 |
Page History
| Wiki Markup |
|---|
{scrollbar:icons=false}
h1. |
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 table 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
...
- "shift
...
- +
...
- I"
...
- to
...
- edit.
...
- The
...
- code.prefix
...
- value
...
- can
...
- be
...
- adjusted,
...
- depending
...
- on
...
- which
...
- Protégé
...
- Instance
...
- is
...
- being
...
- used
...
- (BiomedGT
...
- or
...
- NCI
...
- Thesaurus).
...
- BiomedGT
...
- uses
...
- 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
...
- BiomedGT.owl
...
- ,
...
- 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.
...
- 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.
...
- 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
...
...
...
- 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
...
- database
...
- GUI
...
- tool
...
- (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
...
- 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.
...
- 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 WorkflowTab
...
- 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.
...
- Once
...
- the
...
- table
...
- is
...
- renamed,
...
- click
...
- 'OK'.
...
- This
...
- process
...
- should
...
- take
...
- a
...
- few
...
- seconds.
...
- From
...
- the
...
- menu
...
- bar,
...
- select
...
- 'LuceneQueryPlugin"
...
- and
...
- select
...
- 'Index
...
- Ontologies.
...
- A
...
- window
...
- will
...
- pop
...
- up.
...
- Check
...
- both
...
- the
...
- 'Phonetic
...
- Indexer'
...
- and
...
- the
...
- 'Standard
...
- Indexer',
...
- and
...
- and
...
- select
...
- 'OK'.
...
- After
...
- indexing
...
- has
...
- completed,
...
- 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
...
...
- that
...
- the
...
- tier's
...
- current
...
- Protege
...
- instance
...
- will
...
- be
...
- brought
...
- down.
...
- To
...
- shutdown,
...
- open
...
- another
...
- reflection
...
- X
...
- window
...
- 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
...
- Changes
...
- with
...
- Reasoner'
...
- 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.
...
- 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 DisplayInList setup instructions.
- 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
...
...
...
...
...
...
...
- to
...
- be
...
- downloaded
...
- by
...
- users.
| Wiki Markup |
|---|
{scrollbar:icons=false} |
