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Protégé Software Updates and Configuring New Database Project
A new project file will need to be created using the raw OWL file located in
...
/app/protégé/data/Protégé_x.x/<PROTÉGÉ
...
INSTANCE>.
...
Usually
...
newer,
...
more
...
fresher
...
data
...
is
...
available
...
by
...
the
...
editors
...
after
...
performing
...
a
...
PROMPT
...
of
...
production
...
data.
...
Each
...
baseline
...
file
...
that
...
is
...
created
...
after
...
each
...
session
...
can
...
be
...
used
...
as
...
test
...
data.
...
If
...
however,
...
for
...
some
...
reason,
...
an
...
OWL
...
file
...
must
...
be
...
created
...
manually,
...
instructions
...
are
...
available
...
on
...
how
...
to
...
...
...
...
...
...
...
.
As long as no changes have been made to the behavior of the startup scripts, the following files and scripts should be copied over from the old Protégé.Server version to the new folder:
Code Block run_rmiregistry.sh run_protege\_ server_nci.sh shutdown_protege_server.sh codegen.properties codegen.dat
...
- If you do need to use new scripts, make sure to adjust the memory upwards from the default in the run_protege_server_nci.sh
...
- script.
...
- The
...
- following
...
...
- displays
...
- how
...
- much
...
- memory
...
- to
...
- allocate
...
- for
...
- each
...
- script,
...
- per
...
- tier.
...
- You
...
- will
...
- also
...
- need
...
- to
...
- adjust
...
- the
...
- rmi.registry
...
- and
...
- rmi.server
...
- ports,
...
- the
...
- hostname
...
- and
...
- the
...
- metaproject
...
- location
...
- in
...
- this
...
- same
...
- file.
...
- Please
...
- view
...
- Appendix
...
- A
...
- for
...
- port
...
- information
...
- for
...
- each
...
- tier.
...
As
...
long
...
as
...
no
...
changes
...
have
...
been
...
made
...
to
...
the
...
behavior
...
of
...
the
...
startup
...
scripts,
...
navigate
...
to
...
the
...
Protégé.Client
...
folder
...
and
...
transfer
...
the
...
following
...
script:
...
Code Block
...
run_protege_BGT.sh (BiomedGT) or run_protege_NCIT.sh (NCIThesaurus)
...
- If you do need to use a new script, make sure the -Xmx memory is adjusted upwards from the default from the table.
As long as no changes have been made to the behavior of the startup scripts, navigate to the Explanation.Server directory and transfer the following files:
Code Block restart_explanation_server.sh stop_explanation_server.sh start_explanation_server.sh
...
The
...
'protege_install'
...
path
...
will
...
need
...
to
...
modified
...
in
...
order
...
to
...
specify
...
the
...
correct
...
Protégé
...
server
...
version.
...
- To
...
- edit,
...
- type
...
- 'vi
...
- _start_explanation_server.sh'
...
- to
...
- view
...
- the
...
- script
...
- from
...
- the
...
- vi
...
- editor.
...
- Type
...
- 'shift
...
- +
...
- I'
...
- and
...
- edit
...
- the
...
- server
...
- number
...
- to
...
- the
...
- correct
...
- version
...
- number.
...
- Press
...
- 'esc',
...
- then
...
- ':wq'
...
- to
...
- save
...
- changes
...
- and
...
- exit
...
- the
...
- editor.
...
- If
...
- you
...
- do
...
- need
...
- to
...
- use
...
- a
...
- new
...
- script,
...
- utilize
...
- the
...
...
- for
...
- the
...
- explanation
...
- server
...
- startup
...
- script.
...
- There
...
- should
...
- be
...
- no
...
- other
...
- edits
...
- that
...
- need
...
- to
...
- be
...
- made.
...
- Navigate
...
- to
...
- the
...
- Protégé
...
- server,
...
- and
...
- open
...
- the
...
- 'codegen.properties'
...
- file
...
- using
...
- a
...
- vi
...
- editor.
...
- To
...
- do
...
- this,
...
- type
...
- 'vi
...
- codegen.properties'.
...
- Once
...
- the
...
- file
...
- is
...
- viewable
...
- from
...
- vi,
...
- type
...
- "
...
- i"
...
- to
...
- edit.
...
- The
...
- code.prefix
...
- value
...
- can
...
- be
...
- adjusted,
...
- depending
...
- on
...
- which
...
- Protégé
...
- Instance
...
- is
...
- being
...
- used
...
- .
...
- BiomedGT
...
- used a
...
- prefix
...
- of
...
- 'B',
...
- while
...
- NCI
...
- Thesaurus
...
- uses
...
- 'C'.
...
- Keep
...
- the
...
- seed
...
- number
...
- at
...
- 100000.
...
- Save
...
- and
...
- exit
...
- the
...
- file
...
- by
...
- typing
...
- 'esc',
...
- then
...
- ':wq'.
...
- Open
...
- the
...
- 'codegen.dat'
...
- file
...
- in
...
- the
...
- vi
...
- editor.
...
- You
...
- will
...
- notice
...
- a
...
- number
...
- which
...
- represents
...
- a
...
- code
...
- that
...
- will
...
- be
...
- assigned
...
- to
...
- the
...
- concept
...
- code
...
- created
...
- in
...
- the
...
- database
...
- project.
...
- Set
...
- this
...
- number
...
- to
...
- 102000.
...
- Save
...
- and
...
- exit
...
- the
...
- file.
...
- Open
...
- the
...
- Protégé
...
- client
...
- folder,
...
- and
...
- click
...
- on
...
- '
...
- run_protege
...
- <PROTEGE-INSTANCE>_'
...
- to
...
- open
...
- the
...
- client.
...
- Once
...
- it
...
- is
...
- open,
...
- click
...
- on
...
- "Create
...
- New
...
- Project".
...
- Select
...
- OWL/RDF
...
- File,
...
- and
...
- check
...
- "Create
...
- from
...
- existing
...
- source".
...
- Click
...
- Next.
...
- A
...
- window
...
- will
...
- open
...
- requesting
...
- the
...
- address
...
- of
...
- the
...
- source
...
- of
...
- the
...
- OWL
...
- file.
...
- Navigate
...
- to
...
- /app/protege/data/Protege_x.x/<PROTEGE-INSTANCE>/
...
- and
...
- select the OWL file, and click next. Leave the next two windows to their default values, then click Finish. Loading the file to the client will take approximately 5-10 minutes.
- The following few steps reference the deprecated BiomedGT project and may be ignored.
Once the file is loaded, the ontology repository settings will need to be changed if configuring a BiomedGT project. From the menu bar, click 'OWL', and 'Ontology Repositories'. The Repository Manager window is now displayed with a list of default project repository locations underneath the 'Project repository' tab. Remove the following URL repositories:
Code Block http://ncicb.nih.gov/xml/owl/EVS/BGTCommonWords.owl http://ncicb.nih.gov/xml/owl/EVS/BGTThesaurusNodes.owl http://ncicb.nih.gov/xml/owl/EVS/External.owl
...
- There should be two URLs remaining, one referencing BFO, and another referencing protege-dc.
...
- Those
...
- will
...
- remain
...
- as
...
- is.
...
- The
...
- removed
...
- repositories
...
- will
...
- then
...
- be
...
- re-added
...
- to
...
- the
...
- list,
...
- but
...
- referenced
...
- locally.
...
- Accessing
...
- local
...
- copies
...
- of
...
- an
...
- external
...
- ontology
...
- increases
...
- performance
...
- as
...
- well
...
- as
...
- dependability
...
- of
...
- the
...
- ontology
...
- (the
...
- ontology
...
- URL
...
- might
...
- be
...
- down).
...
- To
...
- read
...
- locally,
...
- click
...
- on
...
- the
...
- white
...
- plus
...
- button
...
- located
...
- at
...
- the
...
- top
...
- right
...
- of
...
- the
...
- window.
...
- Follow
...
- the
...
- wizard
...
- by
...
- specifying
...
- the
...
- location
...
- of
...
- your
...
- local
...
- folder.
...
- Ensure
...
- that
...
- the
...
- 'Force
...
- Read-Only'
...
- box
...
- is
...
- unchecked.
...
- Once
...
- the
...
- window
...
- is
...
- closed,
...
- a
...
- pop-up
...
- window
...
- is
...
- displayed
...
- prompting
...
- you
...
- to
...
- save
...
- the
...
- settings
...
- and
...
- to
...
- reload
...
- the
...
- data
...
- into
...
- the
...
- client.
...
- Select
...
- the
...
- 'Reload'
...
- button,
...
- and
...
- the
...
- client
...
- should
...
- save
...
- the
...
- settings
...
- and
...
- reload
...
- the
...
- client.
...
- This
...
- step
...
- should
...
- anywhere
...
- from
...
- 10-20
...
- minutes,
...
- depending
...
- on
...
- your
...
- machine's
...
- resources.
...
- End of steps pertaining to BiomedGT
- Once loaded (the GUI should be visible with the OWL file displayed), the project file can now be converted to a Clark & Parsia OWL/RDF database. Click File, Convert Project to Format, Clark & Parsia OWL / RDF database.
- In the database info window, enter all requested database info and click finish. Give the Project name the following naming convention: <PROTEGE INSTANCE>-YYMMDD-DB.pprj
...
- .
...
- Note
...
- that
...
- the
...
- JDBC
...
- URL
...
- must
...
- be
...
- in
...
- the
...
- following
...
- format:
...
- jdbc:mysql://<databasehostname>:<port>/<database
...
- name> (Please look at the database info for each instance and tier). Give the table name the following naming convention: <PROTEGE-INSTANCE>_<YYMMDD>_<tier>_<release number>. Conversion can take anywhere up to 2.5 hours.
- After conversion of the project file, you can verify that the database has been created by utilizing a DBMS (such as DB Visualizer) to view if the table has been created. Once verified, the project is now ready to be configured from the client.
- Set transitivity by clicking the properties tag, and perform a search for the 'Anatomic_Structure_Has_Location'
...
- property.
...
- Select,
...
- and
...
- check
...
- the
...
- box
...
- marked
...
- transitive.
...
- Repeat
...
- the
...
- same
...
- step
...
- for
...
- the
...
- 'Anatomic_Structure_Is_Physical_Part_Of'
...
- property.
...
- Set
...
- the
...
- display
...
- slots
...
- by
...
- clicking
...
- the
...
- NCIEdit
...
- tab,
...
- and
...
- clicking
...
- 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
...
- 'rdfs:label'.
...
- Next,
...
- click
...
- the
...
- Properties
...
- tab,
...
- and
...
- click
...
- the
...
- "F"
...
- tab
...
- on
...
- the
...
- very
...
- right.
...
- Click
...
- 'OK'
...
- for
...
- the
...
- forms
...
- dialogue
...
- box.
...
- On
...
- the
...
- left
...
- hand
...
- menu,
...
- click
...
- on
...
- 'owl:DatatypeProperty,
...
- and
...
- set
...
- its 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.
...
- Click
...
- 'OWL'
...
- on
...
- the
...
- menu
...
- tab,
...
- and
...
- select
...
- 'preferences'.
...
- On
...
- the
...
- General
...
- tab,
...
- Disable
...
- the
...
- drag
...
- and
...
- drop
...
- feature,
...
- and
...
- set
...
- the
...
- explanation
...
- server
...
- URL
...
- to
...
- 'http://<Protege
...
- Server
...
- Address>:<port>/explain.
...
- The
...
- correct
...
- port
...
- per
...
- tier
...
- can
...
- be
...
- determined
...
- from
...
- the
...
...
...
...
- .
- In the Tests tab, disable test of deprecated classes/properties.
...
- This
...
- should
...
- be
...
- the
...
- fifth
...
- entry
...
- down.
- Click on the visibility tab from the window, and disable all the boxes in the MetaClasses section. Close the window.
- Click 'EditTab' on the menu bar, and select 'preferences'. Click on the 'panels' tab, and ensure that all four checkboxes are checked (Retire, Split, Merge, and Copy). Click the close button.
Click 'Project' on the menu bar, and select 'configure'. On the Tab Widgets tab, enable only the following boxes from the Widgets tab and put in the following order:
Code Block NCIEditTab LuceneQueryPlugin OWLPropertiesTab OWLMetadataTag ChangesTab ExplanationTab
...
- Click on the 'options'
...
- tab
...
- and
...
- enable
...
- journaling
...
- and
...
- disable
...
- redo/undo.
...
- After
...
- closing
...
- the
...
- configurations
...
- window,
...
- a
...
- changes
...
- ontology
...
- window
...
- will
...
- appear
...
- prompting
...
- you
...
- to
...
- select
...
- how
...
- to
...
- configure
...
- the
...
- annotations
...
- project.
...
- Currently,
...
- all
...
- annotations
...
- and
...
- changes
...
- are
...
- being
...
- stored
...
- into
...
- a
...
- database
...
- table.
...
- Select
...
- the
...
- radio
...
- option
...
- to
...
- create
...
- a
...
- changes
...
- ontology
...
- to
...
- a
...
- database
...
- table
...
- (Should
...
- be
...
- the
...
- 2nd
...
- button).
...
- A
...
- window
...
- will
...
- appear
...
- requesting
...
- all
...
- database
...
- information,
...
- Keep
...
- all
...
- fields
...
- to
...
- their
...
- default
...
- values,
...
- except
...
- the
...
- table
...
- name.
...
- Another
...
- name
...
- will
...
- need
...
- to
...
- be
...
- assigned
...
- to
...
- distinguish
...
- the
...
- annotations table. It is good practice to prefix the name of this table "annotation_[tablename]". Once the table is renamed, click 'OK'.
...
- This
...
- process
...
- should
...
- take
...
- a
...
- few
...
- seconds.
...
- From
...
- the
...
- menu
...
- bar,
...
- select
...
- '
...
- Lucene"
...
- and
...
- select
...
- 'Index
...
- Ontologies.
...
- A
...
- window
...
- will
...
- pop
...
- up. Accept all slots.
...
- Check
...
- both
...
- the
...
- 'Phonetic
...
- Indexer'
...
- and
...
- the
...
- 'Standard
...
- Indexer',
...
- and
...
- and
...
- select
...
- 'OK'.
...
- After
...
- indexing
...
- has
...
- completed (this should take less than 20 minutes on a Production quality machine), a new Lucene folder will be stored in the same directory as your database project file.
- At this point, if a previous version of the Protege and Explanation servers are running, they will need to be shutdown. For best practices, the RMI registry will need to be shutdown as well. Advertise via email that the tier's current Protege instance will be brought down. To shutdown, open another SSH connection to the same server. Type 'ps -ef | grep server' to see view the current protege processes running. If both explanation and Protege servers are running, shutdown the explanation server first.
- Type 'cd /usr/local/protege/Protege_x.x/<PROTEGE
...
- INSTANCE>Explanation.Server-x.x.x.
...
- Type
...
- _'./stop_explanation_server.sh
...
- http:localhost:<port>/explain/'.
...
- After
...
- the
...
- executing,
...
- the
...
- following
...
- message
...
- should
...
- be
...
- displayed
...
- in
...
- the
...
- console:
...
- '_Request
...
- sent
...
- to
...
- server.'
...
- This
...
- message
...
- indicates
...
- that
...
- the
...
- explanation
...
- server
...
- has
...
- successfully
...
- communicated
...
- with
...
- the
...
- Protege
...
- server
...
- that
...
- it
...
- will
...
- be
...
- shutting
...
- down.
...
- Next,
...
- do
...
- a
...
- 'ps
...
- -ef
...
- |
...
- grep
...
- server'
...
- to
...
- see
...
- if
...
- the
...
- explanation
...
- server
...
- was
...
- killed.
...
- Navigate
...
- to
...
- the
...
- previous
...
- version
...
- Protege
...
- server
...
- folder
...
- by
...
- typing
...
- 'cd
...
- ../Protege.Server-x.x.x'.
...
- Once
...
- in
...
- the
...
- directory,
...
- type
...
- './shutdown_protege_server.sh
...
- localhost:<server
...
- port>.
...
- A
...
- message
...
- will
...
- appear
...
- on
...
- the
...
- console
...
- that
...
- the
...
- server
...
- has
...
- been
...
- shut
...
- down.
...
- The
...
- RMI
...
- registry
...
- is
...
- also
...
- shutdown
...
- from
...
- this
...
- directory.
...
- Unfortunately,
...
- there
...
- is
...
- no
...
- script
...
- to
...
- shutdown
...
- the
...
- RMI
...
- registry,
...
- however,
...
- can
...
- be
...
- killed
...
- manually.
...
- To
...
- determine
...
- which
...
- port
...
- you
...
- want
...
- to
...
- kill,
...
- refer
...
- to
...
- the
...
...
...
...
- .
...
- Once
...
- the
...
- correct
...
- port
...
- has
...
- been
...
- determined,
...
- type
...
- 'ps
...
- -ef
...
- |
...
- grep
...
- rmi'
...
- to
...
- figure
...
- out
...
- which
...
- process
...
- ID
...
- is
...
- running
...
- the
...
- port
...
- that
...
- needs
...
- to
...
- be
...
- killed.
...
- To
...
- kill
...
- the
...
- process,
...
- type
...
- '
...
- kill -9
...
- <RMI
...
- Process
...
- ID>'.
...
- Once
...
- executed,
...
- type
...
- ps
...
- -ef
...
- |
...
- grep
...
- rmi
...
- again
...
- to
...
- see
...
- if
...
- the
...
- process
...
- has
...
- been
...
- terminated.
...
- Now
...
- that
...
- the
...
- all
...
- servers
...
- from
...
- the
...
- previous
...
- version
...
- have
...
- been
...
- shutdown,
...
- the
...
- explanation
...
- servers
...
- for
...
- the
...
- latest
...
- version
...
- must
...
- now
...
- be
...
- restarted.
...
- Navigate
...
- to
...
- the
...
- latest
...
- version's
...
- explanation
...
- server
...
- folder
...
- by
...
- typing
...
- 'cd
...
- /usr/local/protege.Protege_x.x/<PROTEGE
...
- INSTANCE>/Explanation.Server-x.x.x.
...
- Once
...
- in
...
- the
...
- directory,
...
- type
...
- '
...
- ./start_explanation_server.sh
...
- --protege-standalone
...
- --port
...
- <port
...
- number>
...
- /app/protege/data/Protege_x.x/<PROTEGE
...
- INSTANCE>/<DB
...
- PROEJCT
...
- NAME>.pprj.
...
- _
...
- After
...
- the
...
- server
...
- has
...
- initiated
...
- start
...
- up,
...
- type
...
- '
...
- tail
...
- -f
...
- nohup.out
...
- '
...
- to
...
- view
...
- start
...
- up
...
- status.
...
- Within
...
- the
...
- nohup.out
...
- file,
...
- the
...
- explanation
...
- server
...
- has
...
- started
...
- when
...
- you
...
- see
...
- "Jena,
...
- Classification,
...
- and
...
- Extracting'
...
- processes
...
- all
...
- complete,
...
- and
...
- a
...
- "Server
...
- started,
...
- listening
...
- on
...
- port
...
- xxxx"
...
- message.
...
- Once
...
- the
...
- server
...
- is
...
- up
...
- and
...
- running,
...
- go
...
- back
...
- to
...
- the
...
- client
...
- GUI,
...
- click
...
- on
...
- the
...
- 'Reasoning'
...
- menu,
...
- and
...
- ensure
...
- that
...
- "Clark&Parsia
...
- Custom
...
- Protege
...
- 3.x
...
- Reasoner"
...
- is
...
- selected
...
- on
...
- the
...
- menu
...
- list.
...
- Click
...
- on
...
- the
...
- 'Reasoning
...
- menu
...
- again,
...
- and
...
- scroll
...
- down
...
- to
...
- "Clark&Parsia
...
- Custom
...
- Protege
...
- 3.x
...
- Reasoner
...
- Details"
...
- and
...
- ensure
...
- that
...
- the
...
- 'Synchronize
...
- on query' box is checked.
...
- Click
...
- 'OK'.
...
- The
...
- Changes
...
- tab
...
- will
...
- now
...
- be
...
- disabled
...
- from
...
- the
...
- GUI,
...
- since
...
- all
...
- changes
...
- will
...
- be
...
- recorded
...
- to
...
- the
...
- database.
...
- To
...
- disable,
...
- click
...
- on
...
- 'Projects',
...
- 'Configure'
...
- and
...
- uncheck
...
- the
...
- 'ChangesTab'
...
- box.
...
- Click
...
- 'OK',
...
- and
...
- the
...
- changes
...
- tab
...
- should
...
- now
...
- be
...
- gone
...
- from
...
- the
...
- GUI.
...
- Click
...
- File,
...
- Save
...
- Project.
...
- Select
...
- File,
...
- Convert
...
- Project
...
- to
...
- Format.
...
- A
...
- window
...
- will
...
- appear
...
- prompting
...
- to
...
- select
...
- a
...
- conversion
...
- file
...
- type.
...
- Select
...
- 'OWL/RDF',
...
- and
...
- store
...
- in
...
- app/protégé/data/Protégé_x.x/<PROTÉGÉ
...
- INSTANCE>.
...
- Label
...
- the
...
- file
...
- with
...
- the
...
- current
...
- date
...
- and
...
- "file".
...
- Example:
...
- BiomedGT-yymmdd-file.pprj.
...
- Set
...
- the
...
- Language
...
- drop-down
...
- field
...
- to
...
- 'XML/RDF
...
- ABREV'.
...
- You
...
- will
...
- notice
...
- a
...
- small
...
- dialogue
...
- box
...
- displaying
...
- the
...
- conversion
...
- progress.
...
- This
...
- step
...
- may
...
- take
...
- approximately
...
- 30
...
- minutes
...
- depending
...
- on
...
- the
...
- size
...
- of
...
- the
...
- database
...
- project.
...
- Once
...
- completed,
...
- the
...
- dialogue
...
- box
...
- should
...
- disappear,
...
- and
...
- the
...
- client
...
- should
...
- display
...
- the
...
- new
...
- file
...
- project.
...
- Close
...
- the
...
- project
...
- WITHOUT
...
- saving
...
- the
...
- file
...
- project
...
- (the
...
- file
...
- project
...
- automatically
...
- gets
...
- saved),
...
- however,
...
- leave
...
- the
...
- Protégé
...
- client
...
- open.
...
- Open
...
- the
...
- nci_metaproject.pprj
...
- located
...
- at
...
- /app/protégé/data/<PROTÉGÉ
...
- INSTACE>/meta/.
...
- Click
...
- on
...
- the
...
- project
...
- tab
...
- underneath
...
- the
...
- SYSTEM-CLASS
...
- tab
...
- on
...
- the
...
- left-hand
...
- side
...
- menu.
...
- Select
...
- the
...
- 'Instances'
...
- tab
...
- at
...
- the
...
- top
...
- of
...
- the
...
- page.
...
- You
...
- will
...
- notice
...
- an
...
- 'Instance
...
- Browser'
...
- section,
...
- and
...
- an
...
- 'Instance
...
- Editor'
...
- section.
...
- The
...
- instance
...
- browser
...
- specifies
...
- the
...
- display
...
- name
...
- of
...
- your
...
- project,
...
- and
...
- the
...
- Instance
...
- Editor
...
- specifies
...
- the
...
- path
...
- of
...
- your
...
- database
...
- project.
...
- Click
...
- on
...
- the
...
- display
...
- project
...
- name
...
- and
...
- set
...
- the
...
- correct
...
- path
...
- to
...
- your
...
- project
...
- files. There should be a project instance for both the main ontology and annotation ontology.
- Within the nci_metaproject,
...
- the
...
- changes
...
- ontology
...
- projects
...
- (annotation
...
- files)
...
- should
...
- also
...
- not
...
- be
...
- made
...
- visible
...
- to
...
- users
...
- when
...
- trying
...
- to
...
- access
...
- a
...
- project
...
- on
...
- the
...
- server.
...
- If
...
- this
...
- has
...
- not
...
- already
...
- been
...
- configured,
...
- please
...
- view
...
- the
...
...
...
- instructions.
- To add users, select the 'User' class and within the Instance Browser, clone an existing user and modify the username and password.
- Save the metaproject and exit the client.
- Verify that the port numbers in the run_protege_server_nci.sh
...
- script
...
- correspond
...
- to
...
- the
...
- port
...
- numbers
...
- in
...
- run_rmiregistry.sh.
...
- Please
...
- refer
...
- to
...
- Appendix
...
- A
...
- for
...
- tier
...
- specific
...
- port
...
- numbers.
...
- Restart
...
- the
...
- RMI
...
- registry
...
- by
...
- running
...
- run_rmiregistry.sh.
...
- Type
...
- 'ps
...
- -ef
...
- |
...
- grep
...
- rmi'
...
- to
...
- see
...
- if
...
- the
...
- rmi
...
- process
...
- has
...
- started.
...
- Restart
...
- the
...
- Protégé
...
- Server,
...
- using
...
- the
...
- run_protege_server_nci.sh
...
- script.
...
- The
...
- console
...
- will
...
- indicate
...
- that
...
- the
...
- server
...
- has
...
- started
...
- and
...
- is
...
- ready
...
- to
...
- accept
...
- connections.
...
- Connect
...
- to
...
- the
...
- server
...
- via
...
- Protégé
...
- client
...
- to
...
- confirm
...
- that
...
- the
...
- project
...
- is
...
- viewable
...
- from
...
- the
...
- GUIrun_protege_<PROTÉGÉ
...
- INSTANCE>.sh.
...
- Enter
...
- proper
...
- login
...
- information.
...
- Select
...
- the
...
- desired
...
- project
...
- from
...
- the
...
- project
...
- display
...
- window.
- The client should now display the database project file, accessed via the Protege server.
- Once tested, the client can now be
posted up on the GForge websiteposted to the sFTP to be downloaded by users.
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