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h1.

NCI

...

Protégé

Section
Column
width55%
Panel
titleContents of this Page
Table of Contents
minLevel2
Include Page
VKC:VKC Quick Links to Include
VKC:VKC Quick Links to Include
Column
Panel
titleAt a Glance Details
  • Version Number and Release Date:
{section} {column:width=55%} {panel:title=Contents of this Page} {toc:minLevel=2} {panel} {include:VKC:VKC Quick Links to Include} {column} {column} {panel:title=At a Glance Details} * Version Number and Release Date:
  • 1.4.3,
  • February
  • 2011
  • (NCI
  • Protégé
  • 1.4
  • requires
  • Protégé
  • 3)
*
  • caBIG®
  • Tool
  • Bundle:
  • None
*
  • Grid
  • Enabled?
  • Supporting
  • tool
*
  • Compatibility
  • Level:
  • Supporting
  • tool
*
  • Installation
  • Level:
  • Intermediate
  • -
  • technical
  • assistance
  • may
  • be
  • required,
  • download
  • may
  • require
  • supporting
  • infrastructure
  • or
  • software
*
  • System
  • Requirements:
  • Protégé
  • runs
  • on
  • platforms
  • that
  • support
  • JDK
  • version
  • 1.4.
  • This
  • includes
  • all
  • modern
  • versions
  • of
  • MS
  • Windows
  • (NT/2000/XP),
  • the
  • common
  • versions
  • of
  • Unix
  • including
  • Linux,
  • Solaris,
  • AIX,
  • and
  • HP-UX,
  • and
  • Mac
  • OS
  • X.
{panel} {column} {section} h2. Tool Overview

Tool Overview

Wiki Markup
{multi-excerpt:name=NCIProtegeSummary}
NCI Protégé is a collection of Protégé plug-ins developed for the NCI-specific editing environment. Protégé is an open-source development environment for ontologies and knowledge based systems. The OWL plug-in extends the environment to support the Web Ontology Language (OWL). Refer to the [Protégé|Protege] page for more information.

The NCI Protégé collection of plug-ins is used to edit the NCI Thesaurus. NCI Protégé provides a customized OWL editing environment, including additional editing and querying capabilities that are not available in the Protégé OWL plug-in. The NCI-specific plug-ins have been implemented as a tabbed interface. Beginning with NCI Protégé 1.3.0. this tool allows imports of ontologies in database mode and enables collaborators to begin "federating" ontologies.
{multi-excerpt}

...

NCI 
...
 Protégé 
...
 runs 
...
 in 
...
 a 
...
 client-server 
...
 environment. 
...
 Current 
...
 editors 
...
 will 
...
 want 
...
 to 
...
 download 
...
 the 
...
 client 
...
 only. 
...
 Others 
...
 may 
...
 wish 
...
 to 
...
 download 
...
 for 
...
 review 
...
 or 
...
 download 
...
 and 
...
 install 
...
 the 
...
 entire 
...
 client-server 
...
 package. 
...
 Links 
...
 to 
...
 both 
...
 are 
...
 provided 
...
 in 
...
 the 
...
tool 
...
 downloads.
Installation and Downloads
The distribution package can be found on GForge.
The package contains the following (this may vary slightly for different versions):
  • The installation folders for the client, Explanation server and Protégé server.
  • A metaproject which contains accounts for editor and administrator by default.
  • Test BiomedGT and NCIThesaurus OWL files to load.
  • An import-repository folder containing OWL files to set up a local ontology repository.
  • A ReadMe file with instructions on how to configure all the necessary scripts from scratch.
When you install a new release, you must configure a new database project, following the instructions on Protege Software Updates and Configuring New Database Project. These instructions reflect the NCI EVS server environment (directory structures, filenames, server hostnames, etc). It is not required, but it is probably easiest, to set up the same directories in a new environment.
 Info
titleDownload for an NCI editor
If you are an NCI editor, you will only need to download the appropriate client, from the list on the downloads page on the GForge site.
 Wiki Markup
{|NCI Protege#Installation and Downloads].

h2. Installation and Downloads

The distribution package can be found [on GForge|http://gforge.nci.nih.gov/frs/?group_id=174 NCI Protégé Public Release Package].

The package contains the following (this may vary slightly for different versions):

* The installation folders for the client, Explanation server and Protégé server. 
* A metaproject which contains accounts for editor and administrator by default. 
* Test BiomedGT and NCIThesaurus OWL files to load. 
* An import-repository folder containing OWL files to set up a local ontology repository. 
* A ReadMe file with instructions on how to configure all the necessary scripts from scratch.

When you install a new release, you must configure a new database project, following the instructions on [Protege Software Updates and Configuring New Database Project]. These instructions reflect the NCI EVS server environment (directory structures, filenames, server hostnames, etc). It is not required, but it is probably easiest, to set up the same directories in a new environment.

{info:title=Download for an NCI editor}If you are an NCI editor, you will only need to download the appropriate client, from the list on the [downloads page on the GForge site|http://gforge.nci.nih.gov/frs/?group_id=174].{info}

{Include:VKC:Code Download Disclaimer to Include}

h2. 
NCI 
...
 Protégé 
...
 Forum 
...
 and Support
 Wiki Markup
 Support

{multi-excerpt-include:pageTitle=NCI Protege Support Links|name=NCIProtegeSupportLinks|nopanel=true}

h2. 
What's 
...
 New
...
The 
...
 final 
...
 version 
...
 of 
...
 NCI 
...
 Protégé 
...
 (1.4.3) 
...
 to 
...
 be 
...
 built 
...
 on 
...
 the 
...
 Protégé 
...
 3.4 
...
 code 
...
 base 
...
 from 
...
 Stanford 
...
 has 
...
 been 
...
 released. 
...
 The 
...
 status 
...
 of 
...
 NCI 
...
 Protégé 
...
 is 
...
 now 
...
 maintenance 
...
 mode. 
...
 Only 
...
 major 
...
 bugs 
...
 that 
...
 appear 
...
 in 
...
 production 
...
 will 
...
 be 
...
 fixed. 
...
 Future 
...
 versions 
...
 of 
...
 NCI 
...
 Protégé 
...
 are 
...
 being 
...
 considered 
...
 for 
...
 the 
...
 Protege 
...
 4 
...
 code 
...
 base.
...
Features
The EVS Protégé distribution includes the NCIEditTab Protégé plug-in 
...
 editing 
...
 client 
...
 (and 
...
 other 
...
 plug-ins), 
...
 a 
...
 highly 
...
 concurrent 
...
 Protégé 
...
 server 
...
 (modified 
...
 from 
...
 the 
...
 base 
...
 Stanford 
...
 distribution), 
...
 and 
...
 an 
...
 Explanation 
...
 server 
...
 that 
...
 includes 
...
 the 
...
 Pellet 
...
 reasoner.
...
Client 
...
 Environment
...
The 
...
 client 
...
 environment 
...
 includes:
...
  • NCIEditTab 
...
  •  plug-in, 
...
  •  supporting 
...
  •  basic 
...
  •  editing 
...
  •  functionality 
...
  •  as 
...
  •  well 
...
  •  as 
...
  •  complex 
...
  •  edits 
...
  •  (merge, 
...
  •  split, 
...
  •  retirement, 
...
  •  and 
...
  •  cloning), 
...
  •  batch 
...
  •  jobs, 
...
  •  report 
...
  •  writing, 
...
  •  and 
...
  •  tree-like 
...
  •  views 
...
  •  of 
...
  •  graphs 
...
  •  built 
...
  •  along 
...
  •  transitive 
...
  •  relationships 
...
  •  (e.g. 
...
  •  part_of). 
...
  •  It 
...
  •  supports 
...
  •  XMLLiterals 
...
  •  for 
...
  •  complex 
...
  •  properties 
...
  •  as 
...
  •  per 
...
  •  configuration, 
...
  •  and 
...
  •  tracks 
...
  •  editing 
...
  •  history 
...
  •  independently 
...
  •  of 
...
  •  the 
...
  •  change 
...
  •  ontology, 
...
  •  which 
...
  •  is 
...
  •  used 
...
  •  in 
...
  •  support 
...
  •  of 
...
  •  Prompt.
...
  • LuceneQuery 
...
  •  tab 
...
  •  plug-in, 
...
  •  supporting 
...
  •  a 
...
  •  variety 
...
  •  of 
...
  •  search 
...
  •  modes 
...
  •  (including 
...
  •  negation) 
...
  •  on 
...
  •  annotations 
...
  •  and 
...
  •  restrictions 
...
  •  as 
...
  •  well 
...
  •  as 
...
  •  indexed 
...
  •  Lucene 
...
  •  "match" 
...
  •  and 
...
  •  "sounds 
...
  •  like" 
...
  •  searching, 
...
  •  plus 
...
  •  reporting 
...
  •  support 
...
  •  for 
...
  •  the 
...
  •  result 
...
  •  sets.
...
  • Explanation 
...
  •  tab 
...
  •  plug-in, 
...
  •  providing 
...
  •  a 
...
  •  description 
...
  •  logic 
...
  •  entailment-explanation 
...
  •  facility 
...
  •  integrated 
...
  •  with 
...
  •  an 
...
  •  incremental 
...
  •  classifier; 
...
  •  classification 
...
  •  results 
...
  •  are 
...
  •  available 
...
  •  to 
...
  •  all 
...
  •  the 
...
  •  clients 
...
  •  in 
...
  •  the 
...
  •  client-server 
...
  •  environment.
...
  • Workflow 
...
  •  tab 
...
  •  plug-in, 
...
  •  supporting 
...
  •  basic 
...
  •  workflow/assignment 
...
  •  functionality, 
...
  •  and 
...
  •  communications 
...
  •  to 
...
  •  Semantic 
...
  •  Media 
...
  •  Wiki 
...
  •  if 
...
  •  set 
...
  •  up 
...
  •  for 
...
  •  collaborative 
...
  •  development.
Roadmap
 Wiki Markup


h3.Roadmap
{multi-excerpt-include:pageTitle=NCI Protege Release Roadmap|name=NCIProtegeReleasestoPresentSummarized|nopanel=true}

h2. 
NCI 
...
 Protégé Presentations
 Wiki Markup
 Presentations

{multi-excerpt-include:pageTitle=NCI Protege Presentations|name=NCIProtegePresentations|nopanel=true}

h2. 
NCI 
...
 Protégé 
...
 Documentation 
...
 and Training
 Wiki Markup
 Training

{multi-excerpt-include:pageTitle=NCI Protege Documentation|name=NCIProtegeDocumentation|nopanel=true}

h2. 
Related 
...
 Tools
 Wiki Markup


* [Protégé|Protege]
* [FCAView Protégé Tab Plug-in|FCAView Protege Tab Plug-in]

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