materials
...
required
...
to
...
build
...
LexBIG
...
product
...
installers.
...
Files
...
are
...
refreshed
...
from
...
the
...
primary
...
development
...
repository
...
(maintained
...
internally
...
by
...
Mayo
...
Clinic)
...
for
...
each
...
milestone
...
release.
...
Development
...
and
...
build
...
processes
...
are
...
not
...
dependent
...
on
...
a
...
particular
...
CVS
...
client
...
or
...
programming
...
environment.
...
However,
...
files
...
with
...
the
...
extension
...
'.classpath'
...
and
...
'.project'
...
have
...
been
...
inserted
...
into
...
each
...
project
...
folder
...
to
...
help
...
facilitate
...
compilation
...
and
...
use
...
within
...
the
...
...
...
...
.
Folder content and purpose
- lbCVSDeploy: Contains build and packaging resources. This includes third party jar files, sample vocabularies, and scripts used to build the LexBIG installer.
- lbAdminDist: Contains source for command-line driven programs related to LexBIG administrative functions.
- lbExamplesDist: Contains source for command-line driven programs used to provide interactive examples of basic operations running against the LexBIG API.
- lbGUIDist: Contains source for the LexBIG graphical user interface.
- lbInterfacesDist: Contains source for the LexBIG API definition.
- lbImplDist: Contains source for the LexBIG API implementation.
- lgModelDist: Contains source for the LexGrid vocabulary data model.
- lbModelDist: Contains source for LexBIG extensions to the LexGrid data model.
- lbTestDist: Contains source for programs used to perform automated validation of the LexBIG runtime environment.
- lgUtilityDist: Contains source for various utility classes (e.g. persistence functions) required by the LexBIG API.
How to produce the installer
- Command line: Download and unzip the latest stable version of Ant from the [Apache site|http://ant.apache.org/bindownload.cgi
...
- .
...
- Check
...
- out
...
- all
...
- project
...
- folders
...
- from
...
- CVS,
...
- and
...
- then
...
- run
...
- the
...
- Ant
...
- command
...
- against
...
- the
...
- build.xml
...
- file
...
- provided
...
- in
...
- lbCVSDeploy.
...
- If
...
- successful,
...
- files
...
- will
...
- be
...
- created
...
- in
...
- /lbCVSDeploy/dist/.
...
- Eclipse:
...
- Open
...
- the
...
- build.xml
...
- file
...
- in
...
- the
...
- Eclipse
...
- Ant
...
- view
...
- and
...
- run
...
- the
...
- default
...
- task.
...
- If
...
- successful,
...
- refresh
...
- the
...
- /lbCVSDeploy
...
- folder;
...
- files
...
- will
...
- be
...
- created
...
- in
...
- /lbCVSDeploy/dist.
...
How
...
to
...
enable
...
ydoc
...
- yDoc offers the capability to add UML diagrams to the generated LexBIG JavaDoc.
If the yDoc directory is present and a valid license is located in the /yDoc/resources directory, the enhanced yDoc support is automatically enabled and used. If not, standard JavaDoc is produced.
Other notes
- Some classpath and jar dependencies have been documented for reference in file /lbCVSDeploy/ClasspathConfig.txt.
...
- Notes
...
- on
...
- the
...
- origin
...
- of
...
- the
...
- files
...
- are
...
- noted
...
- in
...
- /lbCVSDeploy/FILESOURCEs.txt.
...
JBoss
...
Memory
...
Settings
...
JBoss
...
tends
...
to
...
run
...
out
...
of
...
memory
...
while
...
running
...
with
...
the
...
default
...
settings
...
of
...
JBoss.
...
To
...
fix
...
the
...
problem,
...
modify
...
the
...
run.conf
...
file
...
under
...
JBOSS_home/bin
...
to
...
change
...
the
...
memory
...
setting
...
and
...
how
...
frequently
...
the
...
rmi
...
garbage
...
collector
...
runs,
...
by
...
editing
...
the
...
JAVA_OPTS
...
line
...
as
...
follows:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{code:none} if [[ "x$JAVA_OPTS" = "x" ]; then JAVA_OPTS="-server -XX:!MaxPermSize=128m -Xms256m -Xmx2000m -Dsun.rmi.dgc.client.gcInterval=120000 -Dsun.rmi.dgc.server.gcInterval=120000" fi {code} h2. Improving Performance on |
Improving Performance on MySQL/Windows
...
MySQL
...
can
...
be
...
passed
...
a
...
jdbc
...
option
...
for
...
the
...
Windows
...
local
...
environment
...
that
...
may
...
improve
...
perfomance
...
30
...
to
...
50%.
...
Try
...
the
...
following
...
values
...
in
...
the
...
config.props
...
file
...
for
...
the
...
DB_URL:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{code:none} SINGLE_DB_MODE=true DB_URL=jdbc:mysql:///<dbname>?socketFactory=com.mysql.jdbc.NamedPipeSocketFactory DB_DRIVER=org.gjt.mm.mysql.Driver DB_USER=root DB_PASSWORD= DB_PREFIX=lb DB_PARAM= {code} |
This
...
uses
...
Windows
...
Named
...
Pipe
...
function
...
and
...
avoids
...
use
...
of
...
the
...
TCP/IP
...
protocol.
...
It
...
only
...
works
...
when
...
connecting
...
with
...
a
...
local
...
iteration
...
of
...
the
...
MySQL
...
database
...
on
...
Windows.
...
Error
...
Connecting
...
to
...
MySQL
...
LexBIG
...
is
...
distributed
...
with
...
an
...
older
...
version
...
of
...
the
...
Java
...
MySQL
...
driver
...
due
...
to
...
licensing
...
concerns.
...
If
...
LexBIG
...
reports
...
an
...
error
...
concerning
...
establishing
...
a
...
connection
...
to
...
the
...
MySQL
...
server
...
yet
...
the
...
MySQL
...
CLI
...
is
...
able
...
to
...
connect,
...
a
...
new
...
version
...
of
...
Connector/J
...
may
...
be
...
required.
...
The
...
latest
...
version
...
of
...
Connector/J
...
is
...
available
...
from
...
MySQL.org.
...
The
...
new
...
jar
...
should
...
be
...
placed
...
in
...
the
...
LexGrid/LexBIG/2.0.0/runtime/sqlDrivers/
...
directory.
...
Remove
...
the
...
existing
...
mm.mysql-2.0.6.jar
...
to
...
ensure
...
that
...
the
...
class
...
loader
...
does
...
not
...
incorrectly
...
load
...
the
...
older
...
driver
...
file.
...
Configuring
...
Manifest
...
Files
...
Using
...
Coding
...
Scheme
...
Manifest
...
Entries
...
LexBIG
...
Release
...
July/Aug
...
2007
...
What
...
is
...
"Coding
...
Scheme
...
Manifest"?
...
A
...
"Coding
...
Scheme
...
Manifest"
...
(or
...
simply
...
"manifest"
...
as
...
used
...
interchangeably
...
in
...
this
...
document)
...
encapsulates
...
the
...
user
...
supplied
...
values
...
to
...
set
...
for
...
a
...
coding
...
scheme
...
while
...
loading
...
or
...
converting
...
an
...
OWL
...
(currently
...
it
...
is
...
supported
...
only
...
for
...
OWL
...
type
...
of
...
files)
...
source
...
to
...
LexGrid
...
format.
...
What
...
is
...
"Coding
...
Scheme"?
...
Coding
...
Scheme
...
is
...
the
...
term
...
that
...
is
...
used
...
to
...
represent
...
an
...
ontology/terminology
...
being
...
loaded
...
or
...
converted.
...
In
...
the
...
LexGrid
...
data
...
model
...
a
...
terminology
...
is
...
represented
...
as
...
a
...
coding
...
scheme
...
and
...
it
...
can
...
reference
...
other
...
coding
...
schemes.
...
An
...
example
...
of
...
coding
...
scheme
...
is
...
"Amino
...
Acid"
...
which
...
is
...
described
...
in
...
the
...
"amino-acid.owl"
...
file.
...
A
...
Coding
...
Scheme
...
has
...
some
...
meta
...
information
...
about
...
it;
...
values
...
like
...
'formal
...
name',
...
'local
...
names',
...
'default
...
language',
...
'version',
...
'copyright',
...
'sources'
...
to
...
name
...
some.
...
Why
...
do
...
we
...
need
...
a
...
"Coding
...
Scheme
...
Manifest"?
...
When
...
a
...
terminology
...
is
...
being
...
converted
...
to
...
the
...
LexGrid
...
data
...
model
...
from
...
its
...
native
...
format
...
(in
...
this
...
case
...
OWL),
...
Coding
...
Scheme
...
information
...
is
...
read
...
from
...
the
...
source
...
file.
...
Sometimes
...
values
...
may
...
be
...
missing
...
(not
...
provided
...
or
...
invalid)
...
or
...
the
...
author/user
...
of
...
the
...
terminology
...
wants
...
to
...
override
...
or
...
set
...
default
...
values
...
despite
...
(or
...
in
...
addition
...
to)
...
what
...
is
...
provided
...
in
...
the
...
source
...
file.
...
This
...
can
...
be
...
accomplished
...
using
...
"manifest"
...
files
...
along
...
with
...
the
...
source
...
file.
...
How
...
do
...
we
...
create
...
a
...
"Coding
...
Scheme
...
Manifest"
...
file?
...
A
...
coding
...
scheme
...
manifest
...
file
...
is
...
a
...
valid
...
XML
...
file,
...
conforming
...
to
...
the
...
schema
...
defined
...
by
...
http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd]
...
.
...
This
...
XML
...
file
...
can
...
define
...
values
...
for
...
one
...
or
...
more
...
coding
...
schemes
...
you
...
are
...
dealing
...
with.
...
Some
...
coding
...
scheme
...
meta-information
...
may
...
not
...
easily
...
map
...
to
...
information
...
in
...
the
...
source
...
file.
...
In
...
this
...
case
...
a
...
manifest
...
file
...
is
...
of
...
great
...
help
...
to
...
bridge
...
the
...
gap
...
and
...
control
...
the
...
information
...
flow
...
while
...
mapping
...
to
...
the
...
LexGrid
...
model.
...
A
...
detailed
...
model
...
of
...
the
...
LexGrid
...
Coding
...
Scheme
...
and
...
its
...
fields
...
can
...
be
...
found
...
online.
...
Structure
...
of
...
the
...
schema
...
for
...
the
...
manifest
...
file
...
is
...
explained
...
in
...
the
...
following
...
table
...
(manifest
...
components
...
refer
...
to
...
the
...
original
...
LexGrid
...
model
...
schema
...
namespaces
...
and
...
types):
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''id'''
...
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- Yes
...
- Override
...
- flag
...
- set:
...
- Not
...
- applicable
...
- Description:
...
The
...
- registered
...
- name
...
- is
...
- the
...
- key
...
- used
...
- to
...
- find
...
- a
...
- coding
...
- scheme
...
- (for
...
- example
...
- a
...
- unique
...
- URL
...
- or
...
- namespace
...
- by
...
- which
...
- other
...
- people
...
- access
...
- same
...
- coding
...
- scheme).
...
- This
...
- String
...
- value
...
- will
...
- be
...
- used
...
- to
...
- identify
...
- the
...
- manifest
...
- entry
...
- in
...
- the
...
- manifest
...
- file
...
- for
...
- the
...
- coding
...
- scheme
...
- too.
...
- For
...
- example
...
- the
...
- registered
...
- name
...
- for
...
- coding
...
- scheme
...
- "Amino-acid"
...
- is
...
...
- .
...
- This
...
- string
...
- is
...
- also
...
- set
...
- as
...
- the
...
- coding
...
- scheme's
...
- registered
...
- name
...
- field
...
- in
...
- the
...
- LexGrid
...
- model.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''codingScheme'''
...
- Type:
...
- lgBuiltin:localId
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''entityDescription'''
...
- Type:
...
- lgCommon:entityDescription
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- description'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''formalName'''
...
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- formal
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''registeredName'''
...
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- registered
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''defaultLanguage'''
...
- Type:
...
- lgCommon:defaultLanguage
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- default
...
- language'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''representsVersion'''
...
- Type:
...
- lgCommon:version
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- version'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''localName'''
...
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- local
...
- names'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- local
...
- names
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''source'''
...
- Type:
...
- lgCommon:source
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- sources'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- sources
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''copyright'''
...
- Type:
...
- lgCommon:text
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- copyright'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''mappings'''
...
- Type:
...
- lgCS:mappings
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- mappings'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- mappings
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- '''associationDefinitions'''
...
- Type:
...
- lgRel:association
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- associations'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- associations
...
- (if
...
- not
...
- there
...
- already).
...
Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
(Note:
...
- This
...
- option
...
- is
...
- used
...
- internally
...
- by
...
- the
...
- system
...
- to
...
- provide
...
- default
...
- recognition
...
- of
...
- some
...
- common
...
- associations.
...
It
...
- is
...
- typically
...
- not
...
- necessary
...
- to
...
- provide
...
- this
...
- value,
...
- however,
...
- since
...
- association
...
- definitions
...
- are
...
- automatically
...
- derived
...
- from
...
- the
...
- source.)
Could you please provide some example entries in a manifest file?
Here are some example coding scheme manifest entries:
| Code Block | ||||
|---|---|---|---|---|
| ||||
_ h3. Could you please provide some example entries in a manifest file? Here are some example coding scheme manifest entries: {code:none} <CodingSchemeManifestList xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd" xmlns:owldef="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList" xmlns="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList"> <entry id="http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#"> <codingScheme>amino</codingScheme> <entityDescription>This is AminoAcide Description from Manifest.</entityDescription> <formalName>Amino Acid Ontology</formalName> <defaultLanguage>en</defaultLanguage> <representsVersion>2005/10/11</representsVersion> <localName>myLocalName</localName> <source subRef="ontologies">COODE</source> <copyright>This is copyright</copyright> <owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes"> <supportedLanguage localId="en" urn="urn:oid:2.16.840.1.113883.6.84:en"/> <supportedFormat localId="text_plain" urn="urn:oid:2.16.840.1.113883.6.10:text_plain"/> <supportedSource localId="COODE" urn="http://www.co-ode.org/"/> </owldef:mappings> <associationDefinitions> <assoc association="testRelation" forwardName="testRelation" reverseName="testRelationInverse" isTransitive="true" isReflexive="true" targetCodingScheme= "http://www.co-ode.org/ontologies/amino-acid/2006/05/18/outside#"/> </associationDefinitions> </entry> <entry id="urn:oid:2.16.840.1.113883.3.26.1.1"> <codingScheme>NCI Thesaurus CS Manifest</codingScheme> <entityDescription>This is NCI Thesaurus Description from Manifest.</entityDescription> <formalName>NCI Thesaurus Formal From Manifest</formalName> <defaultLanguage>en</defaultLanguage> <representsVersion>manifestVersion</representsVersion> <localName>NCILocalName</localName> <source subRef="ontologies" >NCIManifestSource</source> <copyright>This is copyright for NCI Thesaurus</copyright> %%% <owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes"> <supportedSource localId="COODE" urn="http://www.co-ode.org/"/> </owldef:mappings> <associationDefinitions> <assoc association="testRelation" forwardName="testRelation" reverseName="testRelationInverse" isTransitive="true" isReflexive="true" targetCodingScheme= "urn:oid:2.16.840.1.113883.3.26.1.1"/> </associationDefinitions> </entry> </CodingSchemeManifestList> {code} h3. What code changes may be required to use a manifest file? Currently a coding scheme manifest file is only supported when loading OWL sources. Support for other formats is in-works. If you want to use the manifest file, you can supply the manifest file URI to the following methods: {code:none} |
What code changes may be required to use a manifest file?
Currently a coding scheme manifest file is only supported when loading OWL sources. Support for other formats is in-works. If you want to use the manifest file, you can supply the manifest file URI to the following methods:
| Code Block | ||||
|---|---|---|---|---|
| ||||
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.load()"
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.validate()"
{code}
|
An
...
example
...
code
...
snippet:
| Code Block | ||||
|---|---|---|---|---|
| ||||
{code:none} LexBIGService lbs = new LexBIGServiceImpl(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); OWL_Loader loader = (OWL_Loader) lbsm.getLoader("OWLLoader"); if (toValidateOnly) { loader.'''validate'''(source, manifest, vl); System.out.println("VALIDATION SUCCESSFUL"); } else { loader.'''load'''(new File("resources/testData/amino-cid.owl").toURI(),%%%new File ("resources/testData/aa-manifest.xml").toURI(), true, true); } {code} h2. |
Generating
...
RRF
...
Files
...
from
...
UMLS
...
When
...
generating
...
source
...
RRF
...
files
...
from
...
the
...
Metathesaurus,
...
the
...
UMLS
...
Metamorphosys
...
tool
...
should
...
be
...
set
...
to
...
output
...
versionless
...
source
...
abbreviations
...
rather
...
than
...
versioned
...
source
...
abbreviations
...
in
...
any
...
RRF
...
subset
...
to
...
be
...
loaded
...
to
...
LexGrid.
...
Failing
...
to
...
do
...
so
...
will
...
create
...
an
...
incomplete
...
database
...
leaving
...
the
...
association
...
and
...
concept
...
tables
...
empty.
| Wiki Markup |
|---|
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