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<h3>Web APIs</h3>
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<h4>How to use</h4>
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<p>
<a href="/research/bionlp/APIs/authors/">API for the PubMed Computed Authors</a><br/>
<a href="https://www.ncbi.nlm.nih.gov/research/pubtator3/api" target="_blank">PubTator APIs usage</a><br/>
<a href="https://www.ncbi.nlm.nih.gov/research/pubtator3/api" target="_blank">PubTator APIs with curl</a><br/>
<a href="/research/bionlp/APIs/BioC-PMC/">API for PubMed Central Open Access in BioC
format</a><br/>
<a href="/research/bionlp/APIs/BioC-PubMed/">API for PubMed in BioC format</a><br/>
<a href="/research/bionlp/APIs/SupplMat/">API for PMC Supplementary Materials in BioC format</a><br/>
<a href="/research/bionlp/APIs/format/">Format description</a>
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<h4>Publication</h4>
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<p>
Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu (2016). <a
href="http://bioinformatics.oxfordjournals.org/content/early/2016/02/29/bioinformatics.btv760"
target="_blank">Beyond accuracy: Creating interoperable and s
calable text mining web services</a>, Bioinformatics, DOI:10.1093/bioinformatics/btv760.
</p>
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<h4>Introduction</h4>
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<p>
We report here our recently developed web-based text mining services for biomedical concept
recognition and normalization. The below Figure describes the overall architecture of our web
services, which use sta
ndard HTTP method calls (often known as RESTful services) and allow two access modes: A) a
batch-oriented processing function for any arbitrary text input (abstract, full text, patent,
etc),
submitted via HTTP POST an
d B) instant retrieval of pre-tagged results of PubMed abstracts via HTTP GET. For the batch
processing function, users may submit one or multiple documents per batch, and large requests
will
be sent to a computer clu
ster for parallel processing. When retrieving pre-tagged results of PubMed abstracts, the
request
only requires the PMIDs of the requested abstracts. This option is provided because annotating
biomedical literature is
the most common use case for such a text-mining service. From a technical stand-point, the
preprocessing is made possible by our previous system PubTator, which stores text-mined
annotations
for every article in PubM
ed and keeps in sync with PubMed via nightly updates.
</p>
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<a href="#" data-featherlight="/research/bionlp/static/main/images/tools/RESTfulAPI.png"><img
src="/research/bionlp/static/main/images/tools/RESTfulAPI.png"
alt="Overview of the NCBI text mining web services"/></a>
<span><b>Figure 1.</b> Overview of the NCBI text mining web services.</span>
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<h4>Performance</h4>
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<tr>
<td><strong>Taggers</strong></td>
<td align="center"><strong>Bioconcepts</strong></td>
<td align="center"><strong>Evaluation corpus</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><a href="/bionlp/Tools/gnormplus" target="_blank">GNormPlus (Wei et al., 2015)</a></td>
<td align="center">Gene</td>
<td align="center"><a
href="http://www.biocreative.org/tasks/biocreative-ii/task-1b-human-gene-normalizati/"
target="_blank">BioCreative II - GN
</a></td>
<td align="center">87.08%</td>
<td align="center">86.41%</td>
<td align="center">86.74%</td>
</tr>
<tr>
<td><a href="/bionlp/Tools/tmchem" target="_blank">tmChem (Leaman et al., 2014)</a></td>
<td align="center">Chemical</td>
<td align="center"><a
href="http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/"
target="_blank">CHEMDNER</a></td>
<td align="center">89.09%</td>
<td align="center">85.75%</td>
<td align="center">87.39%</td>
</tr>
<tr>
<td><a href="/bionlp/Tools/dnorm" target="_blank">DNorm (Leaman et al., 2013)</a></td>
<td align="center">Disease</td>
<td align="center"><a href="/CBBresearch/Dogan/DISEASE/"
target="_blank">NCBI Disease corpus</a></td>
<td align="center">80.30%</td>
<td align="center">76.30%</td>
<td align="center">78.20%</td>
</tr>
<tr>
<td><a href="/bionlp/Tools/tmvar" target="_blank">tmVar (Wei et al., 2013)</a></td>
<td align="center">Mutation</td>
<td align="center"><a
href="http://sourceforge.net/projects/mutationfinder/files/latest/download"
target="_blank">MutationFinder</a></td>
<td align="center">98.80%</td>
<td align="center">89.62%</td>
<td align="center">93.98%</td>
</tr>
<tr>
<td><a href="/bionlp/Tools/sr4gn" target="_blank">SR4GN (Wei et al., 2012)</a></td>
<td align="center">Species</td>
<td align="center"><a
href="http://sourceforge.net/projects/linnaeus/files/Corpora/manual-corpus-species-1.0.tar.gz/download"
target="_blank">Linnaeus corpus</a></td>
<td align="center">85.82%</td>
<td align="center">85.28%</td>
<td align="center">85.55%</td>
</tr>
</tbody>
</table>
<span><b>Table 1.</b> Results of our individual taggers when benchmarked on public test collections.</span>
<table class="customtable">
<tbody>
<tr>
<td><strong>Taggers</strong></td>
<td align="center">HTTP Submission Method</td>
<td align="center">Description</td>
<td align="center">Throughput<br>(seconds per article; averaged over 5000 articles)</td>
</tr>
<tr>
<td>PubTator</td>
<td align="center">GET</td>
<td align="center"><p class="style4" nowrap="">Return Pre-Annotations</td>
<td align="center">0.044s</td>
</tr>
<tr>
<td nowrap="">GNormPlus<sup>*</sup></td>
<td align="center">POST</td>
<td align="center" rowspan="4">On-Demand Processing</td>
<td align="center">0.127s</td>
</tr>
<tr>
<td>tmChem</td>
<td align="center">POST</td>
<td align="center">0.008s</td>
</tr>
<tr>
<td>DNorm</td>
<td align="center">POST</td>
<td align="center">0.007s</td>
</tr>
<tr>
<td>tmVar</td>
<td align="center">POST</td>
<td align="center">0.090s</td>
</tr>
</tbody>
</table>
<span><b>Table 2.</b> Estimated processing time of our web services on NCBI clusters (subject to availability).<br/>
* SR4GN is used by GNormPlus. The results of GNormPlus include both gene and species.
</span>
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<h4>Supplementary</h4>
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<p>
We provide below several sample codes to show how to use our RESTful API service via
programs.<br/>
<a href="/CBBresearch/Lu/Demo/tmTools/download/RESTfulAPI.client.zip"
target="_blank">RESTful sample codes avaliable in Perl, Python and Java.</a><br/>
We also provide a <a
href="/CBBresearch/Lu/Demo/tmTools/download/FormatChecking.zip"
target="_blank">script for input formats (i.e., BioC, PubTator and JSON) checking.</a>
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