Journal article Open Access

DrugProt corpus genes and proteins annotation guidelines [GPRO - Biocreative 5.2]

Rabal, Obdulia; Krallinger, Martin


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    <dct:title>DrugProt corpus genes and proteins annotation guidelines [GPRO - Biocreative 5.2]</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2021</dct:issued>
    <dcat:keyword>NLP</dcat:keyword>
    <dcat:keyword>biomedical NLP</dcat:keyword>
    <dcat:keyword>biocreative</dcat:keyword>
    <dcat:keyword>NER</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-15</dct:issued>
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    <dct:description>&lt;p&gt;Annotation guidelines&amp;nbsp;used for the&amp;nbsp;annotations of gene and protein-related objects of the CHEMDNER, ChemProt and DrugProt&amp;nbsp;corpora.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Introduction&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;The&amp;nbsp;annotation guidelines have been refined after iterative cycles of annotations of sample documents. It also incorporated suggestions made by curators as well as observations of annotation inconsistencies encountered when comparing results from different human curators.&lt;/p&gt; &lt;p&gt;In brief, the annotated GPROs include genes, gene products&lt;br&gt; (proteins, RNA), DNA/protein sequence elements and protein families, domains and complexes. The aim of the iterative manual annotation cycles was to improve the quality and consistency of the guidelines, in order to make them more intuitive and easier to follow.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;Please, cite:&lt;/p&gt; &lt;p&gt;@article{perez2016markyt,&amp;nbsp;title={The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge},&amp;nbsp;author={P{\&amp;#39;e}rez-P{\&amp;#39;e}rez, Martin and P{\&amp;#39;e}rez-Rodr{\&amp;#39;\i}guez, Gael and Rabal, Obdulia and Vazquez, Miguel and Oyarzabal, Julen and Fdez-Riverola, Florentino and Valencia, Alfonso and Krallinger, Martin and Louren{\c{c}}o, An{\&amp;#39;a}lia},&amp;nbsp;journal={Database},&amp;nbsp;volume={2016},&amp;nbsp;year={2016},&amp;nbsp;publisher={Oxford Academic}}&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Related Resources:&lt;/strong&gt;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&lt;a href="https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/"&gt;Web&lt;/a&gt;&lt;/li&gt; &lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4955410"&gt;DrugProt corpus&lt;/a&gt;&lt;/li&gt; &lt;li&gt;&lt;a href="https://github.com/tonifuc3m/drugprot-evaluation-library"&gt;Evaluation library&lt;/a&gt;&lt;/li&gt; &lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4957137"&gt;Relations annotation guidelines&lt;/a&gt;&lt;/li&gt; &lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4957518"&gt;Chemicals and drugs annotation guidelines&lt;/a&gt;&lt;/li&gt; &lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.5042178"&gt;DrugProt FAQ&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt;</dct:description>
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