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Extenstions
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Protégé
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This page is meant as an explanation of the NCI Protégé Extensions, why they were implemented and what they do.
The Editor's Guide for the most recent version of the NCI Protégé extensions can be found on GForge. This provides the user with instructions on how to edit within the NCI Edit tab, how to do searches using the Advanced Search tab, how to handle workflow, pull reports, etc.
EVS Protégé Extensions Introduction and History
Version 1.2.3.25
...
is
...
the
...
first
...
public
...
release
...
of
...
the
...
EVS
...
Protégé
...
Extensions.
...
There
...
have
...
been
...
multiple
...
revisions
...
released,
...
tested
...
and
...
used
...
internally
...
over
...
the
...
past
...
year.
...
The
...
current
...
version
...
is
...
considered
...
stable
...
and
...
reliable
...
and
...
suitable
...
for
...
external
...
release.
...
These
...
extensions
...
were
...
created
...
in
...
response
...
to
...
a
...
need
...
for
...
an
...
open-source
...
editing
...
tool
...
that
...
could
...
be
...
customized
...
to
...
the
...
needs
...
of
...
the
...
EVS
...
content
...
editors.
...
In
...
addition,
...
EVS
...
wanted
...
the
...
ability
...
to
...
exchange
...
and
...
share
...
editable
...
content
...
with
...
external
...
collaborators.
...
The
...
Protégé
...
editing
...
tool,
...
developed
...
by
...
Stanford,
...
was
...
used
...
as
...
the
...
basis
...
and
...
extended
...
to
...
meet
...
these
...
needs.
...
The
...
extensions
...
are
...
built
...
on
...
the
...
Protégé
...
3.1
...
codebase
...
and
...
utilize
...
pellet
...
1.5.
...
Some
...
improvements
...
to
...
the
...
Protégé
...
software
...
were
...
required
...
to
...
meet
...
the
...
needs
...
of
...
EVS,
...
but
...
these
...
have
...
already
...
been
...
merged
...
into
...
the
...
Protégé
...
trunk.
...
Both
...
Protégé
...
and
...
Pellet
...
are
...
included
...
within
...
the
...
download.
...
The
...
Explanation
...
Server
...
was
...
developed
...
in
...
collaboration
...
with
...
Clark
...
&
...
Parsia
...
LLC.
...
The
...
Protégé
...
and
...
the
...
extensions
...
are
...
built
...
and
...
expect
...
to
...
run
...
on
...
Java
...
1.5.
...
EVS
...
Protégé
...
Extensions
...
packages
...
The
...
EVS
...
Protégé
...
Extensions
...
are
...
broken
...
into
...
three
...
separate
...
packages.
...
The
...
Explanation
...
Server
...
provides
...
classification
...
and
...
explanation
...
functionality.
...
The
...
Protégé
...
Server
...
provides
...
access
...
to
...
a
...
central
...
editing
...
project
...
for
...
multiple
...
users.
...
The
...
Protégé
...
Client
...
is
...
the
...
end-user
...
application
...
for
...
accessing
...
the
...
Protégé
...
Server
...
and
...
editing
...
content.
...
Explanation
...
Server
...
The
...
Explanation
...
Server
...
is
...
used
...
to
...
do
...
classification
...
of
...
the
...
ontology
...
and
...
provide
...
explanations
...
on
...
demand
...
to
...
the
...
Protégé
...
Client
...
gui.
...
It
...
runs
...
directly
...
against
...
the
...
database,
...
independently
...
of
...
the
...
Protégé
...
Server.
...
The
...
Protégé
...
Server
...
queries
...
the
...
Explanation
...
Server
...
for
...
information
...
when
...
needed
...
and
...
controls
...
requests
...
for
...
classification,
...
so
...
multiple
...
clients
...
cannot
...
try
...
and
...
classify
...
at
...
the
...
same
...
time.
...
Protégé
...
Server
...
The
...
Protégé
...
Server
...
provides
...
multi-user
...
access
...
to
...
a
...
single
...
ontology
...
stored
...
in
...
a
...
database.
...
It
...
coordinates
...
and
...
controls
...
user
...
activities
...
and
...
resource
...
allocation.
...
It
...
stores
...
a
...
history
...
of
...
user
...
actions
...
for
...
use
...
in
...
tracking
...
changes
...
and
...
resolving
...
conflicts.
...
The
...
server
...
also
...
provides
...
a
...
centralized
...
means
...
of
...
enforcing
...
business
...
rules
...
and
...
configurations
...
upon
...
client
...
applications.
...
EVS
...
has
...
extended
...
the
...
Protégé
...
Server
...
to
...
allow
...
tracking
...
of
...
workflow
...
and
...
assigning
...
of
...
editing
...
tasks.
...
Protégé Client
The Protégé Client is a java-swing
...
based
...
gui
...
used
...
for
...
editing
...
an
...
ontology.
...
EVS
...
uses
...
the
...
client
...
to
...
connect
...
to
...
the
...
Protégé
...
Server
...
application,
...
allowing
...
multiple
...
editors
...
to
...
share
...
the
...
same
...
ontology.
...
The
...
Protégé
...
client
...
can
...
also
...
be
...
used
...
in
...
standalone
...
mode
...
to
...
edit
...
a
...
single
...
ontology
...
but
...
some
...
of
...
the
...
client-server
...
specific
...
extensions
...
are
...
then
...
disabled.
...
The
...
client
...
is
...
used
...
in
...
standalone
...
mode
...
by
...
managers
...
to
...
perform
...
Prompt
...
comparisons
...
and
...
terminology
...
exports.
...
Protégé
...
Business
...
Rules
...
The
...
following
...
are
...
EVS
...
business
...
rules
...
that
...
the
...
NCI
...
Edit
...
tab
...
was
...
programmed
...
to
...
enforce.
...
These
...
rules
...
are
...
a
...
major
...
reason
...
why
...
it
...
was
...
necessary
...
to
...
write
...
an
...
extension
...
rather
...
than
...
using
...
the
...
default
...
Protégé
...
editor.
...
Rules
...
for
...
Editing
...
- Each
...
- concept
...
- must
...
- have
...
- one
...
- and
...
- only
...
- one
...
- NCI/PT
...
- Full-Syn
...
- Each
...
- concept
...
- must
...
- have
...
- one
...
- and
...
- only
...
- one
...
- Preferred_Name
...
- HD,
...
- AQ
...
- and
...
- PT
...
- are
...
- equivalent
...
- Full-Syn
...
- term
...
- types.
...
- (i.e.
...
- an
...
- NCI/AQ
...
- can
...
- take
...
- the
...
- place
...
- of
...
- an
...
- NCI/PT)
...
- NCI/PT
...
- value
...
- must
...
- match
...
- the
...
- Preferred_Name
...
- Properties
...
- cannot
...
- be
...
- duplicated
...
- within
...
- a
...
- concept
...
- Roles
...
- cannot
...
- be
...
- duplicated
...
- within
...
- a
...
- concept
...
- Role
...
- groups
...
- cannot
...
- be
...
- duplicated
...
- within
...
- a
...
- concept
...
- Superclasses
...
- cannot
...
- be
...
- duplicated
...
- within
...
- a
...
- concept
...
- The
...
- last
...
- superclass
...
- of
...
- a
...
- concept
...
- cannot
...
- be
...
- deleted
...
- Cannot
...
- create
...
- a
...
- restriction
...
- pointed
...
- at
...
- a
...
- retired,
...
- pre-retired,
...
- or
...
- pre-merged
...
- class
...
- If
...
- concept
...
- has
...
- Def_Curator
...
- property
...
- present,
...
- only
...
- authorized
...
- users
...
- can
...
- create,
...
- modify
...
- or
...
- delete
...
- the
...
- DEFINITION
...
- If
...
- concept
...
- has
...
- Def_Curator
...
- property
...
- present,
...
- only
...
- authorized
...
- users
...
- can
...
- modify
...
- or
...
- delete
...
- the
...
- Def_Curator
...
- Def_Curators
...
- must
...
- exist
...
- in
...
- a
...
- configuration
...
- file.
...
- No
...
- "dummy"
...
- Def_Curators
...
- Each
...
- DEFINITION
...
- must
...
- have
...
- 1
...
- review
...
- date,
...
- 1
...
- review
...
- name,
...
- 0
...
- or
...
- 1
...
- attributes,
...
- and
...
- no
...
- source
...
- Only
...
- single
...
- spaces
...
- allowed
...
- in
...
- a
...
- DEFINITION
...
- unless
...
- preceeded
...
- by
...
- !,
...
- ?
...
- or
...
- .
...
- No
...
- leading
...
- or
...
- trailing
...
- spaces
...
- allowed
...
- in
...
- properties
...
- Only
...
- single
...
- spaces
...
- allowed
...
- between
...
- tokens
...
- in
...
- properties
...
- (except
...
- for
...
- DEFINITION)
...
- Properties
...
- cannot
...
- include
...
- the
...
- characters
...
- :,
...
- !,?
...
- or
...
- @
...
- (except
...
- for
...
- DEFINITION
...
- which
...
- allows
...
- !
...
- and
...
- ?)
...
Retire
- Pre-retired
...
- concepts
...
- are
...
- retired
...
- under
...
- the
...
- preretired_concepts
...
- bin
...
- Pre-retire
...
- process
...
- forces
...
- dependent
...
- classes
...
- to
...
- be
...
- fixed
...
- (children
...
- retreed,
...
- incoming
...
- roles
...
- re-pointed)
...
- Pre-retire
...
- concept
...
- must
...
- have
...
- and
...
- Editor_Note
...
- added
...
- explaining
...
- the
...
- retirement
...
- Only
...
- the
...
- lead
...
- editor
...
- may
...
- do
...
- the
...
- final
...
- retire
...
- on
...
- a
...
- concept
...
- Only
...
- the
...
- lead
...
- editor
...
- may
...
- edit
...
- retired
...
- concepts
...
- Roles
...
- in
...
- the
...
- retiring
...
- concept
...
- converted
...
- to
...
- annotation
...
- properties
...
- called
...
- OLD_ROLE
...
- Retiring
...
- concept
...
- deprecated
...
- using
...
- owl:deprecatedClass
...
Merge
- Pre-merge
...
- retiring
...
- concepts
...
- are
...
- double-treed
...
- under
...
- premerged_concepts
...
- bin
...
- Pre-merge
...
- identifying
...
- properties
...
- (Merge_From,
...
- Merge_To)
...
- are
...
- added
...
- to
...
- the
...
- surviving
...
- and
...
- retiring
...
- concepts
...
- Pre-merge
...
- retiring
...
- concept
...
- must
...
- have
...
- an
...
- Editor_Note
...
- added
...
- explaining
...
- the
...
- merge
...
- Only
...
- the
...
- lead
...
- editor
...
- may
...
- do
...
- the
...
- final
...
- merge
...
- on
...
- a
...
- concept
...
- Non-redundant
...
- roles
...
- and
...
- properties
...
- of
...
- the
...
- retiring
...
- concept
...
- are
...
- added
...
- to
...
- the
...
- surviving
...
- concept
...
- Non-redundant
...
- incoming
...
- roles
...
- pointed
...
- at
...
- the
...
- retiring
...
- concept
...
- are
...
- re-pointed
...
- at
...
- the
...
- surviving
...
- concept
...
- Roles
...
- in
...
- the
...
- retiring
...
- concept
...
- converted
...
- to
...
- annotation
...
- properties
...
- called
...
- OLD_ROLE
...
- Retiring
...
- concept
...
- deprecated
...
- using
...
- owl:deprecatedClass
...
History Record Generation
All edits done on the vocabulary are recorded in an audit log in the database. The data recorded includes the username, type of edit, date and time of edit, and reference concepts. This raw audit log is processed to remove any identifying information using Prompt. The scrubbed version is called concept_history and is published on a monthly basis.
The fields in these files are conceptcode|editaction|editdate|referencecode.
...
- conceptcode
...
- is
...
- the
...
- unique,
...
- permanent,
...
- alphanumeric
...
- identifier
...
- of
...
- the
...
- concept
...
- editaction
...
- is
...
- the
...
- activity
...
- being
...
- recorded
...
- (create,
...
- modify,
...
- split,
...
- merge,
...
- retire)
...
- editdate
...
- is
...
- the
...
- date
...
- the
...
- activity
...
- occurred
...
- referencecode
...
- is
...
- the
...
- identifier
...
- for
...
- a
...
- concept
...
- affected
...
- by
...
- or
...
- influencing
...
- the
...
- action,
...
- as
...
- detailed
...
- below
...
The
...
record
...
will
...
normally
...
just
...
be
...
a
...
single
...
line
...
and
...
will
...
look
...
like
...
this:
...
C#####|create|dd-mon-yy|(null)
...
or
...
C#####|modify|dd-mon-yy|(null)
...
Special
...
Edits
...
In
...
the
...
particular
...
cases
...
of
...
Split,
...
Merge
...
and
...
Retirement
...
there
...
are
...
multiple
...
rows
...
written
...
with
...
reference
...
codes
...
included.
...
Splits
In a split,
...
a
...
single
...
concept
...
is
...
split
...
into
...
two.
...
The
...
original
...
concept
...
survives
...
and
...
a
...
new
...
concept
...
is
...
generated.
...
Two
...
split
...
records
...
are
...
written
...
for
...
the
...
original
...
concept
...
with
...
reference
...
codes
...
for
...
the
...
resulting
...
concepts
...
and
...
a
...
create
...
history
...
record
...
is
...
written
...
for
...
the
...
new
...
concept.
...
In
...
the
...
case
...
of
...
C11111
...
being
...
split
...
into
...
C11111
...
and
...
C22222
...
the
...
history
...
will
...
appear
...
as
...
follows:
...
C22222|create|dd-mon-yy|(null)
...
C11111|split|dd-mon-yy|C22222
...
C11111|split|dd-mon-yy|C11111
...
Retires
In a retirement the concept is moved from its old location in the tree hierarchy into the Retired_Kind.
...
A
...
retire
...
record
...
is
...
written
...
for
...
the
...
retiring
...
concept
...
with
...
a
...
reference
...
code
...
of
...
the
...
old
...
superconcept.
...
If
...
a
...
concept
...
has
...
multiple
...
superconcepts,
...
then
...
a
...
retire
...
record
...
is
...
written
...
for
...
each
...
reference.
...
In
...
the
...
case
...
of
...
retiring
...
concept
...
C11111
...
which
...
has
...
two
...
superconcepts
...
(C22222
...
and
...
C33333),
...
the
...
history
...
will
...
appear
...
as
...
follows:
...
C11111|retire|dd-mon-yy|C22222
...
C11111|retire|dd-mon-yy|C33333
...
Merges
In a merge,
...
two
...
concepts
...
are
...
merged
...
into
...
one.
...
One
...
of
...
the
...
two
...
concepts
...
survives
...
and
...
the
...
other
...
concept
...
is
...
retired.
...
A
...
merge
...
history
...
record
...
is
...
written
...
for
...
both
...
of
...
the
...
concepts
...
with
...
a
...
reference
...
code
...
of
...
the
...
surviving
...
concept
...
and
...
a
...
retire
...
record
...
is
...
written
...
for
...
the
...
concept
...
that
...
retires.
...
In
...
the
...
case
...
of
...
C11111
...
merging
...
with
...
C22222
...
and
...
C11111
...
surviving,
...
the
...
history
...
will
...
appear
...
as
...
follows:
...
C11111|merge|dd-mon-yy|C11111
...
C22222|merge|dd-mon-yy|C11111
...
C22222|retire|dd-mon-yy|(null)
...
Protégé
...
Editing
...
History
...
Application
...
There
...
are
...
a
...
couple
...
of
...
simple
...
web
...
applications
...
that
...
are
...
made
...
available
...
to
...
allow
...
editors
...
to
...
review
...
the
...
evs_history
...
and
...
concept_history
...
tables.
...
The
...
evs_history
...
is
...
written
...
in
...
real-time,
...
as
...
edits
...
are
...
occurring.
...
The
...
concept_history
...
is
...
written
...
during
...
the
...
Prompt
...
cycle.
...
The
...
applications
...
allow
...
access
...
to
...
both
...
the
...
Production
...
and
...
QA
...
tiers
...
of
...
both
...
BiomedGT
...
and
...
NCI
...
Thesaurus.
...
...
| Wiki Markup |
|---|
Query|http://cbvapp-d1007.nci.nih.gov:19580/QueryHistory/]
* [Concept History Query|http://cbvapp-d1007.nci.nih.gov:19580/ConceptHistoryQuery/]
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