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Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3

Farré, Eulàlia; González, Gloria; Mas, Toni; Miranda-Escalada, Antonio; Krallinger, Martin


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  <identifier identifierType="DOI">10.5281/zenodo.4121183</identifier>
  <creators>
    <creator>
      <creatorName>Farré, Eulàlia</creatorName>
      <givenName>Eulàlia</givenName>
      <familyName>Farré</familyName>
      <affiliation>Barcelona Supercomputing Center</affiliation>
    </creator>
    <creator>
      <creatorName>González, Gloria</creatorName>
      <givenName>Gloria</givenName>
      <familyName>González</familyName>
      <affiliation>Bitac</affiliation>
    </creator>
    <creator>
      <creatorName>Mas, Toni</creatorName>
      <givenName>Toni</givenName>
      <familyName>Mas</familyName>
      <affiliation>Bitac</affiliation>
    </creator>
    <creator>
      <creatorName>Miranda-Escalada, Antonio</creatorName>
      <givenName>Antonio</givenName>
      <familyName>Miranda-Escalada</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5654-001X</nameIdentifier>
      <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>Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>NLP</subject>
    <subject>guidelines</subject>
    <subject>annotatation</subject>
    <subject>clinical</subject>
    <subject>neoplasm morphology</subject>
    <subject>cieo</subject>
    <subject>oncology</subject>
    <subject>NER</subject>
    <subject>normalization</subject>
    <subject>ICD-O</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-06-05</date>
  </dates>
  <language>es</language>
  <resourceType resourceTypeGeneral="Text">Report</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4121183</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3878178</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/medicalnlp</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.3</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The Cantemist corpus was manually annotated by clinical experts following the Cantemist guidelines. &amp;nbsp;These guidelines contain rules for annotating morphology neoplasms in Spanish oncology clinical cases; as well as for mapping these annotations to&lt;a href="https://eciemaps.mscbs.gob.es/ecieMaps/browser/index_o_3.html"&gt; CIEO-3&lt;/a&gt; (Spanish version of &lt;a href="https://www.who.int/classifications/icd/adaptations/oncology/en/"&gt;ICD-O-3&lt;/a&gt;).&lt;/p&gt;

&lt;p&gt;Guidelines were created de novo by clinical experts in three phases:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&amp;nbsp;First, a zero version of guidelines after the clinical experts reviewed neoplasm morphology annotations in SPACCC corpus see Codiesp guidelines(https://zenodo.org/record/3730567).&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;Second, a stable version of guidelines was reached while annotating sample sets of Cantemist corpus iteratively until quality control was satisfactory.&lt;/li&gt;
	&lt;li&gt;&amp;nbsp;Third, guidelines are iteratively refined as manual annotation continues.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Please cite if you use this resource:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Miranda-Escalada, A., Farr&amp;eacute;, E., &amp;amp; Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In&amp;nbsp;&lt;em&gt;Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings&lt;/em&gt;.&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;@inproceedings{miranda2020named,
  title={Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results},
  author={Miranda-Escalada, A and Farr{\'e}, E and Krallinger, M},
  booktitle={Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings},
  year={2020}
}&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Resources:&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;strong&gt;&lt;a href="https://temu.bsc.es/cantemist/"&gt;Web&lt;/a&gt;&lt;/strong&gt;&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;Citation:&amp;nbsp;&lt;/strong&gt;Miranda-Escalada, A., Farr&amp;eacute;, E., &amp;amp; Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In&amp;nbsp;&lt;em&gt;Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings&lt;/em&gt;.&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.3773228"&gt;&lt;strong&gt;Gold Standard corpus&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://doi.org/10.5281/zenodo.4010899"&gt;&lt;strong&gt;Silver Standard corpus&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://www.youtube.com/playlist?list=PL5uSCzf1azhC24g5dsp5eVMp8BZFWCraX"&gt;&lt;strong&gt;YouTube presentations&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://temu.bsc.es/cantemist/?p=4606"&gt;&lt;strong&gt;Participant codes&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;For more information, visit &lt;a href="https://temu.bsc.es/cantemist/?p=4362"&gt;https://temu.bsc.es/cantemist/?p=4362&lt;/a&gt;&amp;nbsp;or email us at encargo-pln-life@bsc.es&lt;/p&gt;</description>
    <description descriptionType="Other">Funded by the Plan de Impulso de las Tecnologías del Lenguaje (Plan TL).</description>
  </descriptions>
</resource>
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