De-Identifying GRASCCO - A Pilot Study for the De-Identification of the German Medical Text Project (GeMTeX) Corpus.

The German Medical Text Project (GeMTeX) is one of the largest infrastructure efforts targeting German-language clinical documents. We here introduce the architecture of the de-identification pipeline of GeMTeX. This pipeline comprises the export of raw clinical documents from the local hospital information system, the import into the annotation platform INCEpTION, fully automatic pre-tagging with protected health information (PHI) items by the Averbis Health Discovery pipeline, a manual curation step of these pre-annotated data, and, finally, the automatic replacement of PHI items with type-conformant substitutes. This design was implemented in a pilot study involving six annotators and two curators each at the Data Integration Centers of the University Hospitals Leipzig and Erlangen. As a proof of concept, the publicly available Graz Synthetic Text Clinical Corpus (GRASSCO) was enhanced with PHI annotations in an annotation campaign for which reasonable inter-annotator agreement values of Krippendorff's α ≈ 0.97 can be reported. These curated 1.4 K PHI annotations are released as open-source data constituting the first publicly available German clinical language text corpus with PHI metadata.

Citation

Christina Lohr, Franz Matthies, Jakob Faller, Luise Modersohn, Andrea Riedel, Udo Hahn, Rebekka Kiser, Martin Boeker, Frank Meineke. De-Identifying GRASCCO - A Pilot Study for the De-Identification of the German Medical Text Project (GeMTeX) Corpus. Studies in health technology and informatics. 2024 Aug 30;317:171-179

Mesh Tags

PMID: 39234720

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