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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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    <subfield code="a">&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;</subfield>
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