GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers
Florian Borchert | Christina Lohr | Luise Modersohn | Jonas Witt | Thomas Langer | Markus Follmann | Matthias Gietzelt | Bert Arnrich | Udo Hahn | Matthieu-P. Schapranow
Proceedings of the Thirteenth Language Resources and Evaluation Conference
Despite remarkable advances in the development of language resources over the recent years, there is still a shortage of annotated, publicly available corpora covering (German) medical language. With the initial release of the German Guideline Program in Oncology NLP Corpus (GGPONC), we have demonstrated how such corpora can be built upon clinical guidelines, a widely available resource in many natural languages with a reasonable coverage of medical terminology. In this work, we describe a major new release for GGPONC. The corpus has been substantially extended in size and re-annotated with a new annotation scheme based on SNOMED CT top level hierarchies, reaching high inter-annotator agreement (γ=.94). Moreover, we annotated elliptical coordinated noun phrases and their resolutions, a common language phenomenon in (not only German) scientific documents. We also trained BERT-based named entity recognition models on this new data set, which achieve high performance on short, coarse-grained entity spans (F1=.89), while the rate of boundary errors increases for long entity spans. GGPONC is freely available through a data use agreement. The trained named entity recognition models, as well as the detailed annotation guide, are also made publicly available.
GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines
Florian Borchert | Christina Lohr | Luise Modersohn | Thomas Langer | Markus Follmann | Jan Philipp Sachs | Udo Hahn | Matthieu-P. Schapranow
Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis
The lack of publicly accessible text corpora is a major obstacle for progress in natural language processing. For medical applications, unfortunately, all language communities other than English are low-resourced. In this work, we present GGPONC (German Guideline Program in Oncology NLP Corpus), a freely dis tributable German language corpus based on clinical practice guidelines for oncology. This corpus is one of the largest ever built from German medical documents. Unlike clinical documents, clinical guidelines do not contain any patient-related information and can therefore be used without data protection restrictions. Moreover, GGPONC is the first corpus for the German language covering diverse conditions in a large medical subfield and provides a variety of metadata, such as literature references and evidence levels. 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.
- Florian Borchert 2
- Christina Lohr 2
- Luise Modersohn 2
- Thomas Langer 2
- Markus Follmann 2
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