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
Abstract
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.- Anthology ID:
- 2022.lrec-1.389
- Volume:
- Proceedings of the Thirteenth Language Resources and Evaluation Conference
- Month:
- June
- Year:
- 2022
- Address:
- Marseille, France
- Editors:
- Nicoletta Calzolari, Frédéric Béchet, Philippe Blache, Khalid Choukri, Christopher Cieri, Thierry Declerck, Sara Goggi, Hitoshi Isahara, Bente Maegaard, Joseph Mariani, Hélène Mazo, Jan Odijk, Stelios Piperidis
- Venue:
- LREC
- SIG:
- Publisher:
- European Language Resources Association
- Note:
- Pages:
- 3650–3660
- Language:
- URL:
- https://aclanthology.org/2022.lrec-1.389
- DOI:
- Cite (ACL):
- Florian Borchert, Christina Lohr, Luise Modersohn, Jonas Witt, Thomas Langer, Markus Follmann, Matthias Gietzelt, Bert Arnrich, Udo Hahn, and Matthieu-P. Schapranow. 2022. GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers. In Proceedings of the Thirteenth Language Resources and Evaluation Conference, pages 3650–3660, Marseille, France. European Language Resources Association.
- Cite (Informal):
- GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers (Borchert et al., LREC 2022)
- PDF:
- https://preview.aclanthology.org/emnlp-22-attachments/2022.lrec-1.389.pdf
- Code
- hpi-dhc/ggponc_annotation