Journal article Open Access

DrugProt corpus relation annotation guidelines [ChemProt - Biocreative VI]

Rabal, Obdulia; López, Jose Antonio; Lagreid, Astrid; Krallinger, Martin


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    <dct:title>DrugProt corpus relation annotation guidelines [ChemProt - Biocreative VI]</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>relation extraction</dcat:keyword>
    <dcat:keyword>biocreative</dcat:keyword>
    <dcat:keyword>drugprot</dcat:keyword>
    <dcat:keyword>biomedical NLP</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 used for the construction of the annotations of chemical-protein interactions&amp;nbsp;between Chemical Entities Mentions (CEMs) and Gene and Protein Related Objects (named as GPROs throughout this manuscript).&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;These guidelines provide curation rules to evaluate if a sentence within an abstract contains a description of a chemical-protein interaction; in particular, if sufficient detail/evidence is provided for co-mentioned CEMs and GPROs. Additionally, it describes curation rules and definitions to assign each identified CHEMPROT to any of the 5 classes and 16 subclasses predefined.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;Please, cite:&amp;nbsp;&lt;br&gt; @inproceedings{krallinger2017overview,&amp;nbsp;title={Overview of the BioCreative VI chemical-protein interaction Track},&amp;nbsp;author={Krallinger, Martin and Rabal, Obdulia and Akhondi, Saber A and P{\&amp;#39;e}rez, Mart{\i}n P{\&amp;#39;e}rez and Santamar{\&amp;#39;\i}a, Jes{\&amp;#39;u}s and Rodr{\&amp;#39;\i}guez, Gael P{\&amp;#39;e}rez and others},&amp;nbsp;booktitle={Proceedings of the sixth BioCreative challenge evaluation workshop},&amp;nbsp;volume={1},&amp;nbsp;pages={141--146},&amp;nbsp; year={2017}}&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.4957576"&gt;Genes and proteins 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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