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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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  <dc:creator>Farré, Eulàlia</dc:creator>
  <dc:creator>González, Gloria</dc:creator>
  <dc:creator>Mas, Toni</dc:creator>
  <dc:creator>Miranda-Escalada, Antonio</dc:creator>
  <dc:creator>Krallinger, Martin</dc:creator>
  <dc:date>2020-06-05</dc:date>
  <dc:description>The Cantemist corpus was manually annotated by clinical experts following the Cantemist guidelines.  These guidelines contain rules for annotating morphology neoplasms in Spanish oncology clinical cases; as well as for mapping these annotations to CIEO-3 (Spanish version of ICD-O-3).

Guidelines were created de novo by clinical experts in three phases:


	 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).
	 Second, a stable version of guidelines was reached while annotating sample sets of Cantemist corpus iteratively until quality control was satisfactory.
	 Third, guidelines are iteratively refined as manual annotation continues.


 

Please cite if you use this resource:

Miranda-Escalada, A., Farré, 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 Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings.

@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}
}

 

Resources:


	Web
	Citation: Miranda-Escalada, A., Farré, 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 Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings.
	Gold Standard corpus
	Silver Standard corpus
	YouTube presentations
	Participant codes


 

For more information, visit https://temu.bsc.es/cantemist/?p=4362 or email us at encargo-pln-life@bsc.es</dc:description>
  <dc:description>Funded by the Plan de Impulso de las Tecnologías del Lenguaje (Plan TL).</dc:description>
  <dc:identifier>https://zenodo.org/record/4121183</dc:identifier>
  <dc:identifier>10.5281/zenodo.4121183</dc:identifier>
  <dc:identifier>oai:zenodo.org:4121183</dc:identifier>
  <dc:language>spa</dc:language>
  <dc:relation>doi:10.5281/zenodo.3878178</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/medicalnlp</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>NLP</dc:subject>
  <dc:subject>guidelines</dc:subject>
  <dc:subject>annotatation</dc:subject>
  <dc:subject>clinical</dc:subject>
  <dc:subject>neoplasm morphology</dc:subject>
  <dc:subject>cieo</dc:subject>
  <dc:subject>oncology</dc:subject>
  <dc:subject>NER</dc:subject>
  <dc:subject>normalization</dc:subject>
  <dc:subject>ICD-O</dc:subject>
  <dc:title>Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3</dc:title>
  <dc:type>info:eu-repo/semantics/report</dc:type>
  <dc:type>publication-report</dc:type>
</oai_dc:dc>
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