Farré, Eulàlia
González, Gloria
Mas, Toni
Miranda-Escalada, Antonio
Krallinger, Martin
2020-06-05
<p>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<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>
<p>Guidelines were created de novo by clinical experts in three phases:</p>
<ul>
<li> 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>
<li> Second, a stable version of guidelines was reached while annotating sample sets of Cantemist corpus iteratively until quality control was satisfactory.</li>
<li> Third, guidelines are iteratively refined as manual annotation continues.</li>
</ul>
<p> </p>
<p><strong>Please cite if you use this resource:</strong></p>
<p>Miranda-Escalada, A., Farré, E., & 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 <em>Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings</em>.</p>
<pre><code>@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}
}</code></pre>
<p> </p>
<p><strong>Resources:</strong></p>
<ul>
<li><strong><a href="https://temu.bsc.es/cantemist/">Web</a></strong></li>
<li><strong>Citation: </strong>Miranda-Escalada, A., Farré, E., & 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 <em>Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings</em>.</li>
<li><a href="https://doi.org/10.5281/zenodo.3773228"><strong>Gold Standard corpus</strong></a></li>
<li><a href="https://doi.org/10.5281/zenodo.4010899"><strong>Silver Standard corpus</strong></a></li>
<li><a href="https://www.youtube.com/playlist?list=PL5uSCzf1azhC24g5dsp5eVMp8BZFWCraX"><strong>YouTube presentations</strong></a></li>
<li><a href="https://temu.bsc.es/cantemist/?p=4606"><strong>Participant codes</strong></a></li>
</ul>
<p> </p>
<p>For more information, visit <a href="https://temu.bsc.es/cantemist/?p=4362">https://temu.bsc.es/cantemist/?p=4362</a> or email us at encargo-pln-life@bsc.es</p>
Funded by the Plan de Impulso de las Tecnologías del Lenguaje (Plan TL).
https://doi.org/10.5281/zenodo.4121183
oai:zenodo.org:4121183
spa
Zenodo
https://zenodo.org/communities/medicalnlp
https://doi.org/10.5281/zenodo.3878178
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
NLP
guidelines
annotatation
clinical
neoplasm morphology
cieo
oncology
NER
normalization
ICD-O
Cantemist guidelines: neoplasms morphology annotation and mapping to CIEO-3
info:eu-repo/semantics/report