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Sharing models and tools for processing German clinical texts

Johannes Hellrich, Franz Matthies, Erik Faessler, Udo Hahn
2015 Studies in Health Technology and Informatics  
We suggest sharing statistical models derived from access-protected clinical documents as a reasonable substitute and provide solutions for sentence splitting, tokenization and POS tagging of German clinical  ...  The automatic processing of non-English clinical documents is massively hampered by the lack of publicly available medical language resources for training, testing and evaluating NLP components.  ...  . / Sharing Models and Tools for Processing German Clinical Texts  ... 
pmid:25991250 fatcat:n76hyqwexvejbkd2nerpx6u3gu

A Domain-adapted Dependency Parser for German Clinical Text

Elif Kara, Tatjana Zeen, Aleksandra Gabryszak, Klemens Budde, Danilo Schmidt, Roland Roller
2018 Conference on Natural Language Processing  
In this work, we present a syntactic parser specialized for German clinical data.  ...  We also show that our model performs well on fictitious clinical data from other subdomains (69.69).  ...  Acknowledgements This research was supported by the German Federal Ministry of Economics and Energy (BMWi) through the project MACSS (01MD16011F).  ... 
dblp:conf/konvens/KaraZGBSR16 fatcat:mgqwknmgdnbuzfharlviguoj3a

A Medical Information Extraction Workbench to Process German Clinical Text [article]

Roland Roller, Laura Seiffe, Ammer Ayach, Sebastian Möller, Oliver Marten, Michael Mikhailov, Christoph Alt, Danilo Schmidt, Fabian Halleck, Marcel Naik, Wiebke Duettmann, Klemens Budde
2022 arXiv   pre-print
This problem is even more evident for non-English languages. Approach: In order to address this situation, we introduce a workbench: a collection of German clinical text processing models.  ...  However, in the context of clinical text processing the number of accessible datasets is scarce -- and so is the number of existing tools. One of the main reasons is the sensitivity of the data.  ...  Concerning existing tools and pre-trained methods to process German clinical text, the situation is similar to the availability of text data.  ... 
arXiv:2207.03885v2 fatcat:5lm3cjdlebc4thfvxhy47v36i4

On the Construction of Multilingual Corpora for Clinical Text Mining

Fabián Villena, Urs Eisenmann, Petra Knaup, Jocelyn Dunstan, Matthias Ganzinger
2020 Studies in Health Technology and Informatics  
Natural language processing is often used in medicine, but the majority of tools used by researchers are developed primarily for the English language.  ...  This applies especially to unstructured data, which are often hard to analyze due to the lack of available tools to process and extract information.  ...  It is often hard to use such unstructured texts for research and other analyses due to the lack of available tools to process and extract information.  ... 
doi:10.3233/shti200180 pmid:32570404 fatcat:bnlle6gchzdlvggtxejnzrp5pu

Louhi 2014: Special issue on health text mining and information analysis

Sumithra Velupillai, Martin Duneld, Aron Henriksson, Maria Kvist, Maria Skeppstedt, Hercules Dalianis
2015 BMC Medical Informatics and Decision Making  
Acknowledgements For partial funding we would like to thank the SSF (Swedish  ...  information from pathology reports [7] , text simplification of clinical text for patient use [8] , as well as pre-processing pipelines and information extraction in tools such as cTAKES [9] .  ...  Kreutzhaler & Schulz describe work on detecting sentence boundaries and abbreviations in German clinical text by developing supervised classifiers (support vector machines) for each task.  ... 
doi:10.1186/1472-6947-15-s2-s1 pmid:26099575 pmcid:PMC4474544 fatcat:scnpu3fwjredjdzy4ftf6yxjvq

Continuous Quality Control and Advanced Text Segment Annotation with WAT-SL 2.0

Christina Lohr, Johannes Kiesel, Stephanie Luther, Johannes Hellrich, Tobias Kolditz, Benno Stein, Udo Hahn
2019 Proceedings of the 13th Linguistic Annotation Workshop  
Today's widely used annotation tools were designed for annotating typically short textual mentions of entities or relations, making their interface cumbersome to use for long(er) stretches of text, e.g  ...  We alleviated these problems by developing WAT-SL 2.0, an open-source web-based annotation tool for long-segment labeling, hierarchically structured label sets and built-ins for quality control.  ...  of Clinical Phenotype Information within the Framework of Healthcare Integrated Biobanking) and the German Federal Ministry of Education and Research (BMBF) within the SMITH project under grant 01ZZ1803G  ... 
doi:10.18653/v1/w19-4025 dblp:conf/acllaw/LohrKLHKSH19 fatcat:3k22cqrujjendehqiykjvfapc4

GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines [article]

Florian Borchert, Christina Lohr, Luise Modersohn, Thomas Langer, Markus Follmann, Jan Philipp Sachs, Udo Hahn, Matthieu-P. Schapranow
2020 arXiv   pre-print
The lack of publicly accessible text corpora is a major obstacle for progress in natural language processing.  ...  By applying and evaluating existing medical information extraction pipelines for German text, we are able to draw comparisons for the use of medical language to other corpora, medical and non-medical ones  ...  We thank our annotators, André Scherag and Danny Ammon from the Jena University Hospital, and all colleagues from the HIGH-MED and SMITH consortia for their constant support.  ... 
arXiv:2007.06400v2 fatcat:f6ajxlib3bcehk7oofcy36vqdi

A Medical Informatics Perspective on Decision Support

P. Ruch
2009 IMIA Yearbook of Medical Informatics  
to process large patient sets; 2. narrow clinical applications focused on in-depth real-time signal processing for a specific population or medical specialty.  ...  and/or natural language processing, remain fairly active in the field.  ...  I also would like to thank Casimir Kulikowski and Antoine Geissbuhler for the inspired discussions we had during the selection process.  ... 
doi:10.1055/s-0038-1638645 fatcat:evnpaip6gjderkurxs6bw56oza

Integrated Tools for Query-driven Development of Light-weight Ontologies and Information Extraction Components

Martin Toepfer, Georg Fette, Philip-Daniel Beck, Peter Kluegl, Frank Puppe
2014 Proceedings of the Workshop on Open Infrastructures and Analysis Frameworks for HLT  
text processing components.  ...  Search support provided by the tool fosters this aspect and is helpful for building natural language processing modules in general.  ...  Acknowledgments This work was supported by the Competence Network Heart Failure, funded by the German Federal Ministry of Education and Research (BMBF01 EO1004).  ... 
doi:10.3115/v1/w14-5210 dblp:conf/coling/ToepferFBKP14 fatcat:cbd3xfpk55fixjf4tkqkw4vija

Designing an openEHR-Based Pipeline for Extracting and Standardizing Unstructured Clinical Data Using Natural Language Processing

Antje Wulff, Marcel Mast, Marcus Hassler, Sara Montag, Michael Marschollek, Thomas Jack
2020 Methods of Information in Medicine  
as standard clinical information models, (2) defining a German dictionary with crucial text markers serving as expert knowledge base for a NLP pipeline, and (3) creating mapping rules between the NLP  ...  We designed a promising approach with potential to be generalized, and implemented a prototype that is extensible and reusable for other use cases concerning German medical free texts.  ...  For the former, and with a focus on the German language, mEX as an information extraction platform for German medical texts 48 as well as the well-known Mayo clinical text analysis and knowledge extraction  ... 
doi:10.1055/s-0040-1716403 pmid:33058101 fatcat:qlzoyv35ybga7ih5siz3mmidqu

DrNote: An open medical annotation service

Johann Frei, Iñaki Soto-Rey, Frank Kramer, Imon Banerjee
2022 PLOS Digital Health  
We introduce DrNote, an open source text annotation service for medical text processing.  ...  In the context of clinical trials and medical research medical text mining can provide broader insights for various research scenarios by tapping additional text data sources and extracting relevant information  ...  For German texts, mEx [20] implements a similar pipeline for clinical texts based on SpaCy [16] , albeit its trained models have not been published.  ... 
doi:10.1371/journal.pdig.0000086 fatcat:5l3xzcgmdvgqviynuyxl7cqg6e

An internet portal for the development of clinical practice guidelines

T. Karge, B. Siegmund, J. Preiss, J.C. Hoffmann, M. Zeitz, U.R. Fölsch, W.J. Höhne
2010 Applied Clinical Informatics  
It is based on a Content Management System and combines different tools for document handling and editing, communication as well as process and team steering.  ...  Methods: An internet portal was developed allowing for a shared workplace to support clinical practice guideline authoring.  ...  Acknowledgements The development and the current operation of the portal have been and are supported by the German Technology, Methods, and Infrastructure for Networked Medical Research Association TMF  ... 
doi:10.4338/aci-2010-04-ra-0027 pmid:23616852 pmcid:PMC3633313 fatcat:4b7b5gnmybf47mhc6gnkgdpa7i

Annotating German Clinical Documents for De-Identification

Tobias Kolditz, Christina Lohr, Johannes Hellrich, Luise Modersohn, Boris Betz, Michael Kiehntopf, Udo Hahn
2019 Studies in Health Technology and Informatics  
We devised annotation guidelines for the de-identification of German clinical documents and assembled a corpus of 1,106 discharge summaries and transfer letters with 44K annotated protected health information  ...  To establish a baseline for automatic de-identification on our corpus, we trained a recurrent neural network (RNN) and achieved F1 scores greater than 0.9 on most major PHI categories.  ...  Acknowledgements This work was supported by the German Federal Ministry of Education and Research (BMBF) within the SMITH project under grant 01ZZ1803G and the Deutsche Forschungsgemeinschaft (DFG) under  ... 
doi:10.3233/shti190212 pmid:31437914 fatcat:qxfits7s3jfavnuyvpvkqadp3e

Recent Advances in Clinical Natural Language Processing in Support of Semantic Analysis

S. Velupillai, D. Mowery, B. R. South, M. Kvist, H. Dalianis
2015 IMIA Yearbook of Medical Informatics  
The creation and release of corpora annotated with complex semantic information models has greatly supported the development of new tools and approaches.  ...  extracting meaning (morphological, syntactic, and semantic subtasks), and 3) leveraging NLP for clinical utility (NLP applications and infrastructure for clinical use cases).  ...  Semantic Building Blocks -Extracting Meaning From Texts Semantic analysis can be a powerful tool for representing information and conveying meaning from clinical texts.  ... 
doi:10.15265/iy-2015-009 pmid:26293867 pmcid:PMC4587060 fatcat:4cqwat2q2jhkphvrfytfowmyge

ELGA Outpatient Clinic Report and ELGA Telehealth Note: Two HL7-CDA®-Based Modular Electronic Documents [chapter]

Stefan Sabutsch, Matthias Frohner, Gabriel Kleinoscheg, Andrea Klostermann, Nina Svec, Stephan Rainer-Sablatnig, Nikola Tanjga
2022 Studies in Health Technology and Informatics  
Objectives: The specification of two harmonized implementation guides with standardized structure for all types of outpatient clinics in hospitals on the one hand and for telemonitoring treatments on the  ...  Template specifications were modelled in ART-DECOR and approved in the course of an HL7 Austria ballot.  ...  The tools used to create the CDA implementation guide were ART-DECOR [7] for the data model and CDA template specification, and a Mediawiki for the accompanying text.  ... 
doi:10.3233/shti220350 pmid:35592963 fatcat:tzl2xqwyo5ervjeoytg5sb36oe
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