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Drupal\mathjax\Plugin\Filter\MathjaxFilter->process('Dataset of 1,000 clinical case reports manually annotated by multiple clinical experts with clinical procedures. The case reports were selected by clinical experts and belong to various medical specialties including, amongst others, oncology, odontology, urology, and psychiatry. They are the same text documents that were used for the corpus and shared task on diseases DisTEMIST, building towards a collection of fully-annotated texts for clinical concept recognition and normalization. In addition to the text annotations, the mentions in the corpus have been normalized to SNOMED CT.', 'en') (Line: 118)
Drupal\filter\Element\ProcessedText::preRenderText(Array)
call_user_func_array(Array, Array) (Line: 101)
Drupal\Core\Render\Renderer->doTrustedCallback(Array, Array, 'Render #pre_render callbacks must be methods of a class that implements \Drupal\Core\Security\TrustedCallbackInterface or be an anonymous function. The callback was %s. See https://www.drupal.org/node/2966725', 'exception', 'Drupal\Core\Render\Element\RenderCallbackInterface') (Line: 788)
Drupal\Core\Render\Renderer->doCallback('#pre_render', Array, Array) (Line: 374)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 88)
__TwigTemplate_46cf2cb5ce1e020fec29c3375b8ffc02->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array, Array) (Line: 46)
__TwigTemplate_324600d6877321ff2411db6617d8bf05->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array, Array) (Line: 43)
__TwigTemplate_f26e8c96f097e3ee46706be5dc2cf95a->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/classy/templates/field/field--text-with-summary.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('field', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 80)
__TwigTemplate_038e0db2e394f2fab4504226b512a0bb->block_content(Array, Array) (Line: 182)
Twig\Template->displayBlock('content', Array, Array) (Line: 68)
__TwigTemplate_038e0db2e394f2fab4504226b512a0bb->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/classy/templates/block/block.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('block', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array) (Line: 446)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 54)
__TwigTemplate_fd1f67f696427df30219cdb6a6f6c651->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/stable/layouts/twocol_section/layout--twocol-section.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('layout__twocol_section', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array) (Line: 446)
Drupal\Core\Render\Renderer->doRender(Array) (Line: 446)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 110)
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Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/classy/templates/content/node.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('node', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array, ) (Line: 242)
Drupal\Core\Render\MainContent\HtmlRenderer->Drupal\Core\Render\MainContent\{closure}() (Line: 580)
Drupal\Core\Render\Renderer->executeInRenderContext(Object, Object) (Line: 243)
Drupal\Core\Render\MainContent\HtmlRenderer->prepare(Array, Object, Object) (Line: 132)
Drupal\Core\Render\MainContent\HtmlRenderer->renderResponse(Array, Object, Object) (Line: 90)
Drupal\Core\EventSubscriber\MainContentViewSubscriber->onViewRenderArray(Object, 'kernel.view', Object)
call_user_func(Array, Object, 'kernel.view', Object) (Line: 142)
Drupal\Component\EventDispatcher\ContainerAwareEventDispatcher->dispatch(Object, 'kernel.view') (Line: 174)
Symfony\Component\HttpKernel\HttpKernel->handleRaw(Object, 1) (Line: 81)
Symfony\Component\HttpKernel\HttpKernel->handle(Object, 1, 1) (Line: 58)
Drupal\Core\StackMiddleware\Session->handle(Object, 1, 1) (Line: 48)
Drupal\Core\StackMiddleware\KernelPreHandle->handle(Object, 1, 1) (Line: 191)
Drupal\page_cache\StackMiddleware\PageCache->fetch(Object, 1, 1) (Line: 128)
Drupal\page_cache\StackMiddleware\PageCache->lookup(Object, 1, 1) (Line: 82)
Drupal\page_cache\StackMiddleware\PageCache->handle(Object, 1, 1) (Line: 48)
Drupal\Core\StackMiddleware\ReverseProxyMiddleware->handle(Object, 1, 1) (Line: 51)
Drupal\Core\StackMiddleware\NegotiationMiddleware->handle(Object, 1, 1) (Line: 23)
Stack\StackedHttpKernel->handle(Object, 1, 1) (Line: 713)
Drupal\Core\DrupalKernel->handle(Object) (Line: 19)

Drupal\mathjax\Plugin\Filter\MathjaxFilter->process('If you have published a result better than those on the list, send a message to odesia-comunicacion@lsi.uned.es indicating the result and the DOI of the article, along with a copy of it if it is not published openly.', 'es') (Line: 118)
Drupal\filter\Element\ProcessedText::preRenderText(Array)
call_user_func_array(Array, Array) (Line: 101)
Drupal\Core\Render\Renderer->doTrustedCallback(Array, Array, 'Render #pre_render callbacks must be methods of a class that implements \Drupal\Core\Security\TrustedCallbackInterface or be an anonymous function. The callback was %s. See https://www.drupal.org/node/2966725', 'exception', 'Drupal\Core\Render\Element\RenderCallbackInterface') (Line: 788)
Drupal\Core\Render\Renderer->doCallback('#pre_render', Array, Array) (Line: 374)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 88)
__TwigTemplate_46cf2cb5ce1e020fec29c3375b8ffc02->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array, Array) (Line: 46)
__TwigTemplate_324600d6877321ff2411db6617d8bf05->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array, Array) (Line: 43)
__TwigTemplate_f26e8c96f097e3ee46706be5dc2cf95a->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/classy/templates/field/field--text-with-summary.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('field', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array) (Line: 446)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 80)
__TwigTemplate_038e0db2e394f2fab4504226b512a0bb->block_content(Array, Array) (Line: 182)
Twig\Template->displayBlock('content', Array, Array) (Line: 68)
__TwigTemplate_038e0db2e394f2fab4504226b512a0bb->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('core/themes/classy/templates/block/block.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('block', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array) (Line: 446)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 115)
__TwigTemplate_d509e6b6442caedd1847c1a3a72daf79->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('themes/custom/b5subtheme/templates/layout/page.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('page', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 479)
Drupal\Core\Template\TwigExtension->escapeFilter(Object, Array, 'html', NULL, 1) (Line: 102)
__TwigTemplate_b99c06e3bc9b6cb3e9f0ac63503b296b->doDisplay(Array, Array) (Line: 405)
Twig\Template->displayWithErrorHandling(Array, Array) (Line: 378)
Twig\Template->display(Array) (Line: 390)
Twig\Template->render(Array) (Line: 55)
twig_render_template('themes/custom/b5subtheme/templates/layout/html.html.twig', Array) (Line: 384)
Drupal\Core\Theme\ThemeManager->render('html', Array) (Line: 433)
Drupal\Core\Render\Renderer->doRender(Array, ) (Line: 204)
Drupal\Core\Render\Renderer->render(Array) (Line: 162)
Drupal\Core\Render\MainContent\HtmlRenderer->Drupal\Core\Render\MainContent\{closure}() (Line: 580)
Drupal\Core\Render\Renderer->executeInRenderContext(Object, Object) (Line: 163)
Drupal\Core\Render\MainContent\HtmlRenderer->renderResponse(Array, Object, Object) (Line: 90)
Drupal\Core\EventSubscriber\MainContentViewSubscriber->onViewRenderArray(Object, 'kernel.view', Object)
call_user_func(Array, Object, 'kernel.view', Object) (Line: 142)
Drupal\Component\EventDispatcher\ContainerAwareEventDispatcher->dispatch(Object, 'kernel.view') (Line: 174)
Symfony\Component\HttpKernel\HttpKernel->handleRaw(Object, 1) (Line: 81)
Symfony\Component\HttpKernel\HttpKernel->handle(Object, 1, 1) (Line: 58)
Drupal\Core\StackMiddleware\Session->handle(Object, 1, 1) (Line: 48)
Drupal\Core\StackMiddleware\KernelPreHandle->handle(Object, 1, 1) (Line: 191)
Drupal\page_cache\StackMiddleware\PageCache->fetch(Object, 1, 1) (Line: 128)
Drupal\page_cache\StackMiddleware\PageCache->lookup(Object, 1, 1) (Line: 82)
Drupal\page_cache\StackMiddleware\PageCache->handle(Object, 1, 1) (Line: 48)
Drupal\Core\StackMiddleware\ReverseProxyMiddleware->handle(Object, 1, 1) (Line: 51)
Drupal\Core\StackMiddleware\NegotiationMiddleware->handle(Object, 1, 1) (Line: 23)
Stack\StackedHttpKernel->handle(Object, 1, 1) (Line: 713)
Drupal\Core\DrupalKernel->handle(Object) (Line: 19)

MedProcNER/ProcTEMIST corpus 2023

Dataset of 1,000 clinical case reports manually annotated by multiple clinical experts with clinical procedures. The case reports were selected by clinical experts and belong to various medical specialties including, amongst others, oncology, odontology, urology, and psychiatry. They are the same text documents that were used for the corpus and shared task on diseases DisTEMIST, building towards a collection of fully-annotated texts for clinical concept recognition and normalization. In addition to the text annotations, the mentions in the corpus have been normalized to SNOMED CT.

Language(s)

Spanish

Dataset description link

https://doi.org/10.5281/zenodo.7817745

Year

2023

Domain

Health

Text types

Clinical notes

Annotations

clinical procedures, SNOMED CT normalization

Annotation guide link

https://doi.org/10.5281/zenodo.7817666

Data access

Public

Data link

https://doi.org/10.5281/zenodo.7817745

Publication

Nentidis, A. et al. (2023). Overview of BioASQ 2023: The Eleventh BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. In: Arampatzis, A., et al. Experimental IR Meets Multilinguality, Multimodality, and Interaction. CLEF 2023. Lecture Notes in Computer Science, vol 14163. Springer, Cham. https://doi.org/10.1007/978-3-031-42448-9_19

Publication link

https://link.springer.com/chapter/10.1007/978-3-031-42448-9_19

License

CC-BY-4.0

NLP Topic

(named) entity recognition

Number of units

1000

Training set size

750

Test set size

250

If you have published a result better than those on the list, send a message to odesia-comunicacion@lsi.uned.es indicating the result and the DOI of the article, along with a copy of it if it is not published openly.