biblicit 2.0.5 → 2.0.6
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- 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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vis.display = (vis.display==''||vis.display=='block')?'none':'block';
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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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<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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<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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306
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+
<INPUT TYPE=CHECKBOX NAME="ris3">RIS
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307
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<INPUT TYPE=CHECKBOX NAME="wordbib3">WordBib
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|
+
</P>
|
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309
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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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313
|
+
|
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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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324
|
+
|
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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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328
|
+
<U>ParsCit: An open-source CRF reference string parsing
|
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329
|
+
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
|
+
<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
|
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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>
|
|
382
|
+
|
|
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:
|
|
507
|
+
<P>
|
|
508
|
+
<CODE>$ cp -Rf * ../../.libs
|
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+
$ cp crf_learn ../../.libs/lt-crf_learn<BR/>
|
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$ cp crf_test ../../.libs/lt-crf_test<BR/>
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</CODE></DD>
|
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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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<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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+
make[1]: *** [node.lo] Error 1
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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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+
The install file mentions that this may fail the first time; unfortunately for me, it keeps failing. any help?</DT>
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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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+
1. Add the line. <CODE>#include<iostream></CODE> in node.cpp and compile crf++ again, or;<BR/>
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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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+
<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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+
release.</SPAN> There is now some heuristic postprocessing code to
|
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+
take care of breaking single or multiple tokens for issues and
|
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528
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+
volumes. </DD>
|
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529
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+
<DT>Separation of author names and publishing year fails</DT>
|
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530
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+
<DD> In some reference data with non-standard sequences of
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+
first names and family names, e.g.
|
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532
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+
<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
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+
Annual Review of Psychology, 50, 471-507
|
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536
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+
</pre>
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+
ParsCit's post processing step may not detect and deal with these
|
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538
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+
problems reliably. We're working to fix these too. </DD>
|
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539
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+
<DT>I passed ParsCit plain text output but in another, non-English
|
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540
|
+
language. I didn't get good results or I got empty results. Can
|
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541
|
+
you help? </DT>
|
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542
|
+
<DD>Aside from English, ParsCit can handle Italian and German to a
|
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543
|
+
limited extent, thanks to the multilingual training data.
|
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544
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+
However, the demo web interface uploads non-ASCII (e.g., UTF-8 or
|
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545
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+
UTF-16 data) as binary data and fails to execute ParsCit.
|
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546
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+
However, if you download a copy of ParsCit, the libraries do work
|
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547
|
+
on such data. Here's a <A
|
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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>
|
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552
|
+
|
|
553
|
+
<DT>How about retraining ParsCit for another language/domain?</DT>
|
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554
|
+
<DD>You can put your supervised exemplar data into the same format
|
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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>
|
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560
|
+
<CODE>$ ../../bin/tr2crfpp.pl tagged_references.txt > parsCit.train.data
|
|
561
|
+
<BR/>
|
|
562
|
+
$ ../crf_learn parsCit.template parsCit.train.data model
|
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|
+
<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.
|
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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>
|
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|
+
|
|
599
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+
<!-- 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>
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|
+
|
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|
+
<HR>
|
|
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|
+
<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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|
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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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| 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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