<div dir="ltr"><div id="gmail-:qky" class="gmail-Ar gmail-Au gmail-Ao" style="display:block"><div id="gmail-:qku" class="gmail-Am gmail-Al editable gmail-LW-avf gmail-tS-tW gmail-tS-tY" aria-label="Cuerpo del mensaje" role="textbox" aria-multiline="true" style="direction:ltr;min-height:376px" tabindex="1"><div class="gmail-adn gmail-ads"><div class="gmail-gs"><div class="gmail-"><div id="gmail-:lt3" class="gmail-ii gmail-gt"><div id="gmail-:lc9" class="gmail-a3s gmail-aiL"><div dir="ltr"><p class="MsoNormal" style="margin:10pt 0cm;text-align:center" align="center"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">DrugProt Shared Task (BioCreative VII track 1- 2021) </span></b><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US"> <span> </span></span><b><span lang="EN-US">Text mining drug-protein/gene interactions (DrugProt) & Large-scale Text Mining <span style="color:black">track</span><br></span></b></span></font></p>
<p class="MsoNormal" style="text-align:center;margin:0cm" align="center"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><a href="https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/" style="color:blue;text-decoration:underline" target="_blank">https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/</a><span></span></span></span></font></p>
<p class="MsoNormal" style="text-align:center;margin:0cm" align="center"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span> </span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span> </span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:rgb(14,16,26)"><span>BioCreative</span>
efforts have
provided highly relevant resources for advancing biomedical text mining
research, including datasets and system evaluations</span><span style="color:rgb(14,16,26)"> <span lang="EN-US">(e.g. BioBERT
benchmark datasets, ChemProt corpus, CHEMDNER corpus, etc.). </span></span><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:12pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US">We
are organizing the DrugProt track focusing on the (1) automatic
extraction of relations between drugs/chemicals and genes/proteins of
interest for drug discovery and biomedicine and (2) <font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US">large-scale text mining</span></span></font>.<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">It is getting increasingly challenging to efficiently exploit drug-related
information described in the growing amount of scientific literature. There are
a range of different types of drug-gene/protein interactions, and their systematic
extraction and characterization is essential to analyze, predict and explore key
biomedical properties underlying high impact biomedical applications.<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:12pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US">We
foresee that the DrugProt track will promote the development NLP techniques to
extract critical health information, generating results useful for:</span><span lang="EN-US"><span></span></span></span></font></p>
<p style="margin:12pt 0cm 12pt 36pt;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US"><span>-<span style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal">
</span></span></span><span lang="EN-US">Drug discovery, drug repurposing
& drug design<span></span></span></span></font></p>
<p style="margin:12pt 0cm 12pt 36pt;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US"><span>-<span style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal">
</span></span></span><span lang="EN-US">Drug-induced adverse
reactions, off target interactions<span></span></span></span></font></p>
<p style="margin:12pt 0cm 12pt 36pt;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US"><span>-<span style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal">
</span></span></span><span lang="EN-US">Molecular medicine, systems
biology and bioinformatics<span></span></span></span></font></p>
<p style="margin:12pt 0cm 12pt 36pt;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span style="color:black" lang="EN-US"><span>-<span style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:normal;font-size-adjust:none;font-kerning:auto;font-feature-settings:normal">
</span></span></span><span lang="EN-US">Biomedical knowledge
graph mining<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Therefore the DrugProt organizers have released a large training corpus
of manually annotated entity mentions for drugs/chemicals as well as genes/proteins
together with their interactions (13 different types of interactions). <br></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><br><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">DrugProt teams participating will be provided with the following corpus:</span></span></font></p><p class="MsoNormal" style="margin:0cm"><br><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">- PubMed abstracts (3500 training, 750 development, 750 test)<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">- Manually annotated Gold Standard chemical compound mentions (> 65000)
<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">- Manually annotated <font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Gold Standard </span></span></font>gene/protein mentions (> 60000)
<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">- Manually annotated <font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Gold Standard </span></span></font>drug/chemical-protein/gene
interactions (> 24000) <span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span></span></span></span></font><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span><br></span></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span><br></span></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span>In addition to the main DrugProt task we also have included an additional sub-track on <b>Large Scale Biomedical Text mining</b>, asking teams to automatically detect interactions from a collection of over <b>2,3 million</b> records with almost <b>54 million</b> entity annotations.</span></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span><br></span></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span><br></span></span></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">Key information:</span></b><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">DrugProt web:</span></b><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><a href="https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/" target="_blank">https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/</a><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">DrugProt Corpus: </span></b><span lang="EN-US"><a href="https://zenodo.org/record/4955411#.YNnWl27tZGb" style="color:blue;text-decoration:underline" target="_blank">https://zenodo.org/record/5119892#.YP_ObO3tZpk</a><br></span></span></font></p><p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">Large-Scale Corpus: </span></b><a href="https://zenodo.org/record/5119879#.YP_Ovu3tZpl">https://zenodo.org/record/5119879#.YP_Ovu3tZpl</a></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">Registration:</span></b><span lang="EN-US"><a href="https://docs.google.com/forms/d/e/1FAIpQLScdMnKFMncL8qDkcRx6aV6lYRm8PbufPs1rIAODwxCcPoLkcg/viewform" style="color:blue;text-decoration:underline" target="_blank">https://docs.google.com/forms/d/e/1FAIpQLScdMnKFMncL8qDkcRx6aV6lYRm8PbufPs1rIAODwxCcPoLkcg/viewform</a><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span> </span></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Evaluation will be done using micro-averaged f-measure
by comparing the automatically extracted relations against previously manually
labelled Gold Standard relations.</span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><br></span></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span style="color:black" lang="EN-US">Important dates</span></b><span lang="EN-US"><span></span></span></span></font></p><pre>✓ Test set release- July 19th 2021
✓ Large scale Text Mining sub-track set release- July 19th 2021
DrugProt Test set prediction submission due: September 15th 2021
Large scale Text Mining subtrack submission due: September 20th 2021
Short technical systems description paper due: October 1st 2021
Revised paper submission due: October 17th 2021
BioCreative VII Workshop (virtual): November 8th-10th, 2021</pre><font size="2"><span style="font-family:arial,sans-serif"><span><span></span></span></span></font>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><span><span> </span></span></span></font></p>
<p class="MsoNormal" style="margin:10pt 0cm;text-align:justify"><font size="2"><span style="font-family:arial,sans-serif"><b><span lang="EN-US">BioCreative
VII workshop proceedings and Journal Special Issue</span></b><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Participating teams will be invited to contribute to the: Proceedings of
the Seventh BioCreative Challenge Evaluation Workshop. Proceedings papers are
free of charge.<span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><br>
A selected number of top performing teams will also be invited to contribute
with a longer system description paper to a special issue on BioCreative VII to
be published in the journal Database.</span></span></font></p><p class="MsoNormal" style="margin:0cm"><br><font size="2"><span style="font-family:arial,sans-serif"></span></font></p><p class="MsoNormal" style="margin:0cm"><br><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><b><span lang="EN-US">Task organizers: <span></span></span></b></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Martin Krallinger, Barcelona Supercomputing Center,
Spain <span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="ES">Antonio Miranda, Barcelona Supercomputing Center, Spain <span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Farrokh Mehryary, University of Turku, Finland <br></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif">Jouni Luoma, University of Turku, Finland <br><span lang="EN-US"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">Sampo Pyysalo, University of Turku, Finland <span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="ES">Alfonso Valencia, Barcelona Supercomputing Center, Spain</span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="ES"><br></span></span></font></p><p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><br><span lang="ES"><span></span></span></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><b><span lang="EN-US">References<span></span></span></b></span></font></p>
<p class="MsoNormal" style="margin:0cm"><font size="2"><span style="font-family:arial,sans-serif"><span lang="EN-US">[1] Krallinger, Martin, et al. "Overview of the
protein-protein interaction annotation extraction task of BioCreative II."
Genome biology 9.2 (2008): 1-19.<br>
[2] Krallinger, Martin, et al. "CHEMDNER: The drugs and chemical names
extraction challenge." Journal of cheminformatics 7.1 (2015): 1-11.<br>
[3] Krallinger, Martin, et al. "Overview of the BioCreative VI
chemical-protein interaction Track." Proceedings of the sixth BioCreative
challenge evaluation workshop. Vol. 1. 2017. <span></span></span></span></font></p><div class="gmail-adL">
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