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{scrollbar:icons=false} h1. Protégé NCI Thesaurus Admin Guide Cheatsheet

Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0

{:=

Panel

title

	Contents

this

Page

} {

Table of Contents

minLevel

=2} {panel} h2. Servers || Name || Description || | cbiows501 \\ | Production (protegeqa user) \\ | | cbvapp-s1005 \\ | Stage (protegeadm user) \\ | | cbapp-q1001 \\ | QA (protegeadm user) \\ | | cbvapp-d1012 \\ | Dev (protegeadm user) \\ | h2. Related Programs/Services * Reflection X (using "Direct" or xterm over SSH connection). * F-Secure SSH Client * F-Secure SSH Transfer * Username and password advertised separately h2. Related Directory Structure in the Various Boxes/VMs h3. Production *

	2

Servers

Name	Description
cbiows501	Production (protegeqa user)
cbvapp-s1005	Stage (protegeadm user)
cbapp-q1001	QA (protegeadm user)
cbvapp-d1012	Dev (protegeadm user)

Related Programs/Services

Reflection X (using "Direct" or xterm over SSH connection).
F-Secure SSH Client
F-Secure SSH Transfer
Username and password advertised separately

Related Directory Structure in the Various Boxes/VMs

Production

/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z

...

/usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z

...

/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z

...

/app/protegeqa/data/

...

[EVS:PROTEGE

...

INSTANCE

...

]

...

Dev,

...

QA,

...

Stage

...

usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Protege.Server-x.y.z
...
usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Protege.Client-x.y.z
...
usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Explanation.Server-x.y.z
...

Dev,

...

QA,

...

Stage

...

File

...

for

...

Builds

...

/app/protege/repo
...

Production

...

Login

...

and

...

Basic

...

Server

...

Operations

...

If
...
the
...
Protégé
...
server
...
is
...
brought
...
down
...
for
...
maintenance,
...
classification,
...
Prompt
...
analysis,
...
and
...
so
...
on,
...
the
...
RMI
...
can
...
continue
...
running.
...
While
...
all
...
the
...
services
...
need
...
to
...
be
...
started
...
(e.g.
...
after
...
a
...
reboot),
...
follow
...
this
...
order
...
(see
...
the
...
following
...
bullets
...
for
...
details):
...
star
...
RMI
...
start
...
explanation
...
server
...
start
...
Protégé
...
server
...
Remote
...
login
...
Use
...
reflection
...
X
...
(or
...
SSH
...
client
...
if
...
running
...
the
...
Protégé
...
client
...
is
...
not
...
required).
...
Start
...
RMI
...
registry
...
(configure
...
script
...
to
...
use
...
port
...
2822
...
in
...
production
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
...
Run
...
./run_rmiregistry.sh
...
Shutdown
...
rmiregistry
...
Kill
...
from
...
OS
...
(identify
...
with
...
ps
...
-ef
...
|
...
grep
...
rmiregistry)
...
Start
...
explanation
...
server
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
...
Run
...
with
...
option
...
to
...
periodically
...
save
...
the
...
reasoner
...
state
...
at
...
a
...
desired
...
time
...
frame:
...
./start_explanation_server.sh
...
--port
...
8092
...
--protege-standalone
...
/path/to/database/project/
...
--persistence
...
<numeric
...
time
...
value>
...
Run
...
w/out
...
checking
...
for
...
any
...
changes
...
in
...
ontology:
...
./start_explanation_server.sh
...
--port
...
8092
...
--protege-standalone
...
/path/to/database/project/
...
--no-ontology-sync
...
Restart
...
explanation
...
server
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
...
Run
...
with
...
option
...
to
...
restore
...
to
...
previous
...
saved
...
state
...
of
...
reasoner,
...
as
...
well
...
as
...
to
...
check
...
for
...
any
...
recent
...
changes
...
in
...
the
...
ontology
...
from
...
the
...
previous
...
saved
...
state:
...
./restart_explanation_server.sh
...
--restore
...
--persistaece
...
Verifying
...
explanation
...
servers
...
is
...
starting
...
up
...
correctly
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
...
Run
...
tail
...
-f
...
nohup.out
...
Shutdown
...
explanation
...
sever
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
...
Run
...
./stop_explanation_server.sh
...
Note
...
-
...
after
...
a
...
shutdown,
...
the
...
server
...
can't
...
be
...
"restarted",
...
it
...
must
...
be
...
"started"
...
instead.
...
Start
...
Protégé
...
Server
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
...
Run
...
./run_protege_server_nci.sh
...
Shutdown
...
Protégé
...
Server
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
...
Run
...
./shutdown_protege_server.sh
...
localhost:2822
...
Verifying
...
Protégé
...
servers
...
is
...
starting
...
up
...
correctly
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
...
Run
...
tail
...
-f
...
console.txt
...
Start
...
Protégé
...
client
...
From
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z
...
Run
...
./run_protege_NCIT.sh
...

Prompt

...

Accept/Reject

...

Cycle

...

Advertise
...
(email/chat)
...
the
...
server
...
is
...
going
...
to
...
be
...
shutdown
...
Clean
...
up
...
Pre-Merged,
...
and
...
Pre-Retired
...
concepts.
...
Remote
...
login
...
to
...
the
...
host
...
computer
...
using
...
Reflection
...
X
...
Shut
...
down
...
Protégé
...
server
...
Shut
...
down
...
explanation
...
server
...
Start
...
Protégé
...
client
...
Connect
...
to
...
database
...
project
...
by
...
following
...
the
...
path:
...
/app/protegeqa/data/Protege_1.2.3/NCIThesaurus/Thesaurus.pprj
...
Enable
...
Prompt
...
Tab
...
in
...
menu
...
(in
...
Project
...
-->
...
Configuration
...
dialog)
...
Compare
...
against
...
previous
...
baseline
...
file
...
/
...
database
...
project
...
(pprj
...
file).
...
Accept/reject
...
changes
...
Save
...
concept
...
history
...
(in
...
"save"
...
icon
...
in
...
'Table
...
View'
...
tab)
...
Disable
...
PromptTab
...
(in
...
Configuration
...
dialog)
...
Adjust
...
baseline
...
version
...
in
...
Metadata
...
tab
...
In
...
the
...
Protégé
...
GUI
...
menu,
...
click
...
'Change',
...
'Clean
...
up
...
Changes
...
Ontology'.
...
Ensure
...
that
...
'Delete
...
Changes'
...
and
...
'Archive
...
Changes'
...
remain
...
checked.
...
Click
...
'OK'.
...
After
...
the
...
process
...
has
...
been
...
completed,
...
click
...
'Change',
...
'Save
...
Changes
...
Ontology'
...
Export
...
file
...
for
...
the
...
next
...
Prompt
...
comparison
...
or
...
publication
...
Click
...
'File'
...
-,
...
'Convert
...
Project
...
to
...
Format',
...
'OWL/RDF
...
Files
...
this
...
creates
...
a
...
new
...
project
...
.pprj
...
file
...
and
...
associated
...
OWL
...
file,
...
give
...
it
...
a
...
name
...
with
...
a
...
date
...
suffix,
...
example:
...
ThesaurusInterim-071120.pprj
...
Close
...
project
...
without
...
saving,
...
and
...
exit
...
client
...
In
...
Reflection
...
X
...
console,
...
navigate
...
to
...
/app/protegeqa/data/Protege_x.x.x/NCIThesaurus
...
and
...
look
...
for
...
any
...
Thesaurus
...
accept
...
files:
...
(Thesaurus-accept.pprj,
...
pjrn,
...
.rdf,
...
rdfs)
...
and
...
remove
...
them
...
from
...
the
...
directory
...
by
...
typing
...
'
...
rm
...
Thesaurus-accept.pprj
...
'
...
and
...
so
...
on
...
for
...
the
...
other
...
files.
...
Start
...
explanation
...
server
...
(always
...
restart
...
explanation
...
server
...
first
...
before
...
the
...
Protégé
...
server)
...
For
...
production
...
tier
...
at
...
the
...
end
...
of
...
the
...
month:
...
Reopen Protégé client
Click 'Project',
...
'Configure',
...
enable
...
'OWL
...
Classes
...
Tab'
...
Click
...
'OWL',
...
'Classify
...
Taxonomy'
...
Save
...
the
...
Inferred
...
Ontology
...
using
...
the
...
save
...
button
...
on
...
the
...
Inferred
...
Hierarchy
...
section.
...
Give
...
the
...
naming
...
convention
...
'Thesaurus-Inferred-YYMMDD.owl
...
Start
...
up
...
Protégé
...
server
...
Verify
...
Protégé
...
server
...
is
...
up
...
Verify
...
explanation
...
tab
...
communicates
...
with
...
the
...
explanation
...
server
...
Exit
...
remote
...
program
...
Advertise
...
that
...
the
...
server
...
is
...
back
...
up
...
For
...
end-of-the-month
...
publications,
...
after
...
performing
...
a
...
prompt,
...
notify
...
Tracy,
...
John,
...
or
...
Rob
...
of
...
the
...
availability
...
of
...
the
...
new
...
baseline
...
In
...
the
...
notification
...
include:
...
(a)
...
the
...
filename
...
of
...
the
...
baseline
...
and
...
(b)
...
the
...
length
...
of
...
the
...
time
...
for
...
the
...
Prompt/export
...
to
...
file
...
to
...
complete.
...
The
...
raw
...
exports
...
(OWL
...
files
...
only)
...
will
...
be
...
archived
...
in
...
the
...
private
...
FTP
...
site,and
...
the
...
processed
...
exports
...
in
...
the
...
anonymous
...
FTP
...
site.
...
This
...
will
...
keep
...
the
...
Protégé
...
server
...
clean
...
and
...
organized.
...

Database

...

Load

...

from

...

File

...

Remote
...
login
...
to
...
the
...
host
...
computer
...
using
...
Reflection
...
X
...
cd
...
to
...
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z
...
Start
...
Protégé
...
client
...
('
...
./run_protege_NCIT.sh'
...
)
...
Load
...
file
...
from
...
/app/protegeqa/data/Protege_x.y.z/NCIThesaurus
...
(new
...
project)
...
Convert
...
project
...
to
...
format
...
(OWL/RDF
...
database)
...
initial
...
project
...
-
...
Thesaurus.pprj
...
(as
...
opposed
...
to
...
baselines)
...
Configure
...
project
...
(see
...
below,
...
include
...
Save,
...
but
...
don't
...
Exit).
...
Exit
...
Protégé
...
without
...
saving
...
(the
...
Save
...
gets
...
done
...
automatically
...
during
...
the
...
conversion)
...

Configuring

...

a

...

New

...

Project

...

(already
...
logged-in
...
in
...
the
...
server
...
box)
...
Enable
...
tabs
...
nciedittab
advanced query
properties
metadata
changes
explanation tab
Disable extra tabs (OWLClasses, OWLInstances, OWLForms)
Configure URL for explanation service.
Enable journaling
Disable redo/undo
Set OWL Preferences to read 'Manchester Syntax'
Set transitivity
Set display slots to read 'Preferred Name' for the NCI Edit tab as well as Property Tag
Disable drag and drop in 'OWL Preferences'
Disable test of deprecated classes/properties
Set Visibility tab to uncheck all MetaData items
Generate Lucene indices
Move lucene index from /app/protegeqa/data/Protege_x.y.z/NCIThesaurus
...
to
...
the
...
Proege
...
server
...
directory
...
Save
...
project
...
Exit
...
Protégé

Configure Protégé Server for a Project

Edit run_protege_server_nci.sh

...

- to

...

- include

...

- the

...

- proper

...

- directory

...

- path

...

- for

...

- the

...

- nci_metaproject

...

- file

...

- /app/protegeqa/data/NCIThesaurusMetaProject/

...

- to

...

- use

...

- the

...

- correct

...

- rmi

...

- port

...

- (use

...

- 2822)

...

Classification

...

(Standalone

...

Mode)

...

Advertise
...
the
...
Protégé
...
server
...
is
...
going
...
to
...
be
...
shutdown
...
Remote
...
login
...
to
...
the
...
host
...
computer
...
using
...
Reflection
...
X
...
username
...
and
...
password
...
are
...
advertised
...
separately
...
Shutdown
...
Protégé
...
server
...
Restart
...
explanation
...
server
...
Start
...
Protégé
...
client
...
Connect
...
to
...
the
...
database
...
project
...
in /app/protegeqa/data/Protege_x.y.z/NCIThesaurus
...
file Thesaurus.pprj
...
Enable
...
OWLClassesTab
...
(results
...
are
...
shown
...
there)
...
From
...
the
...
OWL
...
menu,
...
select
...
'
...
Classify
...
Taxonomy',
...
it
...
takes
...
about
...
20
...
minutes
...
Once
...
classification
...
is
...
complete,
...
an
...
inferred
...
hierarchy
...
panel
...
and
...
a
...
list
...
panel
...
are
...
displayed
...
Accept
...
retreeing
...
suggestions
...
in
...
the
...
list
...
panel
...
as
...
per
...
guideline.
...
Generate
...
table
...
to
...
pass
...
around
...
to
...
editors
...
and
...
mail
...
it
...
Process
...
table
...
from
...
previous
...
classification
...
(accept/reject)
...
Close
...
project
...
withtout
...
saving
...
Start
...
Protégé
...
server
...
Verify
...
Protégé
...
server
...
is
...
running
...
connect
...
to
...
server
...
from
...
the
...
client
...
exit
...
the
...
client
...
Exit
...
console
...
Exit
...
Reflection
...
X
...

Classification

...

(Client/Server)

...

Mode

...

From

...

client

...

GUI,

...

enable

...

OWLClassesTab

...

(results

...

shown

...

there)

...

From

...

menu,

...

select

...

Classify

...

Taxonomy'

...

takes

...

about

...

minutes

...

Once

...

classification

...

complete,

...

inferred

...

hierarchy

...

panel

...

list

...

panel

...

displayed.

...

retreeing

...

suggestions

...

list

...

panel

...

guideline

...

Generate

...

table

...

pass

...

around

...

editors

...

mail

...

Process

...

table

...

from

...

classification

...

(accept/reject)

...

project

...

without

...

saving

...

Exit

...

client.

Wiki Markup
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Content

Space Tools

Page History

Versions Compared

Old Version 11

New Version 12

Key

Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0

Servers

Related Programs/Services

Related Directory Structure in the Various Boxes/VMs

Production

Dev,

QA,

Stage

usr/local/protege/Protege_x.x.x/...[EVS:PROTEGE ... INSTANCE...]/Protege.Server-x.y.z...usr/local/protege/Protege_x.x.x/...[EVS:PROTEGE ... INSTANCE...]/Protege.Client-x.y.z...usr/local/protege/Protege_x.x.x/...[EVS:PROTEGE ... INSTANCE...]/Explanation.Server-x.y.z...

Dev,

QA,

Stage

File

Directory

for

Builds

/app/protege/repo...

Production

Login

and

Basic

Server

Operations

Prompt

Accept/Reject

Cycle

Database

Load

from

File

Configuring

a

New

Project

Configure Protégé Server for a Project

Classification

(Standalone

Mode)

Classification

(Client/Server)

Mode

usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Protege.Server-x.y.z
...
usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Protege.Client-x.y.z
...
usr/local/protege/Protege_x.x.x/
...
[EVS:PROTEGE
...
INSTANCE
...
]/Explanation.Server-x.y.z
...

/app/protege/repo
...