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NCI Protégé

...

1.2.3

...

Release

...

Notes

{:=

Panel

title

	Contents

this

Page

} {

Table of Contents

minLevel

=2} {panel} May

	2

May 27,

...

2008

...

National

...

Cancer

...

Institute

...

Center

...

for

...

Bioinformatics

...

and

...

Information

...

Technology

...

1.0

...

Release

...

History

...

Release
Date
1.0
...
June
...
2007
...
1.1
...
Sept
...
2007
1.2.0.
...
December
...
2007
...
1.2.1.
...
February
...
2008
...
1.2.2
...
May
...
2008
1.2.3
...
July
...
2008

Release	Date
1.0

2.0

...

New

...

Features

...

and

...

Updates

...

This
...
release
...
contains
...
3
...
new
...
features
...
-
...
(1)
...
Run
...
time
...
classification;
...
(2)
...
Advanced
...
Query
...
Plugin
...
reporting
...
capability;
...
(3)
...
additional
...
configurability
...

Run

...

Time

...

Classification

...

This
...
new
...
functionality
...
allows
...
editors
...
to
...
classify
...
BiomedGT,
...
or
...
NCIT,
...
in
...
the
...
Protege
...
client-server
...
environment
...
used
...
by
...
the
...
EVS.
...
It
...
depends
...
on
...
an
...
explanation
...
server
...
running
...
independently
...
of
...
the
...
Protege
...
server.
...
The
...
explanation
...
server
...
is
...
initialized
...
with
...
the
...
same
...
data
...
served
...
by
...
the
...
Protege
...
server,
...
and
...
is
...
maintained
...
synchronized
...
with
...
the
...
database
...
as
...
editing
...
occurs
...
by
...
the
...
Protege
...
client.
...
Because
...
of
...
initialization
...
activities,
...
the
...
first
...
classification
...
action
...
by
...
a
...
client
...
will
...
take
...
a
...
number
...
of
...
minutes;
...
subsequent
...
classifications
...
will
...
be
...
faster.
...
Salient
...
points:
...
Enhanced
...
detection
...
of
...
exceptional
...
conditions
...
allowing
...
better
...
error
...
handling
...
and
...
explanation
...
services
...
Parallel
...
improvements
...
on
...
the
...
Explanation
...
Tab
...
GUI
...
to
...
make
...
explanations
...
easier
...
to
...
interpret
...
Performance
...
increase
...
due
...
to
...
improved
...
memory
...
management
...
and
...
optimizations
...
in
...
the
...
classification
...
and
...
extraction
...
algorithms
...
Known
...
issues:
...
A
...
side
...
effect
...
of
...
the
...
requirement
...
for
...
synchronization
...
with
...
the
...
explanation
...
server
...
is
...
that
...
batch
...
loads
...
and
...
edits
...
can
...
take
...
longer
...
and
...
throw
...
exceptions.
...
Batch
...
loads
...
and
...
edits
...
need
...
to
...
be
...
conducted
...
under
...
controlled
...
conditions:
...
the
...
recommendation
...
is
...
for
...
the
...
workflow
...
manager
...
to
...
conduct
...
these
...
batch
...
actions
...
in
...
standalone
...
database
...
mode
...
and
...
with
...
the
...
explanation
...
server
...
shut
...
down.
...
Limited
...
concurrency.
...
On
...
a
...
classification
...
action
...
by
...
the
...
RTC,
...
there
...
will
...
be
...
a
...
period
...
of
...
time
...
in
...
which
...
the
...
DB
...
is
...
locked
...
for
...
writing.
...
The
...
suggested
...
workaround
...
is
...
for
...
one
...
editor,
...
perhaps
...
the
...
workflow
...
manager,
...
to
...
conduct
...
the
...
classification
...
action
...
and
...
advertise
...
to
...
the
...
editors
...
to
...
cease
...
editing
...
while
...
classification
...
is
...
ongoing.
...
This
...
would
...
still
...
allow
...
browsing
...
of
...
the
...
database
...
by
...
other
...
editors.
...
High
...
network
...
communications
...
overhead.
...
The
...
classification
...
time
...
will
...
be
...
significantly
...
increased
...
on
...
classifications
...
by
...
remote
...
editors.
...
The
...
last
...
two
...
issues
...
will
...
be
...
addressed
...
in
...
a
...
future
...
patch.
...
However,
...
a
...
"remote
...
access"
...
server
...
is
...
being
...
set
...
up
...
that
...
will
...
alleviate
...
communications
...
overhead.
...

Reporting

...

functionality

...

added

...

to

...

the

...

Advanced

...

Query

...

Plugin

...

An
...
export
...
function
...
(leveraged
...
from
...
an
...
existing
...
plugin
...
in
...
Protege)
...
has
...
been
...
added
...
to
...
the
...
AQP
...
which
...
allows
...
very
...
detailed
...
reports
...
to
...
be
...
produced
...
in
...
a
...
tabular
...
format.
...
This
...
function
...
doesn't
...
replace
...
the
...
Report
...
Writer.
...

Increased

...

Configurability

...

Although
...
written
...
to
...
support
...
editing
...
activities
...
in
...
the
...
EVS,
...
the
...
NCIEditTab
...
plugin
...
has
...
introduced
...
various
...
user
...
interfaces
...
and
...
behaviors
...
that
...
make
...
it
...
an
...
attractive
...
plugin
...
to
...
other
...
editing
...
groups.
...
Hence
...
configurability
...
has
...
been
...
a
...
background
...
refactoring
...
activity
...
as
...
development
...
progressed.
...
This
...
is
...
noted
...
here
...
because
...
with
...
the
...
EVS
...
now
...
editing
...
BiomedGT
...
and
...
NCIT,
...
this
...
aspect
...
becomes
...
very
...
important
...
as
...
the
...
internal
...
format
...
of
...
annotations
...
in
...
BGT
...
is
...
expected
...
to
...
start
...
deviating
...
significantly
...
from
...
NCIT's
...
in
...
the
...
near
...
future.
...
Some
...
features
...
related
...
to
...
display
...
labels
...
remain
...
to
...
be
...
implemented.
...
Salient
...
points:
...
Specifies
...
what
...
properties
...
are
...
qualified
...
and
...
hence
...
need
...
to
...
be
...
edited
...
in
...
one
...
of
...
the
...
complex
...
panels
...
of
...
the
...
NCIEditTab,
...
where
...
qualified
...
properties
...
are
...
properties
...
with
...
multiple
...
xml-delimited
...
subfields
...
as
...
their
...
value.
...
Maps
...
xml
...
elements
...
of
...
qualified
...
annotation
...
properties
...
to
...
fields
...
in
...
editing
...
panels.
...
Specifies
...
properties
...
and
...
concepts
...
required
...
by
...
the
...
business
...
logic
...
of
...
the
...
various
...
functions
...
in
...
the
...
NCIEditTab
...
(e.g.
...
properties
...
supporting
...
retirement
...
actions).
...
Specifies
...
external
...
sources
...
requiring
...
restricted
...
editing
...
privileges.
...
Specifies
...
external
...
Semantic
...
Media
...
Wiki
...
servers
...
supporting
...
collaborative
...
development
...

3.0

...

Enhancements

...

and

...

Bug

...

Fixes

...

Since

...

Last

...

Release

{:=

Note

title

	Note

}

The

addition

copy-and-paste

the

collaborative

panel,

GUI

and

behavior

enhancements

the

workflow

plugin,

increased

support

for

semantic

types.

{note} h3. Enhancements * 2604 Real Time Classification * 11962 Chat window in Protege

Enhancements

2604 Real Time Classification
11962 Chat window in Protege 1.2.0.12

...

cosmetic

...

change

...

request

...

12735

...

Extra

...

start

...

scripts

...

showing

...

Protege.Server

...

directory

...

12809

...

Improve

...

readability

...

"Modeler's

...

Note"

...

12810

...

Word

...

wrap

...

tooltip

...

text

...

"Modeler's

...

Note"

...

12811

...

allow

...

user

...

mark

...

"Completed"

...

without

...

having

...

done

...

work

...

12816

...

Provide

...

user

...

visual

...

indication

...

when

...

workflow

...

assignments

...

available

...

12823

...

Error

...

Filler

...

value

...

numeric

...

13270

...

Unable

...

pull

...

concepts

...

within

...

an association (Documentation)

...

13430

...

Workflow

...

assignment

...

13518

...

Prompt

...

missing

...

Semantic_Type

...

13806

...

UnRetire

...

button

...

functionality

...

Preretire

...

needs

...

removing

...

14053

...

Export

...

function

...

added

...

14108

...

Typo

...

error

...

message

...

Batch

...

Editor

...

14426

...

Need

...

different

...

Review

...

icon

...

Split/Pre-Merge/Copy/Workflow

...

tabs

...

Bugs

8376 Need Review button in Copy tab
8634 Error when input an ampersand or less than character
11414 Batch load creates duplicates if parent has no children
12069 Not adding prefix of Proposed_ in tree
12081 Duplication of the Concept_Type property not always recognized by the batch editor
12321 Save does not update status to Updated
12322 Closing and reopening project results in blank NCI Edit Tab
12473 Workflow - Last Updated date does not retain seconds
12560 archive not working correctly
12818 Column formatting for assignment table
13220 Cannot save some modifications made to concepts
13257 Error message following 'save' of concept duplicated of 13220
13337 RE: Frozen interface after Batch Loader action
13389 Drops downs in dialogs should be controlled by ncitab.xml
13424 Weird behavior during split
13493 C-NOCODE on creation of a new class
13518 Prompt for missing Semantic_Type
13520 Right click on an Association in the Copy Tab does not allow Delete
13716 association persists after being deleted
13723 Edit Concept loads incorrect concept when using suggested assignment
13810 NCIWorkflow - Manager can not Delete SUGGESTED item
13819 (duplicate of 14414) Problem with Split function in NCIt instance
13823 No warning when leaving Copy pane
13831 NCIWorkflow - Modeler can not delete SUGGESTED items
13834 NCIWorkflow - Adding a note at the same workflow item at the same time
13849 Entire batch fails to load if contains one error
13862 Changing superclass to owl:Thing results in missing framework
13950 code C_NOCODE
14002 exceptions when creating new users in workflow
14056 NullPointer exception thrown when editing NCI Drug Dictionary definition
14057 no copy-and-paste capability in collaboration panel
14103 RTC fails
14290 Problem tracking changes of defining relations if more than one restriction is present
14331 Lower pane review button disabled if do Copy or Split
14343 Unable to add definitions of various kinds
14404 If character in slot matches delimiter then export misaligns values
14405 Change default delimiters of AQP export
14406 AQP search results display properties
14414 Lower Split pane not visible after Clone in Copy tab
14481 Invalid Concept Successfully Created from a Batch Load
14486 Advanced Query report output shows display slot rather than slot name
14829 Edit Concept loads incorrect concept for the manager
14926 5 to 10 minutes to start client
15001 After UnMerge the concept remains a child of Premerged_Concepts
15002 PreRetired concept doesn't appear under Preretired_Concepts

4.0 Known Issues

Re: GForge #14533 - Batch load in client server mode -- Please give batch loads of over 200 concepts to workflow manager to load in standalone mode -- known issues with large batch loads in client server mode. The loads are quick, about 10 minutes for 250.
Special Review User needs to be created for NCI Thesaurus, and config file modified to give this user privilege to edit those definitions. (Batch load may still work for loading these definitions.)
Export from AQP -- When exporting concepts that contain properties that have values that contain commas (such as definition) the data will display incorrectly.
Exporting from AQP -- HINT - When you export to Excel, if you are using the new Excel 7.0, you need to import the file first.
Export from AQP -- HINT - When you export to Excel, if you don't like the file and want to make a change, get out of Excel before creating a new export, or save the new file with a different name because Excel will lock the file.

GForge #14507- Prompt reports all concepts changed - concepts get new properties added
Gforge #13614 - Missing frame node in tree
GForge #14406 - AQP search results display properties

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Page History

Versions Compared

Old Version 11

New Version Current

Key

NCI Protégé

1.2.3

Release

Notes

1.0

Release

History

Release Date 1.0 ... June ... 2007 ... 1.1 ... Sept ...2007 1.2.0. ... December ... 2007 ... 1.2.1. ... February ... 2008 ... 1.2.2 ... May ...2008 1.2.3 ... July ...2008

2.0

New

Features

and

Updates

This ... release ... contains ... 3 ... new ... features ... - ... (1) ... Run ... time ... classification; ... (2) ... Advanced ... Query ... Plugin ... reporting ... capability; ... (3) ... additional ... configurability...

Run

Time

Classification

Reporting

functionality

added

to

the

Advanced

Query

Plugin

Increased

Configurability

3.0

Enhancements

and

Bug

Fixes

Since

Last

Release

Enhancements

Bugs

4.0 Known Issues

Release
Date
1.0
...
June
...
2007
...
1.1
...
Sept
...
2007
1.2.0.
...
December
...
2007
...
1.2.1.
...
February
...
2008
...
1.2.2
...
May
...
2008
1.2.3
...
July
...
2008

This
...
release
...
contains
...
3
...
new
...
features
...
-
...
(1)
...
Run
...
time
...
classification;
...
(2)
...
Advanced
...
Query
...
Plugin
...
reporting
...
capability;
...
(3)
...
additional
...
configurability
...