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<h3>BioC API for PubMed</h3>
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<h4>Accessing PubMed in BioC format (click <a href="/research/bionlp/APIs/BioC-PMC/">here</a> for accessing PMC articles)</h4>
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All the PubMed articles are available in the <a href="http://bioc.sourceforge.net" target="_blank">BioC</a> format. This provides a large number of research articles for text mining and information retrieval research. BioC is a simple format designed for straightforward text processing.
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These articles are available in BioC XML or BioC JSON, in Unicode or ASCII.
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<p>
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If you use this resource, please cite:
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<ul class="dot-list">
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<li>Comeau DC, Wei CH, Dogan RI, and Lu Z. PMC text mining subset in BioC: about 3 million full text articles and growing, <i>Bioinformatics</i>, 2019</li>
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</ul>
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<h4>Instructions</h4>
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<pre><code>https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_[format]/[PMID]/[encoding]</code></pre>
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The parameters are:
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<ul class="dot-list">
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<li><b>format</b>: xml or json</li>
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<li><b>PMID</b></li>
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<li><b>encoding</b>: unicode or ascii</li>
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</ul>
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Sample URL:<br/>
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<a href="https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/unicode" target="_blank">
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https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/unicode
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</a>
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</p>
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<p>
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Same article in ASCII:<br/>
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<a href="https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/ascii" target="_blank">
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https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_xml/17299597/ascii
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</a><br/>
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Obviously, no Unicode to ASCII translation is perfect. We have found this one useful.
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</p>
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<p>
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JSON instead of XML:<br/>
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<a href="https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_json/17299597/unicode" target="_blank">
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https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pubmed.cgi/BioC_json/17299597/unicode
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</a><br/>
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BioC JSON follows the same structure as BioC XML.
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<h4>More information</h4>
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General information about BioC XML structure:<br/>
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<a href="ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/BioC.dtd" target="_blank">
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ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/BioC.dtd
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</a>
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</p>
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<p>
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Specific information about BioC PubMed:<br/>
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<a href="ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/pubmed.key" target="_blank">
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ftp://ftp.ncbi.nlm.nih.gov/pub/wilbur/BioC-PMC/pubmed.key
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</a>
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<p>
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Main BioC web page:<br/>
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<a href="http://bioc.sourceforge.net" target="_blank">
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http://bioc.sourceforge.net
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</a>
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<h4>Caution</h4>
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If you experience any problems, please share them with us: <a href="mailto:donald.comeau@nih.gov">donald.comeau@nih.gov</a> or <a href="mailto:zhiyong.lu@nih.gov">zhiyong.lu@nih.gov</a>.
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