publicdata/nih-gov
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions
nih-gov/www.ncbi.nlm.nih.gov/bionlp/Tools/tmchem

353 lines
No EOL
15 KiB
Text
Raw Blame History

<!DOCTYPE html>
<html lang="en" >
<head >
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<!-- Mobile properties -->
<meta name="HandheldFriendly" content="True">
<meta name="MobileOptimized" content="320">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Stylesheets -->
<link href="/research/bionlp/static/django_uswds/uswds/css/uswds.css" rel="stylesheet" />
<title>
tmChem: a high performance approach for chemical named entity recognition and normalization
</title>
<link rel="stylesheet" href="/research/bionlp/static/main/css/uswds.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/header.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/footer.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/form.css">
<!-- Labs template -->
<link rel="stylesheet" href="/research/bionlp/static/main/css/atoms.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/docsum.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/media.css">
<!-- Additional template -->
<link rel="stylesheet" href="/research/bionlp/static/main/css/journals.molecules.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/custom.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/journals.journal-page.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/iconic-glyphs.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/featherlight.min.css">
<link rel="stylesheet" href="/research/bionlp/static/main/css/styles.css">
<!--[if lt IE 9]>
<link rel="stylesheet" href="/research/bionlp/static/main/css/iconic-glyphs-legacy.css">
<![endif]-->
<!-- Some JS -->
<script src="/research/bionlp/static/main/js/jquery.js"></script>
<script src="/research/bionlp/static/main/js/modernizr.js"></script>
<script src="/research/bionlp/static/main/js/featherlight.min.js"></script>
<script src="/research/bionlp/static/main/js/custom.js"></script>
</head>
<body >
<div>
<a class="skipnav" href="#maincontent">
Skip to main page content
</a>
<header class="ncbi-page-header" role="banner">
<div class="prefix">
<span class="nih" title="National Institutes of Health">
<a href="https://www.nih.gov/" title="To NIH homepage">
<img src="/research/bionlp/static/base/images/nih-logo-header.svg" alt="NIH">
</a>
</span>
<span class="nlm">
<a href="https://www.nlm.nih.gov/" title="To NLM homepage">U.S. National Library of Medicine</a>
</span>
</div>
<div class="ncbi">
<!-- <abbr class="abbr">
<a href="https://www.ncbi.nlm.nih.gov/" title="To NCBI homepage">NCBI</a>
</abbr>
<span class="name">
<a href="https://www.ncbi.nlm.nih.gov/" accesskey="1" title="To NCBI homepage">National Center for Biotechnology Information</a>
</span> -->
<!-- <abbr class="abbr">
<a href="https://www.nlm.nih.gov/research/index.html" title="To DIR homepage">DIR</a>
</abbr> -->
<span class="name">
<a href="https://www.nlm.nih.gov/research/index.html" accesskey="1" title="To DIR homepage">Division of Intramural Research</a>
</span>
<div class="right">
<a id="in" href="/research/bionlp/accounts/login/?next=/research/bionlp/">Log in</a>
</div>
</div>
</header>
<!--app-specific header, something that might want to take full width of screen -->
<a class="skipnav" href="#maincontent">
Skip to main page content
</a>
<div class="breadcrumbs-container menu">
<div class="usa-grid-full">
<ul class="topnav" accesskey="4">
<li class="current">
<a href="/research/bionlp/" title="Home">
Home
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Zhiyong-Lu" title="Zhiyong Lu">
Zhiyong Lu
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/News" title="Media">
Media
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Team" title="Team">
Team
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Research" title="Research">
Research
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Publications/" title="Publications">
Publications
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Tools/" title="Tools">
Tools
</a>
</li>
<li>
<a href="/research/bionlp/APIs/" title="Tools">
Web APIs
</a>
</li>
<li class="separator"></li>
<li>
<a href="/research/bionlp/Data/" title="Data">
AI Datasets
</a>
</li>
<li>
<a href="/research/bionlp/Visiting-us" title="Visiting us">
Visiting us
</a>
</li>
<li class="icon">
<a href="#">&#9776;</a>
</li>
</ul>
</div>
</div>
<!-- asign css class in case app will need to alter styles of this div -->
<div id="maincontent" class="usa-grid-full ncbi-base-page-container">
<div class="labs-pagecontent">
<div class="usa-width-one-whole">
<main class="usa-grid journals-lists">
<h3>tmChem: a high performance approach for chemical named entity recognition and normalization</h3>
<main class="usa-width-one-whole journal-container">
<div>
<div class="issue labs-docsums labs-content-box wrappall">
<h4>Authors: <a href="https://scholar.google.com/citations?user=FLnUx4cAAAAJ" target="_blank">Robert
Leaman</a>, <a href="https://sites.google.com/site/chihhsuanwei/" target="_blank">Chih-Hsuan Wei</a> and
<a href="/bionlp/" target="_blank">Zhiyong Lu</a> (PI)</h4>
<h4>Research highlights</h4>
<div class="usa-width-one-whole">
<p>
tmChem is an open-source software tool for identifying chemical names in biomedical literature,
including chemical identifiers, drug brand and trade names and also systematic formats. tmChem uses
conditional random fields with a rich feature set and rule-based post processing modules for
resolving local abbreviations and improving consistency. tmChem achieved the highest performance of
any submission to the BioCreative IV CHEMDNER task (over 87% F-measure).
</p>
</div>
</div>
<div class="issue labs-docsums labs-content-box wrappall">
<h4>Method overview</h4>
<div class="usa-width-one-whole">
<p>
The tmChem system combines two linear chain conditional random fields (CRF) models employing
different tokenizations and feature sets. Model 1 is an adaptation of the BANNER named entity
recognizer. It uses the MALLET toolkit and is implemented in Java. Model 2 is repurposed from part
of the tmVar system for locating genetic variants. It uses the CRF++ toolkit and is implemented in
Perl and C++. Both models employ multiple post processing steps.
</p>
</div>
</div>
<div class="issue labs-docsums labs-content-box wrappall">
<h4>Results</h4>
<div class="usa-width-one-whole">
<p>
tmChem was evaluated on the CHEMDNER test set, using the CEM task (named entity recognition) and
several strategies to combine the output of the two models.
</p>
<table class="customtable">
<tbody>
<tr>
<td align="center"><strong>Method</strong></td>
<td align="center"><strong>Precision</strong></td>
<td align="center"><strong>Recall</strong></td>
<td align="center"><strong>F-measure</strong></td>
</tr>
<tr>
<td align="center">Model 1</td>
<td align="center">0.8595</td>
<td align="center">0.8721</td>
<td align="center">0.8657</td>
</tr>
<tr>
<td align="center">Model 2</td>
<td align="center" class="best">0.8909</td>
<td align="center">0.8575</td>
<td align="center" class="best">0.8739</td>
</tr>
<tr>
<td align="center" nowrap="">Naive combination</td>
<td align="center">0.8192</td>
<td align="center">0.9209</td>
<td align="center">0.8671</td>
</tr>
<tr>
<td align="center" nowrap="">Heuristic combination</td>
<td align="center">0.8516</td>
<td align="center">0.8906</td>
<td align="center">0.8706</td>
</tr>
<tr>
<td align="center" nowrap="">High recall combination</td>
<td align="center">0.7672</td>
<td align="center" class="best">0.9212</td>
<td align="center">0.8372</td>
</tr>
</tbody>
</table>
<span><b>Table 1.</b> Evaluation of tmChem on the CHEMDNER test set using micro-averaged precsion, recall and F-measure.</span>
</div>
</div>
<div class="issue labs-docsums labs-content-box wrappall">
<h4>Downloads</h4>
<div class="usa-width-one-whole">
<p>
<a href="/CBBresearch/Lu/Demo/tmTools/download/tmChem/tmChemM1-0.0.2.tgz"
target="_blank">Model 1 Source Code (Java)</a><br/>
<a href="/CBBresearch/Lu/Demo/tmTools/download/tmChem/tmChem.M2.ver02.zip"
target="_blank">Model 2 Source Code (Perl/C++)</a><br/>
tmChem-tagged PubMed results in <a href="/CBBresearch/Lu/Demo/PubTator/"
target="_blank">PubTator</a><br/>
<a href="/research/bionlp/APIs/">tmChem
RESTful API</a>
</p>
</div>
</div>
<div class="issue labs-docsums labs-content-box wrappall">
<h4>Please cite</h4>
<div class="usa-width-one-whole">
<ul class="dot-list">
<li>Leaman R, Wei C-H, Lu Z. <a href="http://www.jcheminf.com/content/7/S1/S3/" target="_blank">tmChem:
a high performance tool for chemical named entity recognition and normalization</a>. Journal of
Cheminformatics, 7(Suppl 1):S3 (2015)
</li>
</ul>
</div>
</div>
</div>
</main>
</main>
</div>
</div>
</div>
<footer class="usa-footer usa-footer-big ncbi-footer" role="contentinfo">
<div class="usa-grid">
<div class="usa-row">
<div class="usa-width-one-half">
<div>
<div class="org-section">
<a href="https://www.hhs.gov/"><img class="usa-footer-logo-img hhs-logo"
src="/research/bionlp/static/base/images/dhhs-logo-white.svg"
alt="U.S. Department of Health & Human Services">
<span class="usa-sr-only">Department of Health and Human Services</span></a>
<a href="https://www.nih.gov/"><img class="usa-footer-logo-img nih-logo"
src="/research/bionlp/static/base/images/nih-logo-white.svg"
alt="National Institutes of Health">
<span class="usa-sr-only">National Institutes of Health</span></a>
<a href="https://www.nlm.nih.gov/"><img class="usa-footer-logo-img nlm-logo"
src="/research/bionlp/static/base/images/nlm-logo-letters-white.svg"
alt="National Library of Medicine">
<span class="usa-sr-only">National Library of Medicine</span></a>
<a href="https://www.usa.gov/"><img class="usa-footer-logo-img usagov-logo"
src="/research/bionlp/static/base/images/usagov-logo-white.svg"
alt="USA.gov"/>
<span class="usa-sr-only">USA.gov</span></a>
</div>
</div>
</div>
<div class="usa-width-one-half">
<div>
<p class="about-links">
<a href="https://www.nlm.nih.gov/research/index.html">About DIR</a>
<a href="https://www.nlm.nih.gov/web_policies.html">Web Policies</a></p>
</div>
</div>
</div>
</div>
</footer>
</div>
<!-- JavaScript -->
<script src="/research/bionlp/static/django_uswds/uswds/js/uswds.js"></script>
<script type="text/javascript" src="/research/bionlp/static/base/header.js"></script>
</body>
</html>
Reference in a new issue View git blame Copy permalink