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Textpresso

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Textpresso logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence


Modified GPL

Resources


About Textpresso

Textpresso is an information extracting and processing (text mining) package for biological literature whose capabilities go far beyond that of a simple keyword search engine. The two key elements are the collection of the full text of scientific articles split into individual sentences, and the implementation of semantic categories, for which a database of articles and individual sentences can be searched. The source of the full text articles are PDFs, and additional bibliographical information that is obtained from other citation databases can be processed as well. Alere is a package of scripts that can be used to construct a corpus (retrieve articles) for use with Textpresso. Textpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # HG004090.


Visit the Textpresso website.


Downloads


Using Textpresso

The package is designed for Linux operating systems and is tested to run on an Intel x86 based hardware. The required minimal disk space is around 6GB per 1000 full text papers; half of it is used by the publicly (via WWW) accessible database, while the other half is needed for database preparation and maintenance. If necessary, the latter can be reduced.

System Requirements

  • Software for a world wide web server such as Apache needs to be installed, and an Internet connection should exist
  • Perl 5.6.1 or higher should be present, and the most common Perl packages.
  • The installation script requires bash
  • XML::Checker::Parser
  • XML::DOM::Parser
  • XML::XQL::DOM
  • XML::Checker::Parser,
  • Mailer::Mail (in MailTools-1.58)
  • PDF::Create (in PDF-Create).
  • If the model organism database is based on ACeDB then AcePerl is required
  • XPDF (http://www.foolabs.com/xpdf/), the pdftotext converter
  • RBT, a part-of-speech tagger developed by Eric Brill (blog, homepagedeprecated). RBT seems to be no longer available at JHU. A copy appears to be available at Københavns Universitet (I didn't download and check it). RBT is distributed free of charge under a license of the Massachusetts Institute of Technology and the University of Pennsylvania. If you want to recompile either of the packages, you additionally need a C compiler.

This package has been tested with the Linux RedHat 9.0 distribution (http://www.redhat.com) and Debian Linux 3.1 (http://www.debian.org) . Both work with a 2.4.20 kernel or higher.


Documentation

Textpresso 2 Extensions

A fork of Textpresso has been created that contains a number of extensions to Textpresso 2. These include

  • Interface overhaul, including AJAX and heavy integration of jQuery DatatTables, user authentication, and a GUI for managing the literature corpus.
  • Modularization and customization for better database support
  • Addition of a plug-in API
  • Speed increase

The extended version of Textpresso 2 is available at SourceForge.

These extensions were written by Nathan Liles of the Hu Lab at Texas A&M University. Nathan presented this work at the January 2010 GMOD Meeting. The Textpresso team plans to fold these extensions back into the main Textpresso code base in the future.



Contacts and Mailing Lists

For support, please contact the Textpresso developer, Hans-Michael Müller.

Textpresso in the wild

Public installations of Textpresso:



More on Textpresso

See Category:Textpresso



Facts about "Textpresso"RDF feed
Available on platformweb +
Has URLhttp://textpresso.org +, http://textpresso.org/downloads.html +, http://textpresso-www.caltech.edu/cgi-bin/celegans/user_guide +, http://whis.caltech.edu/textpresso/ +, http://textpresso.yeastgenome.org/textpresso/ + and http://www.textpresso.org/celegans/ +
Has descriptionTextpresso is an information extracting anTextpresso is an information extracting and processing (text mining) package for biological literature whose capabilities go far beyond that of a simple keyword search engine. The two key elements are the collection of the full text of scientific articles split into individual sentences, and the implementation of semantic categories, for which a database of articles and individual sentences can be searched. The source of the full text articles are PDFs, and additional bibliographical information that is obtained from other citation databases can be processed as well. Alere is a package of scripts that can be used to construct a corpus (retrieve articles) for use with Textpresso. Textpresso is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # HG004090. National Institutes of Health # HG004090. +
Has development statusactive +
Has input formatPlain text +, PDF + and html +
Has licenceModified GPL +
Has logoTextpressoLogo.jpg +
Has output formatXML + and text +
Has software maturity statusmature +
Has support statusactive +
Has titleTextpresso User Guide +, Textpresso for Sea Urchin +, Textpresso for S. cerevisiae + and Textpresso for C. elegans +
Has topicTextpresso +
Is open sourceCaveats apply +
Link typewebsite +, download +, documentation + and wild URL +
Tool functionality or classificationLiterature tools + and Text mining +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.Textpresso#http://textpresso.org +, Textpresso#http://textpresso.org/downloads.html +, Textpresso#http://textpresso-www.caltech.edu/cgi-bin/celegans/user_guide +, Textpresso#http://whis.caltech.edu/textpresso/ +, Textpresso#http://textpresso.yeastgenome.org/textpresso/ + and Textpresso#http://www.textpresso.org/celegans/ +