biblicit 2.0.5 → 2.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +1 -0
- data/lib/biblicit/version.rb +1 -1
- data/parscit/INSTALL +29 -7
- data/parscit/bin/parsHed/redo.parsHed.pl +3 -2
- data/parscit/bin/redo.parsCit.pl +3 -2
- data/parscit/bin/sectLabel/genericSect/crossValidation.rb +1 -1
- data/parscit/bin/sectLabel/genericSectExtract.rb +1 -1
- data/parscit/bin/sectLabel/redo.sectLabel.pl +3 -2
- data/parscit/doc/index.html +692 -0
- data/parscit/lib/ParsCit/Config.pm +1 -1
- data/parscit/lib/ParsCit/Tr2crfpp.pm +1 -1
- data/parscit/lib/ParsHed/Config.pm +1 -1
- data/parscit/lib/ParsHed/Tr2crfpp.pm +1 -1
- data/parscit/lib/ParsHed/Tr2crfpp_token.pm +1 -1
- data/parscit/lib/SectLabel/AAMatching.pm +1949 -0
- data/parscit/lib/SectLabel/Config.pm +1 -1
- data/parscit/lib/SectLabel/Tr2crfpp.pm +2 -2
- metadata +5 -8
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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 3.0//EN">
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<HTML><HEAD>
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<META HTTP-EQUIV="Keywords" NAME="Keywords" CONTENT="citations, citation parser, references, reference parser, bibliography parser, reference string parser, bibtex, citation, citation extraction, logical structure, document logical structure">
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<LINK REL="stylesheet" HREF="parsCit.css"><TITLE>ParsCit: An open-source CRF Reference String and Logical Document Structure Parsing Package</TITLE>
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function toggleLayer( whichLayer ) {
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else if( document.all ) // this is the way old msie versions work
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elem = document.all[whichLayer];
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else if( document.layers ) // this is the way nn4 works
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elem = document.layers[whichLayer];
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vis = elem.style;
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// if the style.display value is blank we try to figure it out here
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if(vis.display==''&&elem.offsetWidth!=undefined&&elem.offsetHeight!=undefined)
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vis.display = (elem.offsetWidth!=0&&elem.offsetHeight!=0)?'block':'none';
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}
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</script>
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</HEAD><BODY BGCOLOR="#FFFFFF">
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<div id="leftcontent">
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[ <A href="http://wing.comp.nus.edu.sg/">WING homepage</A> ]<br/>
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[ <A href="http://wing.comp.nus.edu.sg/portal/web-services.html">WING web services</A> ]<br/>
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<BR/>
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[ <A href="#d">Download</a> ]<br/>
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[ <A href="#ws">Web Service</a> ]</br/>
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[ <A href="#wd">Web Demo</a> ]<br/>
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[ <A href="#p">Publications</a> ]<br/>
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[ <A href="#gsiso">Input and Output</a> ]<br/>
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[ <A href="#gm">Group Members</a> ]<br/>
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[ <A href="#faq">FAQ</a> ]<br/>
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[ <A href="#t">Troubleshooting</a> ]<br/>
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<br/>
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<script type="text/javascript"
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src="http://feedjit.com/serve/?vv=932&tft=3&dd=0&wid=0804fba767d140cd&pid=0&proid=0&bc=FFFFFF&tc=000000&brd1=012B6B&lnk=135D9E&hc=FFFFFF&hfc=2853A8&btn=C99700&ww=200&wne=10&wh=WING+Live+Traffic+Feed&hl=0&hlnks=0&hfce=0&srefs=1&hbars=0"></script><noscript><a
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href="http://feedjit.com/">Feedjit Live Blog Stats</a></noscript>
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</div>
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<div id="centercontent">
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<IMG ALIGN="LEFT" SRC="parsCit.png" WIDTH="200px" ALT="Picture of ParsCit Swami">
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<CENTER><H1>ParsCit: An open-source CRF Reference String and Logical Document Structure Parsing Package</H1></CENTER>
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<P>This is the home page of the ParsCit project, which performs two
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tasks: 1) reference string parsing, sometimes also called citation
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parsing or citation extraction, and 2) logical structure parsing of
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scienfific documents. It is architected as a supervised machine
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learning procedure that uses Conditional Random Fields as its learning
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mechanism. You can download the code below, parse strings online, or
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send batch jobs to our web service. The code contains both the
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training data, feature generator and shell scripts to connect the
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system to a web service (used on this web site).</P>
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<P>Some definitions (thanks to Robert Dale for Citations and Reference
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Strings):
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<DL>
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<DT>Reference String:</DT><DD>A text string in the bibliography or
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reference section of a work, usually at the end of the document that
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refers to a unique document. Usually occurs with other reference
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strings that point to other documents. May also appear as
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footnotes.</DD>
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<DT>Citation:</DT><DD>A text string (usually explicit) in the
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document body that points to a corresponding reference string at the
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end of the document. Several citations may co-refer to a single
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reference string.</DD>
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<DT>Document Logical Structure:</DT><DD> A hierarchy of logical
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components, for example, titles, authors, affiliations, abstracts,
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sections, etc., according to (Mao, Rosenfeld &
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Kanungo,2003). Our logical structure is more comprehensive,
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comprising not only header metadata and references, but also the
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logical structure of the internals of the document -- sections,
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subsections, figures, tables, equations, footnotes and
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captions. </DD>
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</DL>
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<P>This project deals with the problem of parsing the reference
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strings and parsing the logical structure of a document. The first
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task is handled by a module with the project namesake, ParsCit, and
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the second task by a separate module SectLabel.
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</P>
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<br clear="all"/>
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<!-- License ---------------------------------------------------------------------- -->
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<A NAME="l"></A><H2>License</H2>
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<P>This software is licensed under the <A
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HREF="http://www.gnu.org/copyleft/lesser.html">Lesser GNU Public
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License</A> (LGPL), which means you are free to use it for any
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purpose, including embedding in commercial products. </P>
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<br clear="all" />
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<!-- Download ---------------------------------------------------------------------- -->
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<A NAME="d"></A><H2>Download</H2>
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<P>You can download the open-source code for ParsCit here. The source requires you to re-compile the CRFPP source code
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and assumes that perl is installed on your system and can be invoked
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using <CODE>perl</CODE> (must be in your path).
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</P>
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<ul>
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<li> Current version <A HREF="parscit-110505b.zip">110505b</A>: Added XML::Twig for XML processing. ParsCit now uses input provided by SectLabel. See <A HREF="CHANGELOG.txt"> CHANGELOG.txt </A>.<BR/>
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The (partially ported) <A HREF="parscit-110505b-win.zip">Windows</A> version is here (provided by Yumichika). See the <A HREF="CHANGES%20FOR%20WINDOWS.txt">CHANGES FOR WINDOWS.txt</A>
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<BR/>
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<BR/>
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We have also pushed a copy of the ParsCit current distribution into <A HREF="http://www.github.com/knmnyn/parscit">GitHub:knmnyn/parscit</A>.
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The Windows version has also been pushed to <A HREF="http://www.github.com/wing-nus/parscit">GitHub:wing-nus/parscit</A>.
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While we'll strive to keep the GitHub version as updated as possible, the versions on this page will remain the most authoritative for major updates.
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<BR/>
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<li> Other versions: <BR/>
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<A HREF="parscit-101101.zip">101101</A>: Incorporated <A HREF="http://github.com/mromanello/BiblioScript">BiblioScript</A> and <A HREF=http://www.scripps.edu/~cdputnam/software/bibutils>BibUtils</A> software. See CHANGELOG.txt; <BR/>
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<A HREF="parscit-100401.zip">100401d</A>: Added SectLabel (logical structure parsing) software from the NUS team, and Iconip training data from Cheong Chi Hong for ParsCit with new ParsCit model retrained. See CHANGELOG.txt; <BR/>
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<A HREF="parscit-090625.zip">090625b</A>: Added documentation for complete re-installation. Improved ParsHed with added line-level CRF model together and post-processing module by NUS team, WSDL file and client for service at NUS and minor bug fixes for ParsCit. See CHANGELOG.txt; <BR/>
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<A HREF="parscit-090316.zip">090316</A>: Incorporation of ParsHed (header parsing) software from the NUS team. See CHANGELOG.txt; <BR/>
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<A HREF="parscit-081201.zip">081201</A>: Bug fixes and incorporation of byte position offset from the Scienstein.org team. See CHANGELOG.txt; <BR/>
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<A HREF="parscit-080917.zip">080917</A>: Minor changes (improved models and mulilingual support), see CHANGELOG.txt; <BR/>
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<A HREF="parscit-080402.zip">080402</A>: First public release. Comes with precompiled linux binaries for CRF++; <BR/>
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<A HREF="parscit-080310.tgz">080310</A>: Beta release.
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<li><A HREF="http://crfpp.sourceforge.net">CRF++</A>: A conditional random fields toolkit that you may need to install, if the compiled one does not work for you. We recommend that you use version 0.51. </ul>
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<!-- Web Service ---------------------------------------------------------------------- -->
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<A name="ws"></a><H2>Web Service</h2>
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<P>More NLP services are now being made available on the web.
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Following this trend you can send your plain text citations to use via
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our web service. We will parse these for you free of charge (as and
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when time and processing power allows, these processes are done with
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lower priority).</P>
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<P CLASS="red">N.B. We keep logs of what's parsed in these demos, to
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improve the accuracy and productivity of ParsCit. If you'd like these
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to be kept private or you find you use this service a lot, why not
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install a local copy of ParsCit for yourself? If you do, please
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let us know where you are so we acknowledge you here and can re-direct
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some traffic your way.
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</P>
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<UL>
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<LI> <A HREF="wing.nus.wsdl">Download the WSDL file</A> for the service at NUS.
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<LI> <A HREF="ParsCitClientWSDL.rb">Download the sample ruby client
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that uses the WSDL file</A> to dynamically generate the ParsCit web
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service call to the NUS server. Edit the file to see how to
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execute it.
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<LI> <A HREF="ParsCitClient.rb">Download sample ruby client code</a>
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for the ParsCit web service at the NUS server. To execute,
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just point it at a local
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text file that represents the text dump of a scholarly article
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(such as one produced by a PDF to text converter):
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<CODE>
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./ParsCitClient.rb ~/public_html/samples/E06-1050.txt
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</CODE>
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<LI><FORM METHOD="post" ACTION="parsCit.cgi"><INPUT TYPE="HIDDEN"
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NAME="ping" VALUE="ping"><INPUT TYPE="SUBMIT" VALUE="Check"> whether
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the web service is up.
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</FORM>
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</UL>
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<!-- Web demo ----------------------------------------------------------------------- -->
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<A name="wd"></a><H2>Web-based Demonstration</H2>
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<P CLASS="red">N.B.: We keep logs of what's parsed in these demos, to
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improve the accuracy and productivity of ParsCit. If you'd like these
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to be kept private, why not install a local copy of ParsCit for
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yourself?</P>
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<P>You can also run ParsCit directly in your browser. The form below
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submits your text input (after suitable cleaning) to the ParsCit
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service to parse the input file or strings. <FONT COLOR="red">
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Note that if system loads gets high, your demo call may not be executed. If you want to run this program in batch, please download your own copy.</FONT>
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</P>
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<P><B>Demo #1: Parsing the header, logical structure and/or reference strings (and citation contexts) from a text file</B></P>
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<DIV STYLE="background-color:D0D0FF; padding: 1em">
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<FORM ENCTYPE="multipart/form-data" METHOD="post" ACTION="parsCit.cgi">
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<P>NB - this demo does not handle PDF input at this time. You can use another web service or software to convert PDFs to text. </P>
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<P style="font-size:small;"><I>Internal key (if applicable):</I> <INPUT TYPE="password" SIZE="4" NAME="key"></P>
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<INPUT TYPE="text" SIZE="80" NAME="demo" value="1" style="display:none;">
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<P>Input Method 1) Enter a URL to a file on the web (e.g., <A HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.txt">http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.txt</A> or <A HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.txt">http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.txt</A>).<BR/>
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<INPUT TYPE="text" SIZE="80" NAME="urlfile">
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</P>
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<P>Input Method 2) Upload a .txt file (ASCII; UTF-8)<BR/>
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<INPUT TYPE="FILE" NAME="datafile">
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</P>
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<P>Input Method 3) Paste the whole file here:
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<br/>
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<TEXTAREA ROWS="4" COLS="80" NAME="textfile">
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</TEXTAREA>
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</P>
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<P>Parse the document using the following options
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<SELECT NAME="ParsCitOptions">
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<OPTION SELECTED VALUE="5">all</OPTION>
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<OPTION VALUE="1">citations</OPTION>
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<OPTION VALUE="2">header</OPTION>
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<OPTION VALUE="4">section</OPTION>
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</SELECT>
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</P>
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<P>Citation export formats
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<INPUT TYPE=CHECKBOX NAME="ads1">ADS
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<INPUT TYPE=CHECKBOX NAME="bib1" CHECKED>BIB
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<INPUT TYPE=CHECKBOX NAME="end1">EndNote
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<INPUT TYPE=CHECKBOX NAME="isi1">ISI
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<INPUT TYPE=CHECKBOX NAME="ris1">RIS
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<INPUT TYPE=CHECKBOX NAME="wordbib1">WordBib
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</P>
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<br/><CENTER><INPUT TYPE="SUBMIT" VALUE="Parse this file!"></CENTER>
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</FORM>
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</DIV>
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<P><B>Demo #2: As above but using XML input (XML must conform to Omnipage output). This demo is slow so please be patient.</B></P>
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<DIV STYLE="background-color:D0D0FF; padding: 1em">
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<FORM ENCTYPE="multipart/form-data" METHOD="post" ACTION="parsCit.cgi">
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<INPUT TYPE="text" SIZE="80" NAME="demo" value="2" style="display:none;">
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<P style="font-size:small;"><I>Internal key (if applicable):</I> <INPUT TYPE="password" SIZE="4" NAME="key"></P>
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<P>Input Method 1) Enter a URL to a file on the web (e.g., <A HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.xml">http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.xml</A> or <A HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.xml">http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.xml</A>).<BR/>
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<INPUT TYPE="text" SIZE="80" NAME="urlfile">
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</P>
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<P>Input Method 2) Upload a .xml file (ASCII; UTF-8)<BR/>
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<INPUT TYPE="FILE" NAME="datafile">
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</P>
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<P>Input Method 3) Paste the whole .xml file here:
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<br/>
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<TEXTAREA ROWS="4" COLS="80" NAME="textfile">
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</TEXTAREA>
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</P>
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<P>Input Method 4) Upload your own .pdf file (less than 50 pages & smaller than 10MB):
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<br/>
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<INPUT TYPE="FILE" NAME="pdffile">
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</P>
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<P>Parse the document using the following options
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<SELECT NAME="ParsCitOptions">
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<OPTION SELECTED VALUE="5">all</OPTION>
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<OPTION VALUE="1">citations</OPTION>
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<OPTION VALUE="2">header</OPTION>
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<OPTION VALUE="4">section</OPTION>
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</SELECT>
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</P>
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<P>Citation export formats
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<INPUT TYPE=CHECKBOX NAME="ads2">ADS
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<INPUT TYPE=CHECKBOX NAME="bib2" CHECKED>BIB
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<INPUT TYPE=CHECKBOX NAME="end2">EndNote
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<INPUT TYPE=CHECKBOX NAME="isi2">ISI
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<INPUT TYPE=CHECKBOX NAME="ris2">RIS
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<INPUT TYPE=CHECKBOX NAME="wordbib2">WordBib
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</P>
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+
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<br/><CENTER><INPUT TYPE="SUBMIT" VALUE="Parse this file!"></CENTER>
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</FORM>
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</DIV>
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<!--
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<P><B>Demo #2b: OCR a PDF file using Omnipage (less than 50 pages & smaller than 10MB).</B></P>
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<DIV STYLE="background-color:D0D0FF; padding: 1em">
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<FORM ENCTYPE="multipart/form-data" METHOD="post" ACTION="upload.cgi">
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<P style="font-size:small;"><I>Internal key (if applicable):</I> <INPUT TYPE="password" SIZE="4" NAME="key"></P>
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<P>File to OCR (PDF only): <INPUT TYPE="FILE" NAME="content"></P>
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<br/><CENTER><INPUT TYPE="SUBMIT" VALUE="OCR this file!"></CENTER>
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</FORM>
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</DIV>
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-->
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<P><B>Demo #3: Parsing individual reference strings only (just <CODE>extract_citations</CODE>)</B></P>
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<DIV STYLE="background-color:D0D0FF; padding: 1em">
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<FORM ENCTYPE="multipart/form-data" METHOD="post" ACTION="parsCit.cgi">
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<INPUT TYPE="text" SIZE="80" NAME="demo" value="3" style="display:none;">
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<P style="font-size:small;"><I>Internal key (if applicable):</I> <INPUT TYPE="password" SIZE="4" NAME="key"></P>
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<P>Input Method 1) Enter a URL to a file on the web in the correct format (each line should be a separate citation; e.g., <A
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HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.cite">http://wing.comp.nus.edu.sg/~wing.nus/samples/E06-1050.cite</A> or <A
|
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|
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HREF="http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.cite">http://wing.comp.nus.edu.sg/~wing.nus/samples/W06-0102.cite</A>).
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<INPUT TYPE="text" SIZE="80" NAME="urllines">
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</P>
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+
|
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<P>Input Method 2) Upload a file (again, each line should be a separate citation)<BR/>
|
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|
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<INPUT TYPE="FILE" NAME="datalines">
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|
+
</P>
|
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295
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+
|
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<P>Input Method 3) Enter a list of plain text citations (again, one per line):<BR/>
|
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<TEXTAREA ROWS="4" COLS="80" NAME="textlines">Isaac G. Councill, C. Lee Giles, Min-Yen Kan. (2008) ParsCit: An open-source CRF reference string parsing package. To appear in the proceedings of the Language Resources and Evaluation Conference (LREC 08), Marrakesh, Morrocco, May.
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</TEXTAREA>
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</P>
|
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+
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<P>Citation export formats
|
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<INPUT TYPE=CHECKBOX NAME="ads3">ADS
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<INPUT TYPE=CHECKBOX NAME="bib3" CHECKED>BIB
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<INPUT TYPE=CHECKBOX NAME="end3">EndNote
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305
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<INPUT TYPE=CHECKBOX NAME="isi3">ISI
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<INPUT TYPE=CHECKBOX NAME="ris3">RIS
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<INPUT TYPE=CHECKBOX NAME="wordbib3">WordBib
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+
</P>
|
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+
|
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<br/><CENTER><INPUT TYPE="SUBMIT" VALUE="Parse these lines!"></CENTER>
|
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</FORM>
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|
+
</DIV>
|
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|
+
|
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314
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<!-- Publications ---------------------------------------------------------------------- -->
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<A name="p"></a><H2>Publications</H2>
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<P><B>Journal Papers:</B>
|
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+
<UL>
|
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318
|
+
<LI> Minh-Thang Luong, Thuy Dung Nguyen and Min-Yen Kan (forthcoming)
|
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319
|
+
<U>Logical Structure Recovery in Scholarly Articles with Rich
|
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320
|
+
Document Features</U>. Forthcoming in the International
|
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321
|
+
Journal of Digital Library Systems. <BR/>
|
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|
+
[ <A HREF="ijdls-SectLabel.pdf">pre-print .pdf</A> ]
|
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|
+
</UL>
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|
+
|
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<P><B>International Referreed Conference Publications:</B>
|
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|
+
<UL>
|
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327
|
+
<LI> Isaac G. Councill, C. Lee Giles, Min-Yen Kan. (2008)
|
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|
+
<U>ParsCit: An open-source CRF reference string parsing
|
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|
+
package</U>. In Proceedings of the Language Resources and
|
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330
|
+
Evaluation Conference (LREC 08), Marrakesh, Morrocco, May.
|
|
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|
+
<BR/> [ <A HREF="lrec08/lrec08.pdf">.pdf</A> ]
|
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|
+
[ <A HREF="lrec08b.png">Poster (.png)</A> ]
|
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|
+
</UL>
|
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|
+
|
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335
|
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<P><B>Others:</B>
|
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|
+
<UL>
|
|
337
|
+
<LI> Yong Kiat Ng. (2004) <U>Citation Parsing Using Maximum Entropy
|
|
338
|
+
and Repairs</U>. Undergraduate thesis. National University of
|
|
339
|
+
Singapore. <BR/>
|
|
340
|
+
[ <A HREF="yongKiatNgThesis.pdf">.pdf</A> ]
|
|
341
|
+
</UL>
|
|
342
|
+
|
|
343
|
+
<!-- Output ---------------------------------------------------------------------- -->
|
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|
+
<A name="gsiso"></a><H2>Gold Standard Input and Sample Output</H2>
|
|
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|
+
|
|
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|
+
<UL>
|
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|
+
<LI>Chunk tagged data for <A HREF="cora.tagged.txt">Cora</A>, <A
|
|
348
|
+
HREF="citeseerx.tagged.txt">CiteSeer<SUP>X</SUP></A>, <A
|
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349
|
+
HREF="flux-cim-cs.tagged.txt">FLUX-CiM</A> and humanities (<A
|
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350
|
+
HREF="it-humanities.tagged.txt">Italian</A>, <A
|
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351
|
+
HREF="en-humanities.tagged.txt">English</A>, and <A
|
|
352
|
+
HREF="mixed-humanities.tagged.txt">mixed language</A>) datasets
|
|
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|
+
(suitable for ParsCit training). For FLUX-CiM data, please try
|
|
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|
+
the original hosting site maintained by Eli Cortez. Credits to
|
|
355
|
+
Matteo Romanello for contributing the humanities datasets.
|
|
356
|
+
<LI> <A HREF="iconip.tagged.txt">Chunk tagged data for some ICONIP
|
|
357
|
+
papers</A>. Contributed by Cheong Chi Hung.
|
|
358
|
+
<LI>Results of running the v080917 version of ParsCit on FLUX-CiM's
|
|
359
|
+
dataset for [ <A HREF="flux-cim-cs.out.xml">300 computer science
|
|
360
|
+
references</A> ] [ <A HREF="flux-cim-med.out.xml">2000 medical
|
|
361
|
+
references</A> ] [ <A HREF="cora.out.xml">on the CORA dataset</A>
|
|
362
|
+
]. Note that these results are considered cheating as current
|
|
363
|
+
version has been trained on this data.
|
|
364
|
+
<LI> Tagged section data for the SectLabel module. <BR/> [ <A
|
|
365
|
+
HREF="sectLabelXML.tagged.txt">XML Format</A> ] [ <A
|
|
366
|
+
HREF="sectLabel.tagged.txt">Plain Text Format</A> ]<BR/>
|
|
367
|
+
[ <A HREF="genericSect.tagged.txt">GenericSect training data</A> ]
|
|
368
|
+
</UL>
|
|
369
|
+
|
|
370
|
+
<!-- Group Members ---------------------------------------------------------------------- -->
|
|
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|
+
<A name="gm"></a><H2>Group Members</H2>
|
|
372
|
+
|
|
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|
+
<UL>
|
|
374
|
+
<LI> <A HREF="http://www.comp.nus.edu.sg/~kanmy">Min-Yen Kan</A> - Project leader, NUS
|
|
375
|
+
<LI> <A HREF="http://www.personal.psu.edu/igc2/">Isaac G. Councill</A>, The Pennsylvania State University
|
|
376
|
+
<LI> <A HREF="http://clgiles.ist.psu.edu/">C. Lee Giles</A>, The Pennsylvania State University
|
|
377
|
+
<LI> <A HREF="http://wing.comp.nus.edu.sg/~lmthang">Minh-Thang Luong</A> - Research Assistant (alumnus), NUS
|
|
378
|
+
<LI> Yong Kiat Ng - Final year undergraduate student (graduated, 2004), NUS
|
|
379
|
+
<LI> Thuy Dung Nguyen - Research Assistant (alumnus), NUS
|
|
380
|
+
<LI> Huy Nhat Hoang Do - Research Assistant, NUS
|
|
381
|
+
</UL>
|
|
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|
+
|
|
383
|
+
<!-- FAQ ---------------------------------------------------------------------- -->
|
|
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|
+
<A name="faq"></a><H2>FAQ</H2>
|
|
385
|
+
<DL>
|
|
386
|
+
<DT>What platforms does ParsCit work on?</DT>
|
|
387
|
+
<DD>ParsCit works on all major platforms: Windows, Linux and MacOS.
|
|
388
|
+
The installation requires ruby and perl and the CRF++ embedded
|
|
389
|
+
package also requires standard UNIX utilities like sed. You
|
|
390
|
+
should have a working knowledge of UNIX and some experience in
|
|
391
|
+
installing UNIX tools. Due to our time constraints, we may not be
|
|
392
|
+
able answer your particular problems with installation. Do let us
|
|
393
|
+
know if there was something important that you had to do to get
|
|
394
|
+
your particular download and installation working; we'll
|
|
395
|
+
incorporate it into the Troubleshooting section below.</DD>
|
|
396
|
+
<DT>What is the difference of SectLabel and previous ParsHed?</DT>
|
|
397
|
+
<DD>SectLabel is a newly-developed module that further extends
|
|
398
|
+
ParsHed in functionality. It not only classifies header metadata,
|
|
399
|
+
but analyzes full documents to output the logical structure of
|
|
400
|
+
the internals of the document -- sections, subsections, figures,
|
|
401
|
+
tables, equations, footnotes and captions. <BR/> For compatibility
|
|
402
|
+
issues, the ParsHed module is still retained in our source code
|
|
403
|
+
and command line options. </DD>
|
|
404
|
+
|
|
405
|
+
<DT>How do I retrain ParsCit for a different language? I saw code in
|
|
406
|
+
lib/ParsCit/PreProcess' to find the beginning of the bibliography
|
|
407
|
+
section, and changed that but it doesn't work.</DT>
|
|
408
|
+
<DD>The current version does not depend on those regular expressions
|
|
409
|
+
anymore, they are for previous versions (e.g., v101101). ParsCit
|
|
410
|
+
now first labels each line using the SectLabel module and
|
|
411
|
+
discovers which lines to parse references for based on the first
|
|
412
|
+
step's output. You need to retrain SectLabel for this, by
|
|
413
|
+
providing labeled data about what class of line each line in your
|
|
414
|
+
training data is. It's also possible to "downgrade" the current
|
|
415
|
+
version to go back to use the rule-based method for identifying
|
|
416
|
+
the reference section.</DD>
|
|
417
|
+
<DT>What is the "genericHeader" in the output of SectLabel? What is
|
|
418
|
+
the difference between "genericSect.tagged" and "SectLabel.tagged"?</DT>
|
|
419
|
+
<DD>Generic headers, such as introduction, methodology, and
|
|
420
|
+
evaluation, represent generic purposes of different sections in a
|
|
421
|
+
scholarly article. We map all section names to generic ones
|
|
422
|
+
(i.e., "5. Text Features" to "Methodology"). This promotes
|
|
423
|
+
comparative viewing of sections with identical purpose across
|
|
424
|
+
articles. For the second question, actually, Generic section is
|
|
425
|
+
a component of SectLabel. It is responsible for classifying the
|
|
426
|
+
section headers of a paper into the generic categories such as
|
|
427
|
+
Introduction, Methodology, Result, etc. For details refer to our
|
|
428
|
+
IJDLS journal paper.
|
|
429
|
+
</DD>
|
|
430
|
+
<DT>Why is there an option to input file in XML format? Which DTD
|
|
431
|
+
should it follow?</DT>
|
|
432
|
+
<DD>SectLabel is a robust logical document structure inference
|
|
433
|
+
system that can handle both rich input (produced by OCR software
|
|
434
|
+
such as font or spatial features) to boost recognition
|
|
435
|
+
performance, but still be able to perform inference on
|
|
436
|
+
impoverished input (plain text) with degraded
|
|
437
|
+
performance. Currently, the XML input must be in the form of
|
|
438
|
+
output from Nuance OmniPage (version 16)'s XML format, and hence,
|
|
439
|
+
should follows the DTD by OmniPage. Note: The ParsCit team is not
|
|
440
|
+
affiliated with Nuance in any way nor does it endorse
|
|
441
|
+
OmniPage.</DD>
|
|
442
|
+
<DT> I need to run ParsCit but I can't get well-formed text from my
|
|
443
|
+
PDF documents. Can you help?</DT>
|
|
444
|
+
<DD> No, we cannot help you with this. We don't perform OCR or text
|
|
445
|
+
extraction from PDF documents. You will have to find your own
|
|
446
|
+
source for doing the extraction or conversion. We've found
|
|
447
|
+
Omnipage useful in our own project work (hence the possibility of
|
|
448
|
+
XML input), but we don't endorse any product.</DD>
|
|
449
|
+
<DT> The OmniPage XML doesn't seem to be well-formed. Is that OK?</DT>
|
|
450
|
+
<DD> Yes. The sample "XML" provided in the links (for Demo 2) are
|
|
451
|
+
actual outputs for a sequence of XML pages (one XML file per
|
|
452
|
+
page). If you use OmniPage to save an XML file for input to
|
|
453
|
+
ParsCit, make sure to save individual pages as separate files,
|
|
454
|
+
then concatenate them to send to ParsCit. You may want to
|
|
455
|
+
download the sample links for inspection (as they are
|
|
456
|
+
concatenations of several XML files, your browser will likely
|
|
457
|
+
complain about them not being well-formed.</DD>
|
|
458
|
+
<DT> I ran Demos 1 and 2 with the default "all" settings, but sections
|
|
459
|
+
don't seem to be detected.</DT>
|
|
460
|
+
<DD> There's no problem. The demo just hides the SectLabel output
|
|
461
|
+
by default. Click "Show SectLabel output" to reveal it.</DD>
|
|
462
|
+
<DT> I ran ParsCit using the OmniPage XML output, but encountered malformed UTF8 character errors.</DT>
|
|
463
|
+
<DD> OmniPage normally outputs XML results in UTF-16 format, a conversion into UTF-8 will solve the problem, see below: </BR>
|
|
464
|
+
<I> iconv --from-code UTF-16 --to-code UTF-8 omnipageOutput.xml > newOmnipageOutput.xml</I>
|
|
465
|
+
</DD>
|
|
466
|
+
</DL>
|
|
467
|
+
|
|
468
|
+
<!-- Troubleshooting ---------------------------------------------------------------------- -->
|
|
469
|
+
<A name="t"></a><H2>Troubleshooting</H2>
|
|
470
|
+
|
|
471
|
+
<P> A list of common problems with ParsCit. If you find problems,
|
|
472
|
+
email the lead developer at <kanmy@comp.nus.edu.sg>. Please use
|
|
473
|
+
the subject "[ParsCit]" to ensure that it reaches our attention. If
|
|
474
|
+
you have hand-corrected tagged data that you don't mind providing us,
|
|
475
|
+
we can use that to further improve ParsCit's extracting capabilities.
|
|
476
|
+
Nevertheless, there are problems with the output occasionally. Below
|
|
477
|
+
are some common problems people have encountered.
|
|
478
|
+
|
|
479
|
+
<DL>
|
|
480
|
+
<DT>ParsCit v110505 seems to be a lot slower when used on Omnipage
|
|
481
|
+
output than the previous versions, why?</DT>
|
|
482
|
+
<DD>You are correct. We are now using XML::Twig to do the XML
|
|
483
|
+
processing correctly, rather than do it ad-hoc ourselves, but this
|
|
484
|
+
requires constructing an exhaustive DOM tree for the Omnipage input.
|
|
485
|
+
This is the timesink that you are experiencing.</DD>
|
|
486
|
+
<DT>I'm running ParsCit on Windows but I can't get it to work, even
|
|
487
|
+
after installing a perl interpreter. Specifically, the
|
|
488
|
+
citeExtract.pl program dies complaining that it Can't open
|
|
489
|
+
"/tmp/...." at line 175. </DT>
|
|
490
|
+
<DD>ParsCit hasn't been fully tested on windows at NUS, so we can't
|
|
491
|
+
vouch for whether it will run correctly. In this specific error
|
|
492
|
+
case, the "/tmp/" directory (a standard place for temporary files in
|
|
493
|
+
UNIX systems) is normally not available in Windows, and may generate
|
|
494
|
+
problems. You may need to change the code and/or create an
|
|
495
|
+
appropriate directory for ParsCit to generate such files.</DD>
|
|
496
|
+
<DT>I tried downloading and running ParsCit but I get complaints
|
|
497
|
+
about /bin/sed and crf not being found. Help?</DT>
|
|
498
|
+
<DD>Please read the INSTALL.txt directions. You need to recompile
|
|
499
|
+
CRF++ for your platform. The paths included with the install are
|
|
500
|
+
for our version, you need to recompile to have the paths point
|
|
501
|
+
correctly.</DD>
|
|
502
|
+
<DT>When running citeExtract.pl I get some errors complaining about
|
|
503
|
+
the wrong ELF class of the binaries. How can I fix this?</DT>
|
|
504
|
+
<DD>This seems to be a problem with the compiled executables of
|
|
505
|
+
CRF++ bundled with the software. Follow the INSTALL instructions
|
|
506
|
+
but after step 1 do:
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+
<P>
|
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+
<CODE>$ cp -Rf * ../../.libs
|
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509
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+
$ cp crf_learn ../../.libs/lt-crf_learn<BR/>
|
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510
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+
$ cp crf_test ../../.libs/lt-crf_test<BR/>
|
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511
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+
</CODE></DD>
|
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512
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+
<DT>I'm trying to install parscit v110505 using the instructions in the install file, and when I get to the point where you're supposed to recompile CRF, it exists with an error:<BR/>
|
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513
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+
|
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514
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+
<PRE>In file included from node.h:13:0,
|
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+
from node.cpp:9:
|
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516
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+
path.h:26:52: error: 'size_t' has not been declared
|
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517
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+
make[1]: *** [node.lo] Error 1
|
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518
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+
make[1]: Leaving directory `/home/agarnett/parscit/crfpp/CRF++-0.51'
|
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519
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+
make: *** [all] Error 2</PRE><BR/>
|
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520
|
+
The install file mentions that this may fail the first time; unfortunately for me, it keeps failing. any help?</DT>
|
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521
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+
<DD>The error is from CRF++ package (not from ParsCit), there are two ways to fix it:<BR/>
|
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522
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+
1. Add the line. <CODE>#include<iostream></CODE> in node.cpp and compile crf++ again, or;<BR/>
|
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523
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+
2. Go to <A HREF="http://crfpp.googlecode.com/svn/trunk/doc/index.html">http://crfpp.googlecode.com/svn/trunk/doc/index.html</A> and download the latest version. The instruction is the same. Hope this helps.</DD>
|
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524
|
+
<DT>Issue numbers don't get extracted.</DT>
|
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+
<DD><SPAN CLASS="red">This issue should be fixed as of the v110505
|
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526
|
+
release.</SPAN> There is now some heuristic postprocessing code to
|
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527
|
+
take care of breaking single or multiple tokens for issues and
|
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528
|
+
volumes. </DD>
|
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529
|
+
<DT>Separation of author names and publishing year fails</DT>
|
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530
|
+
<DD> In some reference data with non-standard sequences of
|
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531
|
+
first names and family names, e.g.
|
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532
|
+
<pre>
|
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533
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+
Baltes, Paul, Ursula Staudinger, Ulmann Lindenberger (1999): Lifespan
|
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534
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+
psychology: theory and application of intellectual functioning; in:
|
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535
|
+
Annual Review of Psychology, 50, 471-507
|
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536
|
+
</pre>
|
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537
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+
ParsCit's post processing step may not detect and deal with these
|
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538
|
+
problems reliably. We're working to fix these too. </DD>
|
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539
|
+
<DT>I passed ParsCit plain text output but in another, non-English
|
|
540
|
+
language. I didn't get good results or I got empty results. Can
|
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541
|
+
you help? </DT>
|
|
542
|
+
<DD>Aside from English, ParsCit can handle Italian and German to a
|
|
543
|
+
limited extent, thanks to the multilingual training data.
|
|
544
|
+
However, the demo web interface uploads non-ASCII (e.g., UTF-8 or
|
|
545
|
+
UTF-16 data) as binary data and fails to execute ParsCit.
|
|
546
|
+
However, if you download a copy of ParsCit, the libraries do work
|
|
547
|
+
on such data. Here's a <A
|
|
548
|
+
HREF="humanities.test.out.xml">sample</A>. We'd love to help make
|
|
549
|
+
a more universal model that can accommodate reference strings in
|
|
550
|
+
other languages. If you're willing to help contribute ground
|
|
551
|
+
truth data, we love to hear from you!</DD>
|
|
552
|
+
|
|
553
|
+
<DT>How about retraining ParsCit for another language/domain?</DT>
|
|
554
|
+
<DD>You can put your supervised exemplar data into the same format
|
|
555
|
+
as tagged_references.txt found in crfpp/traindata/. Once you have
|
|
556
|
+
this file you can generate the appropriate model for ParsCit, by
|
|
557
|
+
using three commands (assumes you are in the crfpp/traindata
|
|
558
|
+
directory):
|
|
559
|
+
<P>
|
|
560
|
+
<CODE>$ ../../bin/tr2crfpp.pl tagged_references.txt > parsCit.train.data
|
|
561
|
+
<BR/>
|
|
562
|
+
$ ../crf_learn parsCit.template parsCit.train.data model
|
|
563
|
+
<BR/>
|
|
564
|
+
$ mv model ../../resources/parsCit.model
|
|
565
|
+
</CODE>
|
|
566
|
+
<P>The first command creates the input feature file that crfpp uses
|
|
567
|
+
from the training data. The second creates the model using the
|
|
568
|
+
crf_learn command. You can then move the model file to the
|
|
569
|
+
resources/ subdirectory where it can be utilized. To replace the
|
|
570
|
+
default model that comes with ParsCit, just execute the final
|
|
571
|
+
command. </DD>
|
|
572
|
+
<DT> Can I retrain the package for a different set of tags if I
|
|
573
|
+
change the tagset in the training data?</DT>
|
|
574
|
+
<DD> Yes, you should be able to change the tagset to suit your
|
|
575
|
+
dataset. You can add, eliminate and change the tagset as you
|
|
576
|
+
wish. You need to retrain the parser system after creating your
|
|
577
|
+
tag data. For more details on the training process, see the
|
|
578
|
+
documentation for CRF++, that is on the web at sourceforge.
|
|
579
|
+
</DD>
|
|
580
|
+
<DT>When retraining I get a "bad_alloc" error. What gives?</DT>
|
|
581
|
+
<DD>We're not entirely sure of this. CRF training is quite memory
|
|
582
|
+
intensive and running a large amount of training data tuples may
|
|
583
|
+
cause the embedded CRF++ package to fail. You can try with less
|
|
584
|
+
training data, or try training on a machine with a larger amount
|
|
585
|
+
of RAM. </DD>
|
|
586
|
+
<DT>Does the web service actually work? I can't seem to run it.</DT>
|
|
587
|
+
<DD>Occasionally our school's networking staff changes the firewall
|
|
588
|
+
settings, so the port for our group's web services may be blocked
|
|
589
|
+
(port 4000 on host wing.comp.nus.edu.sg). If you find you can't
|
|
590
|
+
reach our services (they time out), please let us know. </DD>
|
|
591
|
+
<DT>I get funny errors with crf_test not being useful. How do I
|
|
592
|
+
fix this?</DT> <DD>The updated README.txt file in the 090625b
|
|
593
|
+
distribution fixes this. Basically you need to recompile CRF++
|
|
594
|
+
0.51 and place the libraries and the executables in the proper
|
|
595
|
+
place. See the README for details.</DD>
|
|
596
|
+
|
|
597
|
+
</DL>
|
|
598
|
+
|
|
599
|
+
<!-- Kudos ---------------------------------------------------------------------- -->
|
|
600
|
+
<H2>Kudos</H2>
|
|
601
|
+
|
|
602
|
+
<p>ParsCit owes its continued maintenance and support from its user
|
|
603
|
+
base. Here we'd like to thank them for their help.</p>
|
|
604
|
+
|
|
605
|
+
<P>Thanks to David Judd who reconfigured how CRF++ is located with
|
|
606
|
+
respect to the main code. Thanks to Alex Garnett in spotting more
|
|
607
|
+
problems with CRF dependencies. Thanks to George E. Raptis and Eric
|
|
608
|
+
Tran for the port to Windows. Thanks to Zhu Ying-Bo
|
|
609
|
+
(yumichika@163.com) from the Language Computing and Web Mining Group,
|
|
610
|
+
Institute of Computer Science and Technology of Peking University for
|
|
611
|
+
the partial port to Windows. Thanks to Yustus Oktian for questions
|
|
612
|
+
about training for another language. Thanks to Madhur Kapoor for
|
|
613
|
+
asking questions about PDF conversion. Thanks to Behrang Qasemizadeh
|
|
614
|
+
for reporting problems with truncation of XML entities in XML output
|
|
615
|
+
(v110505). Thanks Tim Brody for his BiblioScript patch. Thanks to
|
|
616
|
+
David Jurgens for suggesting that remove temporary files after runs
|
|
617
|
+
(v110505). Thanks Nikolay Nikolov for suggesting the conversion of
|
|
618
|
+
OmniPage XML results from UTF-16 to UTF-8 to avoid encoding
|
|
619
|
+
problems. Thanks to Matteo Romanello for the suggestion and permission
|
|
620
|
+
to incorporate BiblioScript software (v101101). Many thanks to Kris
|
|
621
|
+
Jack for pointing out problems with the ELF binaries and an
|
|
622
|
+
appropriate fix. Thanks to Cheong Chi Hong for fixing problems with
|
|
623
|
+
Preprocess.pm (v100401) and contributing the ICONIP training data and
|
|
624
|
+
XML entity problems in reference string parsing (v100401). Thanks to
|
|
625
|
+
Priya Venkateshan for pointing out sudo/root installation
|
|
626
|
+
possibilities (v100401). Thanks to Mario Lipinski for reporting
|
|
627
|
+
punctuation stripping problems in reference string parsing (v100401).
|
|
628
|
+
Thanks to Artemy Kolchinsky for fixes in Preprocess.pm
|
|
629
|
+
(v090625). Thanks to Matteo Romanello for the humanities training
|
|
630
|
+
datasets. Thanks to Dain Kaplan for helping us fix the Preprocess.pm
|
|
631
|
+
bug. Thanks to Ayeh Bandeh-Ahmadi for correcting the warning in
|
|
632
|
+
parseRefString.pl. Thanks to Nick Friedrich and Jöran Beel of
|
|
633
|
+
scienstein.org for all fixes in the v081201 version of ParsCit. Also
|
|
634
|
+
thanks to Madian Khabsa for indicating problems with installation to
|
|
635
|
+
MacOS.</p>
|
|
636
|
+
|
|
637
|
+
<P>ParsCit is used by many projects worldwide, and not just in
|
|
638
|
+
experimental, research and academic places, but in commercial
|
|
639
|
+
snterprises as well. <A HREF="http://www.mendeley.com/">Mendeley</A>
|
|
640
|
+
is using ParsCit to parse references from contributed papers, as is
|
|
641
|
+
the <A HREF="http://citec.repec.org/">Citations in Economics
|
|
642
|
+
(CitEc)</A> project.
|
|
643
|
+
|
|
644
|
+
|
|
645
|
+
<!-- Related Links ---------------------------------------------------------------------- -->
|
|
646
|
+
<H2>Related Links</H2>
|
|
647
|
+
|
|
648
|
+
<P>Other, open-source citation parsers:
|
|
649
|
+
|
|
650
|
+
<UL>
|
|
651
|
+
<LI> <A
|
|
652
|
+
HREF="http://freecite.library.brown.edu/welcome">FreeCite</A>:
|
|
653
|
+
supported by the Mellon Foundation and Brown University. Written in
|
|
654
|
+
Ruby on Rails, with the same CRF++ backend.
|
|
655
|
+
<LI> An <A
|
|
656
|
+
HREF="http://purl.net/net/egh/hmm-citation-extractor/">Hidden Markov
|
|
657
|
+
Model Citation Extractor</A>: written by Erik Hetzner of the
|
|
658
|
+
California Digital Library.
|
|
659
|
+
</UL>
|
|
660
|
+
|
|
661
|
+
<P> Other related links. Contact Min below to get your other related
|
|
662
|
+
software listed here. Thanks!
|
|
663
|
+
|
|
664
|
+
<UL>
|
|
665
|
+
<LI> Perhaps you're interested in open source code for libraries?
|
|
666
|
+
If so try the <A
|
|
667
|
+
HREF="http://dewey.library.nd.edu/mailing-lists/code4lib/">CODE4LIB
|
|
668
|
+
mailing list</A>.
|
|
669
|
+
|
|
670
|
+
<LI> <A
|
|
671
|
+
HREF="https://wiki.birncommunity.org:8443/display/NEWBIRNCC/LATISI+-+Literature+Annotation+Tool+from+the+Information+Sciences+Institute">LATISI
|
|
672
|
+
- Literature Annotation Tool from the Information Sciences
|
|
673
|
+
Institute</A>. A related project from ISI, using MBL instead of CRF.
|
|
674
|
+
<LI> <A HREF="http://www.scienstein.org">Scienstein.org</A>: A
|
|
675
|
+
recommendation system for papers.
|
|
676
|
+
<LI> PdfBox: An open-source package for extracting text information
|
|
677
|
+
from PDF files. Does not deal with problems with custom font
|
|
678
|
+
encodings.
|
|
679
|
+
</UL>
|
|
680
|
+
|
|
681
|
+
<HR>
|
|
682
|
+
<H5><ADDRESS><A HREF="http://www.comp.nus.edu.sg/~kanmy">Min-Yen Kan</A> <<A HREF="mailto:kanmy@comp.nus.edu.sg">kanmy@comp.nus.edu.sg</A>></ADDRESS>
|
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|
+
Created on: Fri Dec 24 01:48:05 SGT 2004
|
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|
+
<!-- hhmts start -->
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| Version: 1.0
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+
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| Last modified:
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+
Mon Mar 4 14:23:46 SGT 2013
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+
<!-- hhmts end -->
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|
+
</H5>
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</div>
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</BODY> </HTML>
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