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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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{
  "inLanguage": {
    "alternateName": "spa", 
    "@type": "Language", 
    "name": "Spanish"
  }, 
  "description": "<p>The Cantemist corpus was manually annotated by clinical experts following the Cantemist guidelines. &nbsp;These guidelines contain rules for annotating morphology neoplasms in Spanish oncology clinical cases; as well as for mapping these annotations to<a href=\"https://eciemaps.mscbs.gob.es/ecieMaps/browser/index_o_3.html\"> CIEO-3</a> (Spanish version of <a href=\"https://www.who.int/classifications/icd/adaptations/oncology/en/\">ICD-O-3</a>).</p>\n\n<p>Guidelines were created de novo by clinical experts in three phases:</p>\n\n<ul>\n\t<li>&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).</li>\n\t<li>&nbsp;Second, a stable version of guidelines was reached while annotating sample sets of Cantemist corpus iteratively until quality control was satisfactory.</li>\n\t<li>&nbsp;Third, guidelines are iteratively refined as manual annotation continues.</li>\n</ul>\n\n<p>&nbsp;</p>\n\n<p><strong>Please cite if you use this resource:</strong></p>\n\n<p>Miranda-Escalada, A., Farr&eacute;, E., &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&nbsp;<em>Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings</em>.</p>\n\n<pre><code>@inproceedings{miranda2020named,\n  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},\n  author={Miranda-Escalada, A and Farr{\\'e}, E and Krallinger, M},\n  booktitle={Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings},\n  year={2020}\n}</code></pre>\n\n<p>&nbsp;</p>\n\n<p><strong>Resources:</strong></p>\n\n<ul>\n\t<li><strong><a href=\"https://temu.bsc.es/cantemist/\">Web</a></strong></li>\n\t<li><strong>Citation:&nbsp;</strong>Miranda-Escalada, A., Farr&eacute;, E., &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&nbsp;<em>Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings</em>.</li>\n\t<li><a href=\"https://doi.org/10.5281/zenodo.3773228\"><strong>Gold Standard corpus</strong></a></li>\n\t<li><a href=\"https://doi.org/10.5281/zenodo.4010899\"><strong>Silver Standard corpus</strong></a></li>\n\t<li><a href=\"https://www.youtube.com/playlist?list=PL5uSCzf1azhC24g5dsp5eVMp8BZFWCraX\"><strong>YouTube presentations</strong></a></li>\n\t<li><a href=\"https://temu.bsc.es/cantemist/?p=4606\"><strong>Participant codes</strong></a></li>\n</ul>\n\n<p>&nbsp;</p>\n\n<p>For more information, visit <a href=\"https://temu.bsc.es/cantemist/?p=4362\">https://temu.bsc.es/cantemist/?p=4362</a>&nbsp;or email us at encargo-pln-life@bsc.es</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@type": "Person", 
      "name": "Farr\u00e9, Eul\u00e0lia"
    }, 
    {
      "affiliation": "Bitac", 
      "@type": "Person", 
      "name": "Gonz\u00e1lez, Gloria"
    }, 
    {
      "affiliation": "Bitac", 
      "@type": "Person", 
      "name": "Mas, Toni"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@id": "https://orcid.org/0000-0002-5654-001X", 
      "@type": "Person", 
      "name": "Miranda-Escalada, Antonio"
    }, 
    {
      "affiliation": "Barcelona Supercomputing Center", 
      "@id": "https://orcid.org/0000-0002-2646-8782", 
      "@type": "Person", 
      "name": "Krallinger, Martin"
    }
  ], 
  "headline": "Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2020-06-05", 
  "url": "https://zenodo.org/record/4121183", 
  "version": "1.3", 
  "keywords": [
    "NLP", 
    "guidelines", 
    "annotatation", 
    "clinical", 
    "neoplasm morphology", 
    "cieo", 
    "oncology", 
    "NER", 
    "normalization", 
    "ICD-O"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.4121183", 
  "@id": "https://doi.org/10.5281/zenodo.4121183", 
  "@type": "ScholarlyArticle", 
  "name": "Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3"
}
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