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Overview
This page serves as an instructional guide as well as a brief history and and overview about Protege to all non-NCI users. Users are able to download a zipped copy of this public release Protege extension package, which contain the necessary installation folders. Within each folder, certain file(s) will need to be configured in order to properly run the application. Once configured in the user should be able to run Protege within their own server environment.
EVS Protege Extensions Introduction and History
Currently, version 1.3.0.188
...
is
...
the
...
third
...
public
...
release
...
of
...
the
...
EVS
...
Protege
...
Extensions.
...
There
...
have
...
been
...
multiple
...
revisions
...
released,
...
tested
...
and
...
used
...
internally
...
over
...
the
...
past
...
year.
...
The
...
current
...
version
...
is
...
considered
...
stable
...
and
...
reliable
...
and
...
suitable
...
for
...
external
...
release.
...
These
...
extensions
...
were
...
created
...
in
...
response
...
to
...
a
...
need
...
for
...
an
...
open-source
...
editing
...
tool
...
that
...
could
...
be
...
customized
...
to
...
the
...
needs
...
of
...
the
...
EVS
...
content
...
editors.
...
In
...
addition,
...
EVS
...
wanted
...
the
...
ability
...
to
...
exchange
...
and
...
share
...
editable
...
content
...
with
...
external
...
collaborators.
...
The
...
Protégé
...
editing
...
tool,
...
developed
...
by
...
Stanford,
...
was
...
used
...
as
...
the
...
basis
...
and
...
extended
...
to
...
meet
...
these
...
needs.
...
The
...
extensions
...
are
...
built
...
on
...
the
...
Protégé
...
3.4
...
Beta
...
508
...
codebase
...
and
...
utilize
...
pellet
...
1.5.
...
Some
...
improvements
...
to
...
the
...
Protégé
...
software
...
were
...
required
...
to
...
meet
...
the
...
needs
...
of
...
EVS,
...
but
...
these
...
have
...
already
...
been
...
merged
...
into
...
the
...
Protégé
...
trunk.
...
Both
...
Protégé
...
and
...
Pellet
...
are
...
included
...
within
...
the
...
download.
...
The
...
Explanation
...
Server
...
was
...
developed
...
in
...
collaboration
...
with
...
Clark
...
&
...
Parsia
...
LLC.
...
The
...
Protégé
...
and
...
the
...
extensions
...
are
...
built
...
and
...
expect
...
to
...
run
...
on
...
Java
...
1.5.
...
EVS
...
Protégé
...
Extensions
...
As
...
metioned
...
above,
...
the
...
EVS
...
Protégé
...
Extensions
...
are
...
broken
...
into
...
three
...
separate
...
packages.
...
The
...
Explanation
...
server
...
provides
...
classification
...
and
...
explanation
...
functionality.
...
The
...
Protégé
...
server
...
provides
...
access
...
to
...
a
...
central
...
editing
...
project
...
for
...
multiple
...
users.
...
The
...
Protégé
...
client
...
is
...
the
...
end-user
...
application
...
for
...
accessing
...
the
...
Protégé
...
server
...
and
...
editing
...
content.
...
Explanation
...
Server
...
The
...
Explanation
...
Server
...
is
...
used
...
to
...
do
...
classification
...
of
...
the
...
ontology
...
and
...
provide
...
explanations
...
on
...
demand
...
to
...
the
...
Protégé
...
Client
...
GUI.
...
It
...
runs
...
directly
...
against
...
the
...
database,
...
independently
...
of
...
the
...
Protégé
...
Server.
...
The
...
Protégé
...
Server
...
queries
...
the
...
Explanation
...
Server
...
for
...
information
...
when
...
needed
...
and
...
controls
...
requests
...
for
...
classification,
...
so
...
multiple
...
clients
...
cannot
...
try
...
and
...
classify
...
at
...
the
...
same
...
time.
...
The
...
Explanation
...
Server
...
is
...
designed
...
to
...
run
...
in
...
the
...
bash
...
shell
...
on
...
a
...
Linux
...
or
...
Unix
...
computer.
...
Please
...
ensure
...
that
...
the
...
JRE
...
is
...
installed
...
on
...
the
...
machine
...
to
...
run
...
the
...
explanation
...
server.
...
Protégé
...
Server
...
The
...
Protégé
...
server
...
provides
...
multi-user
...
access
...
to
...
a
...
single
...
ontology
...
stored
...
in
...
a
...
database.
...
It
...
coordinates
...
and
...
controls
...
user
...
activities
...
and
...
resource
...
allocation.
...
It
...
stores
...
a
...
history
...
of
...
user
...
actions
...
for
...
use
...
in
...
tracking
...
changes
...
and
...
resolving
...
conflicts.
...
The
...
server
...
also
...
provides
...
a
...
centralized
...
means
...
of
...
enforcing
...
business
...
rules
...
and
...
configurations
...
upon
...
client
...
applications.
...
EVS
...
has
...
extended
...
the
...
Protégé
...
server
...
to
...
allow
...
tracking
...
of
...
workflow
...
and
...
assigning
...
of
...
editing
...
tasks.
...
The
...
Protégé
...
server
...
is
...
designed
...
to
...
run
...
in
...
the
...
bash
...
shell
...
on
...
a
...
Linux
...
or
...
Unix
...
computer.
...
Please
...
ensure
...
that
...
the
...
JRE
...
is
...
installed
...
on
...
the
...
machine
...
to
...
run
...
the
...
explanation
...
server.
...
Protégé
...
Client
...
The
...
Protégé
...
client
...
is
...
a
...
java-swing
...
based
...
GUI
...
used
...
for
...
editing
...
an
...
ontology.
...
EVS
...
uses
...
the
...
client
...
to
...
connect
...
to
...
the
...
Protégé
...
server
...
application,
...
allowing
...
multiple
...
editors
...
to
...
share
...
the
...
same
...
ontology.
...
The
...
Protégé
...
client
...
can
...
also
...
be
...
used
...
in
...
standalone
...
mode
...
to
...
edit
...
a
...
single
...
ontology
...
but
...
some
...
of
...
the
...
client-server
...
specific
...
extensions
...
are
...
then
...
disabled.
...
The
...
client
...
is
...
used
...
in
...
standalone
...
mode
...
by
...
managers
...
to
...
perform
...
Prompt
...
comparisons
...
and
...
terminology
...
exports.
...
The
...
Protégé
...
client
...
is
...
designed
...
to
...
run
...
in
...
the
...
bash
...
shell
...
on
...
a
...
Linux
...
or
...
Unix
...
computer
...
or
...
on
...
a
...
Windows
...
computer.
...
The
...
JRE
...
has
...
been
...
set
...
for
...
the
...
Protégé
...
client
...
to
...
run
...
on
...
a
...
Windows
...
machine,
...
however,
...
this
...
JRE
...
folder
...
is
...
not
...
needed
...
for
...
the
...
client
...
residing
...
on
...
the
...
server,
...
the
...
Linux
...
server
...
should
...
have
...
a
...
JRE
...
setup.
...
Installation instructions
The instructions below will allow the user to build an environment to match the one used by EVS. Some of the configurations are optional and will be labeled as such. The zip package contains folders for the client, Protégé server and explanation server. All of these should be copied to the Linux/Unix machine where you will be serving Protégé. A copy of the client should also reside on a local Windows machine for use in accessing the server data.
Metaproject
Any multi-user Protégé server-client configuration requires a metaproject. The server application references this metaproject to determine what ontologies to make available for editing and what users have rights to do various tasks. EVS has made available an example metaproject that includes all the privileges and groups required for the NCI edit tab. A base metaproject is located in the Protégé.Server-1.4.0.267/examples/server
...
folder.
...
Protégé
...
Client
...
Folder
...
Before
...
the
...
vocabulary
...
can
...
be
...
accessed
...
by
...
the
...
server
...
it
...
must
...
be
...
loaded
...
into
...
a
...
project
...
using
...
the
...
Protégé
...
Client
...
GUI.
...
The
...
OWL
...
source
...
is
...
loaded
...
first
...
as
...
a
...
Protégé
...
file
...
project
...
and
...
then
...
converted
...
to
...
a
...
database
...
project.
...
Steps
...
to
...
load
...
a
...
new
...
Protégé
...
project
...
and
...
convert
...
in
...
to
...
a
...
database
...
project
...
are
...
below.
...
The
...
Protégé
...
application
...
will
...
create
...
the
...
necessary
...
tables
...
in
...
the
...
database.
...
You,
...
or
...
course,
...
need
...
to
...
have
...
a
...
database
...
ready
...
and
...
able
...
to
...
be
...
written
...
to
...
before
...
you
...
start
...
the
...
load.
...
These
...
steps
...
can
...
be
...
performed
...
on
...
a
...
Windows
...
machine
...
but
...
all
...
the
...
files
...
generated
...
or
...
modified
...
would
...
then
...
need
...
to
...
be
...
copied
...
up
...
to
...
the
...
Linux
...
server.
...
The
...
directions
...
below
...
assume
...
the
...
user
...
is
...
running
...
the
...
client
...
on
...
the
...
actual
...
Linux
...
server.
...
Files
...
to
...
configure
...
in
...
the
...
Protégé
...
client
...
folder:
...
run_protege.sh
...
(Linux)
...
- JAVA_HOME
...
- =
...
- must
...
- be
...
- set
...
- to
...
- the
...
- proper
...
- path.
...
- Insert
...
- the
...
- path
...
- to
...
- your
...
- JDK
...
- folder
...
- here
...
- (NCI
...
- Protege
...
- uses
...
- Java
...
- 1.5).
...
- For
...
- the
...
- client
...
- folder
...
- residing
...
- on
...
- the
...
- Linux
...
- server,
...
- set
...
- MAX_MEMORY
...
- value
...
- to
...
- a
...
- suitable
...
- size
...
- (NCI
...
- Prod
...
- -
...
- 7GB,
...
- QA
...
- -
...
- 7GB,
...
- Dev
...
- 2.5GB).
...
run_protege.bat
...
(Windows)
...
Used
...
only
...
for
...
windows
...
machines.
...
All
...
that
...
needs
...
to
...
be
...
done
...
here
...
is
...
to
...
set
...
MAX_MEMORY
...
to
...
700MB.
...
An
...
important
...
note
...
is
...
that
...
if
...
you
...
are
...
using
...
the
...
client
...
from
...
a
...
Windows
...
machine,
...
be
...
sure
...
to
...
insert
...
a
...
copy
...
of
...
a
...
JRE
...
folder
...
within
...
the
...
Protégé
...
client
...
folder.
...
The
...
batch
...
file
...
will
...
not
...
run
...
unless
...
it
...
can
...
detect
...
a
...
JRE.
...
PromptNCIPlugins.properties
...
Examine
...
the
...
PromptNCIPlugins.properties
...
file
...
to
...
verify
...
correct
...
database
...
information.
...
This
...
is
...
only
...
necessary
...
if
...
Prompt
...
is
...
going
...
to
...
be
...
used
...
to
...
export
...
history
...
records
...
to
...
the
...
concept_history
...
table:
...
nci.prompt.ipAddress=<hostname>:<port>
...
nci.prompt.dataBaseName=<db
...
name>
...
nci.prompt.dbEVSHistoryTable=<tablename>
...
nci.prompt.userName=<username>
...
nci.prompt.password=<password>
...
Explanation Server Folder
The Explanation Server can connect with either the Protégé database or to a raw OWL file. Files to configure:
start_explanation_server.sh
...
- Allocate
...
- a
...
- decent
...
- max_heap_size.
...
- (default
...
- is
...
- set
...
- to
...
- 12gigs,
...
- however,
...
- less
...
- memory
...
- can
...
- be
...
- used
...
- for
...
- test
...
- machines
...
- (i.e.
...
- 8GB
...
- for
...
- QA)).
...
- Enusre
...
- that
...
- the
...
- explanation
...
- server
...
- is
...
- pointing
...
- to
...
- the
...
- correct
...
- Protege.Server
...
- folder:
...
- (protege_install=/path/to/new/Protege
...
- server
...
- folder).
...
- This
...
- allows
...
- the
...
- Explanation
...
- server
...
- to
...
- use
...
- jars
...
- found
...
- in
...
- the
...
- Protege.Server
...
- folder.
...
- Make
...
- sure
...
- the
...
- path
...
- to
...
- the
...
- java
...
- server
...
- is
...
- correct
...
- (replace
...
- <PATH
...
- TO
...
- JRE
...
- BIN>
...
- with
...
- the
...
- actual
...
- jre/bin/java.exe
...
- location.
...
- The
...
- command
...
- to
...
- connect
...
- the
...
- explanation
...
- server
...
- to
...
- a
...
- database
...
- project:
...
- './start_explanation_server.sh
...
- --port
...
- <PORT>
...
- --protege-standalone
...
- /path/to/databaseProject.pprj
...
- '.
...
- The
...
- command
...
- to
...
- connect
...
- to
...
- a
...
- raw
...
- OWL
...
- file:
...
- *'./sh
...
- start_explanation_server.sh
...
- --urls
...
- file:///home/user/path/to/file.owl'*
...
- The
...
- Explanation
...
- Server
...
- is
...
- ready
...
- when
...
- you
...
- see
...
- "Jena,
...
- Classification,
...
- and
...
- Extracting'
...
- as
...
- well
...
- as
...
- a
...
- final
...
'Server
...
- started,
...
- listening
...
- on
...
- port
...
- ....'
...
- message.
...
- The
...
- Explanation
...
- Server
...
- should
...
- be
...
- allowed
...
- to
...
- start
...
- completely
...
- before
...
- starting
...
- the
...
- Protege
...
- Server.
...
Protégé
...
Server
...
Folder
...
run_rmiregistry.sh
...
- JAVA_HOME
...
- must
...
- be
...
- set
...
- in
...
- the
...
- script.
...
- The
...
- very
...
- last
...
- line
...
- has
...
- a
...
- port
...
- number
...
- that
...
- will
...
- need
...
- to
...
- match
...
- the
...
- Protégé
...
- Server:
...
- $JAVA_PATH/rmiregistry
...
- <PORT>
...
- &
run_protege_server.sh
...
- JAVA_HOME
...
- must
...
- be
...
- set.
...
- Set
...
- MAX_MEMORY
...
- to
...
- a
...
- suitable
...
- size
...
- to
...
- run
...
- adequately
...
- (i.e.
...
- NCI
...
- Production
...
- -
...
- 7.5
...
- GB,
...
- QA
...
- -
...
- 7GB,
...
- Dev
...
- -
...
- 3GB).
...
- Ensure
...
- RMI_REG_PORT
...
- number
...
- matches
...
- port
...
- number
...
- in
...
- 'run_rmiregistry.sh'
...
- script.
...
- Set
...
- RMI_SERV_PORT
...
- to
...
- any
...
- desired
...
- open
...
- port.
...
- HOSTNAME_PARAM=-Djava.rmi.server.hostname=<hostname>
...
- should
...
- be
...
- edited
...
- with
...
- the
...
- actual
...
- server
...
- hostname
...
- where
...
- the
...
- rmi
...
- registry
...
- server
...
- will
...
- be
...
- running.
...
- The
...
- "localhost"
...
- address
...
- will
...
- not
...
- work
...
- properly,
...
- it
...
- needs
...
- to
...
- be
...
- the
...
- actual
...
- server
...
- name.
...
- Set
...
- METAPROJECT
...
- with
...
- the
...
- location
...
- of
...
- the
...
- Metaproject
...
- file.
...
codegen.properties
...
The
...
codegen.seed
...
number
...
should
...
be
...
set
...
at
...
a
...
figure
...
higher
...
than
...
the
...
highest
...
concept
...
number
...
in
...
your
...
vocabulary.
...
The
...
codegen
...
prefix
...
and
...
codegen.suffix
...
values
...
are
...
optional.
...
The
...
optional
...
codegen
...
delimeter
...
will
...
set
...
the
...
character
...
to
...
be
...
inserted
...
between
...
prefix
...
and
...
code
...
or
...
code
...
and
...
suffix.
...
Example:
...
prefix=B,
...
delimiter=-,
...
suffix=cs,
...
seed=100.
...
The
...
first
...
code
...
generated
...
will
...
be
...
B-100-cs.
...
A
...
'codegen.dat'
...
file
...
will
...
then
...
be
...
generated
...
within
...
the
...
Protégé
...
server
...
folder
...
and
...
will
...
be
...
updated
...
to
...
"100"
...
and
...
will
...
iterate
...
the
...
concept
...
code
...
number
...
from
...
that
...
point.
...
PromptNCIPlugin.properties
...
Verify
...
correct
...
database
...
information
...
for
...
saving
...
to
...
the
...
evs_history
...
table.
...
This
...
information
...
should
...
match
...
the
...
PromptNCIplugin
...
info
...
residing
...
in
...
the
...
Protégé
...
client
...
folder:
...
nci.prompt.ipAddress=<hostname>:<port>
...
nci.prompt.dataBaseName=<db
...
name>
...
nci.prompt.dbEVSHistoryTable=<tablename>
...
nci.prompt.userName=<username>
...
nci.prompt.password=<password>
...
protege.properties
...
Verify
...
that
...
the
...
protege.properties
...
file
...
points
...
to
...
the
...
correct
...
Protégé
...
server
...
as
...
well
...
as
...
the
...
URL
...
for
...
the
...
explanation
...
server:
...
edu.stanford.smi.protege.server.ServerPanel.host_name=serverhostname\:port
...
edu.stanford.smi.protegex.owl.jena.reasoner.URL=http\://serverhostname\:port/explain/
...
The
...
first
...
line
...
should
...
be
...
the
...
Protégé
...
server
...
hostname
...
with
...
the
...
desired
...
RMI
...
port
...
number.
...
The
...
second
...
line
...
is
...
read
...
by
...
the
...
explanation
...
server,
...
and
...
should
...
be
...
the
...
same
...
address
...
or
...
hostname
...
as
...
the
...
Protégé
...
server.
...
However,
...
the
...
port
...
number
...
will
...
be
...
different.
...
The
...
backslashes
...
in
...
the
...
hostname
...
represent
...
escape
...
character
...
in
...
Linux
...
for
...
the
...
colons.
...
To
...
edit,
...
use
...
your
...
editor
...
to
...
open
...
the
...
properties
...
file.
...
Insert
...
proper
...
server
...
hostname
...
and
...
port
...
number
...
values,
...
save,
...
and
...
exit
...
the
...
properties
...
file.
...
Nothing
...
else
...
should
...
be
...
modified
...
in
...
this
...
file.
...
Protégé
...
Database
...
Project/Configuration
...
Files
...
All
...
files
...
should
...
now
...
be
...
configured
...
and
...
ready
...
to
...
be
...
used.
...
At
...
this
...
point,
...
a
...
new
...
database
...
project
...
will
...
need
...
to
...
be
...
created
...
and
...
configured
...
for
...
the
...
Protégé
...
server
...
to
...
connect
...
with
...
the
...
database.
...
Follow
...
the
...
Instructions
...
for
...
creating
...
and
...
configuring
...
a
...
new
...
Protégé
...
database
...
project.
...
Loading the OWL file into a Project
Open the Protégé client, run 'run_protege.sh',
...
and
...
click
...
on
...
"Create
...
New
...
Project".
...
Select
...
OWL/RDF
...
File,
...
and
...
check
...
"Create
...
from
...
existing
...
source".
...
Click
...
"Next".
...
A
...
window
...
will
...
display
...
requesting
...
the
...
address
...
of
...
the
...
source
...
OWL
...
file.
...
Navigate
...
to
...
where
...
the
...
OWL
...
file
...
is
...
stored
...
and
...
click
...
"Finish".
...
The
...
OWL
...
file
...
may
...
take
...
some
...
time
...
to
...
load
...
into
...
the
...
client,
...
dpending
...
on
...
the
...
file size.
Converting a File-Based
...
Project
...
into
...
a
...
Database
...
Project
...
Once
...
the
...
OWL
...
file
...
is
...
visible
...
in
...
the
...
GUI,
...
it
...
can
...
now
...
be
...
converted
...
to
...
an
...
OWL/RDF
...
database.
...
Click
...
"File",
...
"Convert
...
Project
...
to
...
Format",
...
and
...
select
...
OWL
...
/
...
RDF
...
database.
...
A
...
new
...
window
...
will
...
open
...
requesting
...
information
...
on
...
the
...
database
...
where
...
the
...
project
...
should
...
be
...
created.
...
Even
...
a
...
database
...
project
...
has
...
a
...
file
...
component
...
that
...
holds
...
settings
...
for
...
the
...
project.
...
The
...
first
...
field
...
in
...
the
...
new
...
window
...
will
...
request
...
the
...
path
...
to
...
the
...
project
...
file.
...
The
...
remaining
...
fields
...
are
...
for
...
database
...
info:
...
*JDBC
...
Driver
...
Class
...
Name
...
-
...
for
...
MySQL,
...
the
...
database
...
used
...
by
...
NCI,
...
this
...
would
...
be
...
com.mysql.jdbc.Driver
...
*JDBC
...
Driver
...
URL
...
-
...
the
...
URL
...
of
...
the
...
database.
...
In
...
MySQL
...
it
...
will
...
look
...
like
...
jdbc:mysql:<server>:<port>/<database>
...
*Table
...
-
...
the
...
name
...
of
...
the
...
table
...
to
...
be
...
created
...
for
...
this
...
project
...
*Username
...
-
...
username
...
for
...
access
...
to
...
the
...
database
...
*Password
...
-
...
password
...
to
...
the
...
database
...
After
...
entering,
...
click
...
"Finish"
...
and
...
the
...
client
...
will
...
the
...
proceed
...
to
...
load
...
the
...
data
...
into
...
the
...
specified
...
database
...
table.
...
This
...
process
...
may
...
take
...
some
...
time
...
depending
...
on
...
the
...
file
...
size.The
...
console
...
will
...
display
...
a
...
completion
...
message
...
indicating
...
that
...
the
...
conversion
...
process
...
is
...
successful.
...
The
...
database
...
project
...
should
...
be
...
visible
...
in
...
the
...
client.
...
The
...
project
...
is
...
now
...
ready
...
to
...
be
...
configured.
...
Configuring the Database Project
Activating the NCIEdit Tab
Click "Project"
...
on
...
the
...
menu
...
bar,
...
and
...
select
...
"Configure".
...
On
...
the
...
Tab
...
Widgets
...
tab,
...
enable
...
the
...
the
...
NcIEdit
...
tab.
...
<Optional>Within
...
the
...
same
...
dialog,
...
click
...
on
...
the
...
Options
...
tab
...
and
...
enable
...
journaling
...
and
...
disable
...
redo/undo.
...
Click
...
"OK"
...
to
...
finish.
...
Changing
...
the
...
Tree
...
Display
...
To
...
set
...
the
...
display
...
slots,
...
click
...
the
...
NCIEdit
...
tab,
...
and
...
click
...
the
...
"F"
...
tab
...
on
...
the
...
very
...
far
...
top
...
right
...
section
...
of
...
the
...
page.
...
You
...
will
...
now
...
be
...
within
...
the
...
Form
...
Editor
...
section.
...
Set
...
the
...
"Display
...
Slot"
...
drop
...
down
...
to
...
the
...
property
...
you
...
wish
...
displayed
...
for
...
the
...
concept
...
(NCI
...
Thesaurus
...
uses
...
"rdfs:label".
...
Changing
...
the
...
display
...
of
...
properties
...
Click
...
the
...
Properties
...
tab,
...
and
...
click
...
the
...
"F"
...
tab
...
on
...
the
...
very
...
right.
...
On
...
the
...
left
...
hand
...
menu,
...
click
...
on
...
"owl:DatatypeProperty",
...
and
...
set
...
it's
...
"Display
...
Slot"
...
drop
...
down
...
to
...
"rdfs:label".
...
Next,
...
click
...
on
...
the
...
owl:ObjectProperty
...
on
...
the
...
left
...
hand
...
menu,
...
and
...
set
...
its
...
"Display
...
Slot"
...
drop
...
down
...
field
...
to
...
'rdfs:label'
...
as
...
well.
...
OWL
...
Preferences
...
Window
...
Click
...
"OWL"
...
on
...
the
...
menu
...
and
...
select
...
"Preferences".
...
On
...
the
...
"General"
...
tab
...
set
...
the
...
explanation
...
server
...
URL
...
to
...
the
...
url
...
where
...
the
...
explanation
...
server
...
will
...
be
...
located.
...
The
...
<hostname>
...
is
...
typically
...
"localhost"
...
and
...
the
...
<port>
...
is
...
set
...
by
...
the
...
user
...
when
...
starting
...
the
...
Explanation
...
server.
...
Example:
...
http://localhost:1234/explain/
...
<Optional>On
...
this
...
same
...
page
...
disable
...
Drag
...
and
...
Drop.
...
It
...
can
...
cause
...
accidental
...
re-treeing
...
of
...
concepts
...
due
...
to
...
errant
...
drags.
...
<Optional>In
...
the
...
"Tests"
...
tab
...
disable
...
"List
...
deprecated
...
classes
...
and
...
properties".
...
This
...
will
...
prevent
...
testing
...
of
...
deprecated
...
classes
...
which
...
can
...
save
...
a
...
lot
...
of
...
time
...
if
...
there
...
are
...
many
...
of
...
them.
...
<Optional>In
...
the
...
"Visibility"
...
tab
...
disable
...
all
...
the
...
boxes
...
in
...
the
...
MetaClasses
...
section.
...
This
...
can
...
eliminate
...
a
...
lot
...
of
...
clutter
...
in
...
the
...
editing
...
view.
...
Click
...
"Close"
...
at
...
the
...
bottom
...
of
...
the
...
dialog
...
box.
...
Activating
...
Other
...
Essential
...
Tabs
...
Click
...
"Project"
...
on
...
the
...
menu
...
bar,
...
and
...
select
...
"Configure".
...
On
...
the
...
Tab
...
Widgets
...
tab,
...
enable
...
the
...
following
...
tabs,
...
and
...
order
...
as
...
shown:
...
- NCIEditTab
- LuceneQueryTab
- OWLPropertiesTab
- OWLMetadataTab
- ChangesTab
- ExplanationTab
- NCIWorkflowTab
Click "OK" to exit. You will notice a window that will automatically display prompting you to choose a source to store all changes and annotations ontology. Changes are records of any type of modification that is done to any concepts within the ontology.
The window will prompt you to select whether to save to a new or existing changes ontology file, or to a database. After selecting, follow the wizard to properly configure the changes ontology source.
Indexing the Ontology
The Lucene Query Tab (LQT) works off of a lucene index. To enable this, click on "Lucene" from the menu bar, and select "Index Ontology". A window will appear with a list of all the properties. By default, all properties are selected, and you may customize indexing by selecting the properties individually as well. Click 'Start', and you will notice a small status window at the top left hand of your screen. Once indexing has completed (Indexing usually completes when the status window disappears), a directory called "lucene" will have been created within the same directory as your new database project. It is essential to keep the newly created lucene directory at this location.
<Optional - but advised> Click on the "Properties" tab and click on the "Annotation" sub tab within the menu pane.
Click "code" in the Annotation Properties list. You should see the properties listed for code' within the "Property Editor" section of the GUI. Enusre that the property 'protégé:readOnly" is labeled as 'true'. This will prevent editors from changing the identifier for a concept once it is assigned.
Saving the New Database Project
Click "File", 'Save Project As.' Name the project and save to a directory on the server.
This act of saving will create an Annotations project in the same directory as the main project. Close the project but leave the
Protégé client open.
Setting up the Metaproject security
The sample Metaproject should be found in the Protege.Server-1.2.3.25/examples/server
...
folder.
...
Open
...
the
...
nci_metaproject.pprj
...
provided.
...
Click
...
on
...
the
...
"Instances"
...
tab
...
and
...
select
...
"Project"
...
in
...
the
...
list
...
to
...
the
...
left.
...
Select
...
"Ontology"
...
from
...
the
...
"Instance
...
Browser"
...
in
...
the
...
middle
...
and
...
click
...
the
...
"View
...
Ontology"
...
button
...
just
...
above
...
(It
...
looks
...
like
...
a
...
magnifying
...
glass).
...
In
...
the
...
window
...
that
...
opens
...
set
...
the
...
name
...
of
...
your
...
ontology
...
as
...
you
...
would
...
like
...
it
...
to
...
appear
...
when
...
people
...
access
...
it
...
from
...
the
...
server.
...
Just
...
below
...
that
...
set
...
the
...
absolute
...
path
...
to
...
the
...
project
...
file
...
created
...
in
...
3.3.3.7.
...
Close
...
just
...
this
...
subwindow
...
using
...
the
...
red
...
"X"
...
in
...
the
...
upper
...
right
...
of
...
the
...
subwindow.
...
Now
...
click
...
on
...
the
...
Annotation_Ontology
...
in
...
the
...
"Instance_Browser",
...
name
...
it
...
and
...
enter
...
the
...
path.
...
Close
...
the
...
subwindow.
...
Click
...
on
...
"User"
...
in
...
the
...
list
...
to
...
the
...
left.
...
Examine
...
the
...
existing
...
users
...
by
...
clicking
...
on
...
them.
...
Make
...
a
...
copy
...
of
...
the
...
_test_editor
...
user
...
and
...
give
...
it
...
a
...
new
...
name
...
and
...
password.
...
Make
...
note
...
of
...
this
...
information
...
for
...
use
...
in
...
logging
...
into
...
the
...
Protégé
...
Server
...
later.
...
Click
...
"File",
...
"Save
...
Project"
...
then
...
"Exit".
...
'ncitab.xml'
...
File
...
The
...
Protégé
...
Client
...
also
...
contains
...
an
...
ncitab.xml
...
file
...
which
...
is
...
used
...
to
...
populate
...
drop
...
down
...
menus
...
with
...
NCI-specific
...
values
...
in
...
the
...
Protégé
...
Client
...
also
...
provides
...
other
...
ontology-specific
...
configurations.
...
Towards
...
the
...
bottom
...
of
...
the
...
file,
...
curatorial
...
authorities
...
can
...
be
...
assigned
...
to
...
specific
...
editors.
...
For
...
example:
...
<authorization
...
prop="curatorial-authority">
...
<entry>
...
<authority>enter_authority_here</authority>
...
<username>enter_username_here</username>
...
</entry>
...
Selected
...
editors
...
can
...
be
...
authrorized
...
to
...
handle
...
specific
...
concepts
...
within
...
the
...
project.
...
NCIHeader.owl
...
File
...
This
...
file
...
is
...
optional,
...
but
...
can
...
be
...
copied
...
over
...
to
...
your
...
OWL
...
file
...
to
...
provide
...
the
...
required
...
NCI
...
properties
...
and
...
concepts.
...
The
...
codes
...
can
...
be
...
adjusted
...
as
...
necessary,
...
as
...
long
...
as
...
it
...
coincides
...
with
...
the
...
ncitab.xml
...
file.
...
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