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

Rabal, Obdulia; Krallinger, Martin


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  <identifier identifierType="DOI">10.5281/zenodo.4957577</identifier>
  <creators>
    <creator>
      <creatorName>Rabal, Obdulia</creatorName>
      <givenName>Obdulia</givenName>
      <familyName>Rabal</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>Krallinger, Martin</creatorName>
      <givenName>Martin</givenName>
      <familyName>Krallinger</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2646-8782</nameIdentifier>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
  </creators>
  <titles>
    <title>DrugProt corpus genes and proteins annotation guidelines [GPRO - Biocreative 5.2]</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>NLP</subject>
    <subject>biomedical NLP</subject>
    <subject>biocreative</subject>
    <subject>NER</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-06-15</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="JournalArticle"/>
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    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/medicalnlp</relatedIdentifier>
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  <version>1.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
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  <descriptions>
    <description descriptionType="Abstract">&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;Please cite if you use any DrugProt resource:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Miranda, Antonio, et al. &amp;quot;Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations.&amp;quot;&amp;nbsp;&lt;em&gt;Proceedings of the seventh BioCreative challenge evaluation workshop&lt;/em&gt;. 2021.&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;@inproceedings{miranda2021overview,
  title={Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations},
  author={Miranda, Antonio and Mehryary, Farrokh and Luoma, Jouni and Pyysalo, Sampo and Valencia, Alfonso and Krallinger, Martin},
  booktitle={Proceedings of the seventh BioCreative challenge evaluation workshop},
  year={2021}
}&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;&amp;nbsp;&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://codalab.lisn.upsaclay.fr/competitions/8293"&gt;Online evaluation (CodaLab)&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4957137"&gt;Relation annotation guidelines&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4957576"&gt;Gene and protein 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.7252201"&gt;DrugProt Silver Standard Knowledge Graph&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.5042178"&gt;FAQ&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.5119878"&gt;DrugProt Large Scale Additional SubTrack&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.5656991"&gt;DrugProt Large Scale document collection protocol&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
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