 |
Page History
| Scrollbar | ||
|---|---|---|
|
Archive - Protégé BiomedGT Admin Guide Cheatsheet v1.1
| Panel | ||||
|---|---|---|---|---|
| ||||
|
Servers
cbiows501 - production
cbapp-q1001 - qa
cbvapp-d1012 - dev (VM)
cbvapp-s1005 - stage (VM)
Related Programs/Services
Reflection X (using "Direct" or xterm over SSH connection)
F-Secure SSH Client
F-Secure SSH File Transfer
Username and password advertised separately.
Relevant Directory Structure in the various boxes/VMs
Production
...
/usr/local/protege/Protege.Server-x.y.z
...
/usr/local/protege/Protege.Client-x.y.z
...
/usr/local/protege/Explanation.Server-x.y.z
...
/app/protégé/data
...
Dev,
...
QA,
...
Stage
...
/usr/local/protege/Protégé_x.x.x/
...
[EVS:PROTÉGÉ
...
INSTANCE
...
]/Protege.Server-x.y.z
...
/usr/local/protege/Protégé_x.x.x/
...
[EVS:PROTÉGÉ
...
INSTANCE
...
]/Protege.Client-x.y.z
...
/usr/local/protege/Protégé_x.x.x/
...
[EVS:PROTÉGÉ
...
INSTANCE
...
]/Explanation.Server-x.y.z
...
Dev,
...
QA,
...
Stage
...
SVN
...
files
...
for
...
builds
...
/app/protege/repo/<protégé
...
release
...
folder>
...
Production
...
login
...
and
...
basic
...
server
...
operations
...
If
...
the
...
protege
...
server
...
is
...
brought
...
down
...
for
...
maintenance,
...
classification,
...
Prompt
...
analysis,
...
and
...
so
...
on,
...
the
...
RMI
...
can
...
continue
...
running.
...
When
...
all
...
the
...
services
...
need
...
to
...
be
...
started
...
(e.g.
...
after
...
a
...
reboot),
...
follow
...
this
...
order
...
(see
...
bullets
...
below
...
for
...
details):
...
- start
...
- rmi
...
- start
...
- Explanation
...
- server
...
- start
...
- Protege
...
- server
...
Remote
...
login
...
- Use
...
- reflection
...
- X
...
- (or
...
- SSH
...
- client
...
- if
...
- running
...
- the
...
- Protege
...
- client
...
- is
...
- not
...
- required)
...
Start
...
rmiregistry
...
(configure
...
script
...
to
...
use
...
port
...
2633
...
in
...
PROD)
...
- From
...
- '/usr/local/protege/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/protege/Explanation.Server-x.y.z
...
- Run
...
- with
...
- option
...
- to
...
- periodically
...
- save
...
- the
...
- reasoner
...
- state
...
- at
...
- a
...
- desired
...
- time
...
- frame:
...
- ./start_explanation_server.sh
...
- --port
...
- 8090
...
- --protege-standalone
...
- /path/to/database/project/
...
- --persistance
...
- <numeric
...
- time
...
- value>
...
- Run
...
- w/out
...
- checking
...
- for
...
- any
...
- changes
...
- in
...
- ontology:
...
- ./start_explanation_server.sh
...
- --port
...
- 8090
...
- --protege-standalone
...
- /path/to/database/project/
...
- --no-ontology-sync
...
Re
...
start
...
Explanation
...
server
...
- From
...
- /usr/local/protege/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
...
- --persistance
...
Verifying
...
Explanation
...
servers
...
is
...
starting
...
up
...
correctly
...
- From
...
- /usr/local/protege/Explanation.Server-x.y.z
...
- Run
...
- tail
...
- -f
...
- nohup.out
...
Shutdown
...
Explanation
...
server
...
- From
...
- /usr/local/protege/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
...
Protege
...
server
...
- From
...
- /usr/local/protege/Protege.Server-x.y.z
...
- Run
...
- ./run_protege_server_nci.sh
...
Shutdown
...
Protege
...
server
...
- From
...
- /usr/local/protege/Protege.Server-x.y.z
...
- Run
...
- ./shutdown_protege_server.sh
...
- localhost:
...
- 2633
...
Verifying
...
Protege
...
servers
...
is
...
starting
...
up
...
correctly
...
- From
...
- /usr/local/protege/Protege.Server-x.y.z
...
- Run
...
- tail
...
- -f
...
- console.txt
...
Start
...
Protege
...
client
...
- From
...
- /usr/local/protege/Protege.Client-x.y.z
...
- Run
...
- ./run_protege_BGT.sh
...
Prompt
...
Accept/Reject
...
cycle
...
- Advertise
...
- (email/chat)
...
- the
...
- server
...
- is
...
- going
...
- to
...
- be
...
- shut
...
- down
...
- Clean
...
- up
...
- Pre-Merged,
...
- and
...
- Pre-Reitred
...
- concepts.
...
- Remote
...
- login
...
- to
...
- the
...
- host
...
- computer
...
- using
...
- Reflection
...
- X
...
- Shut
...
- down
...
- Protege
...
- server
...
- Shut
...
- down
...
- Explanation
...
- server.
...
- Start
...
- Protege
...
- client.
...
- Connect
...
- to
...
- database
...
- project
...
- by
...
- following
...
- the
...
- path:
...
- /app/protege/data/BiomedGT.pprj.
...
- Enable
...
- PromptTab
...
- 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).
...
- 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
...
- next
...
- Prompt
...
- comparison
...
- or
...
- publication.
...
- Convert
...
- Project
...
- to
...
- Format
...
- ->
...
- OWL
...
- /
...
- RDF
...
- Files.
...
- This
...
- creates
...
- a
...
- new
...
- project
...
- .pprj
...
- and
...
- associated
...
- OWL
...
- file,
...
- give
...
- it
...
- a
...
- name
...
- with
...
- a
...
- date
...
- suffix,
...
- example
...
- BiomedGTFile-071128.pprj.
...
- Close
...
- project
...
- without
...
- saving,
...
- and
...
- exit
...
- the
...
- client.
...
- In
...
- the
...
- Reflection
...
- X
...
- console,
...
- navigate
...
- to
...
- /app/protege/data/
...
- and
...
- look
...
- for
...
- any
...
- BiomedGT
...
- accept
...
- files:
...
- (BiomedGT-accept.pprj,
...
- .pjrn,
...
- .rdf,
...
- .rdfs)
...
- and
...
- remove
...
- them
...
- from
...
- the
...
- directory
...
- by
...
- typing
...
- 'rm
...
- BiomedGT-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:
...
i)
...
- Reopen
...
- Protégé
...
- client.
...
ii)
...
- Click
...
- 'Project',
...
- 'Configure',
...
- enable
...
- 'OWLClasses
...
- Tab'.
...
iii)
...
- Click
...
- 'Reasoning',
...
- 'Classify
...
- Taxonomy'.
...
iv)
...
- Save
...
- the
...
- Inferred
...
- Ontolgoy
...
- using
...
- the
...
- save
...
- button
...
- in
...
- the
...
- Inferred
...
- Hierarchy
...
- section.
...
- Give
...
- the
...
- naming
...
- convention
...
- 'BiomedGT-Inferred-YYMMDD.owl'
...
- *
...
- Startup
...
- Protege
...
- server.
...
- Verify
...
- Protege
...
- server
...
- is
...
- up.
...
- Verify
...
- Explanation
...
- tab
...
- communicates
...
- with
...
- 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:
...
- i)
...
- the
...
- filename
...
- of
...
- the
...
- baseline
...
- and
...
- (ii)
...
- the
...
- length
...
- of
...
- 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
...
- help
...
- keep
...
- the
...
- Protégé
...
- server
...
- clean
...
- and
...
- organized.
...
Database
...
Load
...
from
...
File
...
- Remote
...
- login
...
- to
...
- the
...
- host
...
- computer
...
- using
...
- Reflection
...
- X.
...
- cd
...
- to
...
- /usr/local/protege/Protege.Client-x.y.z.
...
- Start
...
- protege
...
- ("./run_protege_BGT.sh").
...
- Load
...
- file
...
- from
...
- /app/protege/data/(new
...
- project).
...
- Convert
...
- project
...
- to
...
- format
...
- (Clark
...
- &
...
- Parsia
...
- owl
...
- /
...
- rdf
...
- database).
...
- initial
...
- project
...
- BiomedGT.pprj
...
- (as
...
- opposed
...
- to
...
- baselines).
...
- Configure
...
- project
...
- (see
...
- below,
...
- include
...
- Save
...
- but
...
- don't
...
- Exit).
...
- Convert
...
- project
...
- to
...
- format
...
- (owl
...
- /
...
- rdf
...
- file)
...
- for
...
- a
...
- file
...
- baseline,
...
- with
...
- date.
...
- Exit
...
- Protege
...
- without
...
- saving
...
- (the
...
- Save
...
- gets
...
- done
...
- automatically
...
- during
...
- the
...
- conversion).
...
Configuring
...
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).
- Enable journaling.
- Disable redo/undo.
- Set OWL Preferences items:
- Configure URL to the correct explanation server.
- Set preferences to read Manchester Syntax.
- Disable drag and drop in owl preferences.
- Disable test of deprecated classes/properties.
- Set Visibility to uncheck all MetaData Items.
- Set Reasoning menu items:
- Click on Reasoning menu, and ensure that Clark & Parsia Custom Protégé 3.x Reasoner is selected on the menu list.
- Click on Reasoning menu, C & P Custom Protégé 3.x Reasoner Details, and ensure the 'Synchronize Changes with Reasoner' box is checked, and click OK.
- Set transitivity.
- Set display slots to read rdfs:label for NCI Edit tab as well as Property Tag.
- Generate Lucene indices from Lucene menu. Ensure both Phonetic and Standard boxes are checked prior to indexing.
- Start explanation server, point to the newly created project. Once the server's up and running, save the project.
- Exit protege.
Configure protege server for a project
- Edit run_protege_server_nci.sh.
...
a)
...
to
...
include
...
the
...
proper
...
directory
...
path
...
for
...
the
...
nci_metaproject
...
file
...
-
...
/app/protege/data/metaproject/.
...
b)
...
to
...
use
...
the
...
correct
...
rmi
...
port
...
(use
...
2633).
...
Classification
...
(Standalone
...
mode)
...
- Advertise
...
- the
...
- protege
...
- server
...
- is
...
- going
...
- to
...
- be
...
- shutdown.
...
- Remote
...
- login
...
- to
...
- the
...
- host
...
- computer
...
- using
...
- Reflection
...
- X.
...
- Username
...
- and
...
- password
...
- are
...
- advertised
...
- separately.
...
- Shutdown
...
- Protege
...
- server.
...
- Restart
...
- Explanation
...
- server.
...
- Start
...
- protege
...
- client.
...
- Connect
...
- to
...
- database
...
- project.
...
- in
...
- /app/protege/data/.
...
- file
...
- -
...
- BiomedGT.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
...
...
- it.
...
- Process
...
- table
...
- from
...
- previous
...
- classification
...
- (accept/reject).
...
- Close
...
- project
...
- without
...
- saving.
...
- Start
...
- protege
...
- server.
...
- Verify
...
- protege
...
- server
...
- is
...
- running.
...
- connect
...
- to
...
- the
...
- server
...
- from
...
- the
...
- client.
...
- exit
...
- the
...
- client.
...
- Exit
...
- terminal.
...
- Exit
...
- reflection
...
- X.
...
Classification
...
(client/server
...
mode)
...
- From
...
- the
...
- GUI,
...
- enable
...
- OWLClassesTab
...
- (results
...
- are
...
- shown
...
- there).
...
- From
...
- the
...
- OWL
...
- menu,
...
- select
...
- "Classify
...
- taxonomy",
...
- it
...
- takes
...
- about
...
- 20
...
- minutes.
...
- Once
...
- classifications
...
- 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
...
...
- it.
...
- Process
...
- table
...
- from
...
- previous
...
- classification
...
- (accept/reject).
...
- Close
...
- project
...
- without
...
- saving.
...
- Exit
...
- the
...
- client.
...
| Scrollbar |
|---|
...
|
...
|
...
