Brief History of U-Compare

We started using UIMA in 2005 at the Tsujii laboratory in the University of Tokyo. Initially our own language resources are made into UIMA compatible. Then the U-Compare platform was developed to facilitate users' tasks such as workflow creation, comparison, and result anaysis. The platform was developed in the University of Tokyo mainly funded by Grant-in-aids for specially promoted research (18002007, PI: Prof. Tsujii), MEXT Japan. The NLP research group in the University of Tokyo (headed by Prof. Jun'ichi Tsujii) worked together with the National Centre for Text Mining at the University of Manchester (headed by Prof. Sophia Ananiadou) and the Center for Computational Pharmacology at the University of Colorado (headed by Prof. Larry Hunter), to collect language resouces to be compatible UIMA components while promoting the U-Compare system for the community to share the resources. The first public version of U-Compare was released in 2008. We have been further broadining the collaboration with more research groups.

Please refer to Contact page for individual contributers.

Update History of U-Compare

March 2011, U-Tokyo web service components temporarily unavailable

Due to the power saving effort at the University of Tokyo, web service components hosted in U-Tokyo are unavailable. Service status is shown as a red "X" icon when unavailable.

March 10th, 2011 Version

U-Compare type system updated, needs update of u-compare.jar file if you use a local copy.
A couple of new components included for the Japanese language.

2011 January 18th, Version

New component "Metaboliner" which annotates named entities of yeast metabolites. Missing libraries for our secondstring matching component are recovered. A few types are added to the type system.

2010/Oct/16 Version 1.1.6

Enhancement in the comparison viewer, now highlights matched annotations when selected. This change might not be compatible with older saved data if created by a comparison workflow. A minor bugfix, needless classpath entry check in startup. Other minor enhancements and bugfixes included.

2010/Sep/02 Open Source License License

We have changed the license, to a dual license of LGPL open source license and a commercial license. Please see our license page for details.

2010/Jul/05 Version

A bug in Mac OSX, sometimes the UI has locked up, was fixed.

2010/Jul/02 Version

Minor bugfixes and improvements in the U-Compare platform and ucloader.jar (UCLoader Launcher).

2009 Oct 23. Forum posting not available (Forum)

Due to very many spam posts, we have disabled new posts in the forum. We will consider workarounds later.

2009 Oct 9. released a new launcher, UCLoader Launcher (Launch U-Compare)

UCLoader Launcher is an executable Jar file, which allows users to launch U-Compare in an easy mannar but runs faster as same as UCLoader.
This is due to the previous Java Web Start launcher was very slow when the network connection is narrow.

2009 Jul 31. Version 1.1.3.

New Comonents: NaCTeM Species Word Detector, morpha, extractabbrev, NaCTeM Species Disambiguator.from Nactem.
ABNER with User Model, NLPBA reader, BioCreative1a reader, BIO (IOB) reader/writer, wrapped by U-Compare.
Annotation Viewer shows comparison groups precisely.. Other debugs.

2009 Jul 31. Documentation Updated.

Updated almost all of the pages in this site, except for the Developer Guide (to be updated)..

2009 May 27. Version 1.1.2

Updated to version 1.1.2. FIX: Language Capability option in Input Text Reader was not working.

2009 May 21. Version 1.1.1

Updated to version 1.1.1. CHANGE: Input Text Reader has Language Capability option. FIX: fixed text encoding bug. FIX: problem using external type system.

2009 May 16. Video Tutorial

A video tutorial available for the first time U-Compare users.

2009 May 13. UCLoader, Website (Launch U-Compare/Link)

Provides new launcher system, UCLoader, faster and in a command line way. See Launch U-Compare page for details. Link page has also updated.

2009 May 4. Publication

Kano, Yoshinobu, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter and Jun'ichi Tsujii U-Compare: share and compare text mining tools with UIMA. Bioinformatics 2009 (in press); doi: 10.1093/bioinformatics/btp289 abstract (journal website) pdf bib enl

See Publications page for details.

2010 Mar 03. Version 1.1.4

The U-Compare type system updated, now released under the Apache license. Include bugfixes in several components.

2009 Oct 23. Updated UCLoader Launcher (Launch U-Compare)

Bugfix: UCLoader Launcher could not start U-Compare when the ucloader.jar file is saved to a path which contains whitespaces. This occurs often when you use Windows and run the jar file directly from the browser, which saves the file to your temporary folder under Documents and Settings.

2009 Apr 30, system

U-Compare released a major update, Version 1.1.0, includes many new features, new components, bugfixes.

  • U-Compare now uses directory [user.home]/.U-Compare, instead of [user.home]/U-Compare. Automatically renames the old directory when the new directory does not exist.
  • Results of U-Compare parallel workflows are not compatible with the previous versions due to the new evaluation pluggable system, loading such old results will fail. Sorry for the inconvenience.
We will notify about the new features and components here, when we update corresponding documents.
Forum location has been moved, please check if you linked to the forum articles directly.

2009 Mar 19, UIMA

OASIS approved the first open specification of the UIMA standard. The members of U-Compare (the University of Tokyo and the University of Manchester/Nactem) are members of the OASIS UIMA Technical Committee, created the standard together with other members.

2009 Feb 4, Java

Sun released Java 6 update 12, supporting Java Web Start in 64bit systems.

2009 Jan 26, system

Version 1.0.5, enhancement in the BioNLP shared task reader, other bugfixes.

2009 Jan 7, system

Version 1.0.4, enhancement and bugfixes of Annotation Viewer.

2008 Dec 22, system/website

U-Compare is officially supporting the BioNLP 09 shared task on event detections, held in NAACL 09 at Boulder, Colorado. In version 1.0.3 below, Shared Task format reader and a workflow for visualization is provided. Along with the later data/evaluation scheme releases from the shared task, we will provide more functions. See the BioNLP 09 page for details, also linked from the menu list on the left.

2008 Dec 22, system/website

Version 1.0.3, added Enju 2.3.1, Akane PPI Detector, StanfordParser and SecondString based dictionary pluggable NER. Annotation Viewer is now showing any links between annotations graphically as arcs. See our forum for details.

2008 Nov 27, system/website

Version 1.0.2, added Nactem Sentence Breaker, Import/Export function bugfix, providing LingPipe importable package again, Annotation Viewer performance improvement, etc. See our forum for details.

2008 Nov 17, system/website

Version 1.0.1, see our forum for details. Also updated developer guide.

2008 Nov 14, system/website

First public release.

2008 Nov 11, system/website

Public beta version for testing purpose.

2008 Oct 17, website

Renewed entire website.