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changes.mady.by.user Frost, Ruth (NIH/NCI) [C]

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Protégé NCI Thesaurus Admin Guide Cheatsheet v1.0

Panel

title	Contents of this Page

Table of Contents

minLevel	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

MobaXterm Professional
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
...

Build Notes

The automated build script will prompt for various configuration items (for files such as the run scripts, PromptNCIPlugin.properties, etc).
Do not use the default localhost for any IP addresses. Always use the machine name, and include the port.
Do not include PromptNCIPlugin.properties with a distributed client.
Set the max code + 1 in codegen.dat

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):
- start RMI
- start explanation server
- start Protégé server

Remote login
- Use MobaXterm (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)

...

- Run kill -9 [rmi pid]

Start explanation server
- From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z

...

- Run

...

- with

...

- option

...

- to

...

- periodically

...

- save

...

- the

...

- reasoner

...

- state

...

- at

...

- 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

...

starting

...

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

...

- 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

...

starting

...

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)

Database reload into an existing project

Preconditions – Thesaurus running normally

Thesaurus tables exist
ChaO tables exist
Metaproject exists
Prompt.properties exists and configured
Ncitab.xml exists and configured
Shell scripts all exist and configured
Prompt complete (if needed)
File exported

Steps

Stop protégé server.
Stop explanation server.
Start Protégé, New Project->Check Create from Exisitng Sources, select OWL/RDF Files->Find file->OWL DL->Finish
Save to temp project Thesaurus_Temp.pprj
Change to database project File->Convert Project to Format-> Select Clark-Parsia Protégé OWL/RDF Database->Enter the JDBC URL using the database ->Table (Thesaurus)-> Username (********)->Password(*******)
1. Overwrite existing database tables.
File->Save Project to the temp project
Close client. Reopen Thesaurus.pprj
1. Check that everything is configured correctly and the database can be reached.
Close client
Start explanation server and monitor
Start protégé server
Start client pointed at server
Reindex
Verify it works and returns queries
Classify

Configuring a New Project

(already logged-in in the server box)
Enable tabs in this order
- NCIEditTab
- LuceneQueryPlugin
- OWLProperties
- OWLMetadataTab
- ChangesTab
- ExplanationTab
Upon enabling the ChangesTab, click OK
- Dialogue will pop up. Select 2nd option 'Create ChAO stored in database' and click enable change tracking. Click OK.
- Create new DB dialogue table gets "annotation_" prefixed
- Enter DB credentials
- Click OK
File->Save Project
Configure->Deselect Changes tab, Options tab->Track changes should be checked
Disable other extra tabs (OWLClasses, OWLInstances, OWLForms)
Set display slots to read 'Preferred Name' for the NCI Edit tab as well as Property Tag within the Forms Tab for:
- owl:Class
- DatatypeProperty
- code
- ObjectProperty
Configure URL for explanation service.
Goto OWL->Preferences
- Disable Drag and Drop, verify reasoner URL is correct
- Visibility->uncheck rdfs:Class, owl:Class, rdf:Property
- Datatypes->rdf:XMLLiteral should be checked
- Tests->uncheck 'Find TODO list items' and 'List deprecated classes and properties'
Reasoning->Select Clark & Parsia
Reasoner Details->Click Synchronize Changes with Reasoner, Reasoner Behavior select Synchronize on query
Set OWL Preferences to read 'Manchester Syntax'
Set transitivity
Generate Lucene indices
- Lucene->Index Ontologies, accept all slots, Use Phoenetic and Standard indexers, click OK (this should take less than 20 minutes in a Production quality envrironment)
- Move lucene index from /app/protegeqa/data/Protege_x.y.z/NCIThesaurus to the Proege server directory
Save project
Exit Protégé

Configuring the Metaproject

Open the metaproject
Instance tab->Click User class
- In the Instance Browser copy an editor (to the number of users needed)
- Enter full name
- Change password
PolicyControlledObject->ProjectClass
- Verify Thesaurus instance Location is edited to the pprj location
- Verify Annotation Thesaurus instance Location is edited to the annotation_Thesaurus... location
  - It should be granted the 'GrpOp(World)' instance that does not contain the 'DisplayInList' instance to prevent it from showing as a selectable project on login
  - See 'DisplayInList' Project Setup Instructions for more details.
- File->Save Project->Exit

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 the client GUI, 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 without saving
Exit the client.

Troubleshooting

Q: After building the database, why am I getting this weird warning and Java RuntimeException?

Weird warning and Java RuntimeException. Image Added

A: You accidentally selected the 'Clark & Parsia Database' option. Start over and select the 'Clark & Parsia OWL/RDF Database' instead.

Q: I exported an owl file from my project, but now the project loads from a file. What's up?

A: When exporting an owl file, rename the project and not the owl file by itself. When renaming the project, your owl export will follow the same naming convention used.

Q: I've started a new project and am trying to enable the Changes tab, but am getting a red box and error similar to 'ncit.annotation_thesaurus doesn't exist'

A: This is due to a hard-coding where the application will attempt to find a project file named annotation_PROJECTNAME.pprj. Rename this project file if it exists so Protege can create a new one and is no longer trying to reference the old file.

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Content

Space Tools

Page History

Versions Compared

Old Version 11

New Version Current

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...

Build Notes

Production Login and Basic Server Operations

Prompt

Accept/Reject

Cycle

Database

Load

from

File

Database reload into an existing project

Configuring a New Project

Configuring the Metaproject

Configure Protégé Server for a Project

Classification (Standalone Mode)

Classification (Client/Server) Mode

Troubleshooting

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
...