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Posts

news

Paper published in Briefings in Bioinformatics

Published:

Our paper “Knowledge bases and software support for variant interpretation in precision oncology” has been published in Briefings in Bioinformatics! Thanks to all collaborators from the HiGHmed consortium.

1st GGPONC User Meeting

Published:

I have organized a workshop with experts from both the German clinical NLP and the clinical guideline communities, to deepen the dialogue that we have started with our GGPONC project. Check out the event website for details.

GGPONC 2.0 @ LREC

Published:

Our paper for the new release of GGPONC 2.0 has been accepted at LREC! The new dataset is currently the largest, freely distributable annotated corpus of German medical text (1.87M tokens, 250K annotations). We also created baseline NER models with HuggingFace transformers.

projects

Mixed Reality

Development of interactive XR applications for HoloLens and other HMDs / mobile devices
Microsoft Hololens

GGPONC

German Guideline Program in Oncology NLP Corpus

publications

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

Published in LOUHI@EMNLP, 2020

Recommended citation: Florian Borchert*, Christina Lohr*, Luise Modersohn*, Thomas Langer, Markus Follmann, Jan Philipp Sachs, Udo Hahn, Matthieu-P. Schapranow. GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines. In Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis, pp. 38–48. Online: Association for Computational Linguistics, 2020. (* equal contribution) [Data Access] [Code]

Knowledge bases and software support for variant interpretation in precision oncology

Published in Briefings in Bioinformatics, 2021

Recommended citation: Florian Borchert*, Andreas Mock*, Aurelie Tomczak*, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P Schapranow. Knowledge Bases and Software Support for Variant Interpretation in Precision Oncology, Briefings in Bioinformatics, Volume 22, Issue 6, November 2021, bbab134 (* equal contribution) IF = 11.6 https://doi.org/10.1093/bib/bbab134.

An Engineering Approach towards Multi-Site Virtual Molecular Tumor Board Software Support

Published in 1st Conference on ICT for Health, Accessibility and Wellbeing, 2021

Recommended citation: Richard Henkenjohann, Benjamin Bergner, Florian Borchert, Nina Bougatf, Hauke Hund, Roland Eils, and Matthieu-P. Schapranow. An Engineering Approach towards Multi-Site Virtual Molecular Tumor Board Software Support. Proceedings of the 1st Conference on ICT for Health, Accessibility and Wellbeing. Springer International Publishing, 2021

GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers

Published in LREC, 2022

Recommended citation: Florian Borchert, Christina Lohr, Luise Modersohn, Jonas Witt, Thomas Langer, Markus Follmann, Matthias Gietzelt, Bert Arnrich, Udo Hahn and Matthieu-P. Schapranow. GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers. LREC 2022 — Proceedings of the Language Resources and Evaluation Conference, pp. 3650‑3660. Marseille, France, European Language Resources Association, 2022 [Data Access] [Code]