CARDIO:DE [V1.01]

Version 7.0
Christoph Dieterich, 2022, "CARDIO:DE [V1.01]", https://doi.org/10.11588/data/AFYQDY, heiDATA, V7
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Description


Version information CARDIO:DE 1.01
  • Resolved minor annotation bugs
  • Updated TSV format (importable to INCEpTION release > 29.7)
  • Added UIMA CAS corpus version
  • Added annotation layer information files for INCEpTION import ( cardiode_[exp]_dependencies_inception.zip)
Abstract:
We present CARDIO:DE, the first freely available and distributable large German clinical corpus from the cardiovascular domain. CARDIO:DE encompasses 500 clinical routine German doctor’s letters from Heidelberg University Hospital, which were manually annotated. Our prospective study design complies well with current data protection regulations and allows us to keep the original structure of clinical documents consistent. In order to ease access to our corpus, we manually de-identified all letters. To enable various information extraction tasks the temporal information in the documents was preserved. We added two high-quality manual annotation layers to CARDIO:DE, (1) medication information and (2) CDA-compliant section classes. To the best of our knowledge, CARDIO:DE is the first freely available and distributable German clinical corpus in the cardiovascular domain. In summary, our corpus offers unique opportunities for collaborative and reproducible research on natural language processing models for German clinical texts.

If you make use of the corpus, please cite the following resource:
Richter-Pechanski, P. et al. CARDIO:DE. heiData https://doi.org/10.11588/data/AFYQDY (2022).

If you cite the related manuscript published at Scientific Data, please cite:
Richter-Pechanski, P., Wiesenbach, P., Schwab, D.M. et al. A distributable German clinical corpus containing cardiovascular clinical routine doctor’s letters. Sci Data 10, 207 (2023). https://doi.org/10.1038/s41597-023-02128-9.


This repository includes two corpora - CARDIO:DE and CARDIO:DE_EXP:
  1. CARDIO:DE (main corpus) contains manual gold standard annotations of:
    • medication information (ActiveIng, Drug, Duration, Form, Frequency, Strength)
    • section types (Abschluss, Anamnese, Anrede, Diagnosen, AufnahmeMedikation, Befunde, EchoBefunde, AktuellDiagnosen, EntlassMedikation, KuBefunde, Labor, Anderes, RisikofaktorenAllergien, Zusammenfassung)
  2. CARDIO:DE_EXP (experimental) contains manual gold standard annotations of:
    • medication information (ActiveIng, Dosage, Drug, Duration, Form, Frequency, Reason, Route, Strength)
    • section types (Abschluss, Anamnese, Anrede, Diagnosen, AufnahmeMedikation, Befunde, EchoBefunde, AktuellDiagnosen, EntlassMedikation, KuBefunde, Labor, Anderes, RisikofaktorenAllergien, Zusammenfassung)
    • NOTE: Medication information classes Dosage, Route and Reason are for experimental purposes only, as these classes achieved a lower inter-annotator agreement score during redundant annotation, see CARDIO:DE publication.

Information about how to access the data, see Terms -> Terms of Use section.
Subject Medicine, Health and Life Sciences
Related Publication Richter-Pechanski, P., Wiesenbach, P., Schwab, D.M. et al. A distributable German clinical corpus containing cardiovascular clinical routine doctor’s letters. Sci Data 10, 207 (2023). doi: https://doi.org/10.1038/s41597-023-02128-9
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cardiode.zip
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Published Dec 15, 2023
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MD5: 8df944b7861214bf9e70ae00ecf45d17
cardiode_dependencies_inception.zip
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Published Dec 20, 2023
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MD5: 144c6fe26e2d78ddfb885d5707dc6182
cardiode_exp.zip
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Published Dec 15, 2023
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MD5: c167cf5db46f36793db6cf4b3b46c6b3
cardiode_exp_dependencies_inception.zip
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Published Dec 20, 2023
61 Downloads
MD5: 9497b092483924979d2d0b72d4672a45
DUA_en.pdf
DUA_en.pdf
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Published Jan 20, 2023
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MD5: 9b3f59448c6360573fe2d24463c69c08
Data Usage Agreement for CARDIO:DE and CARDIO:DE_EXP
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Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

Terms of Use, see our data usage agreement (DUA). See files tab: DUA_en.pdf

The corpus must be formally requested following three steps:

  1. Sending a data request mail to the stdy director (christoph.dieterich@uni-heidelberg.de) including a signed DUA form, addressing information about correct data usage and security standards. Under this licence, it is clearly prohibited, to identify individuals or try to contact or advertise them.
  2. including a group description and a project description (details, see below).
  3. After a positive decision by the CARDIO:DE study director Christoph Dieterich (CARDIO:DE supervisor), the data requestor will receive detailed instructions how to download the corpus via heiDATA.

Data approval will require at least one week.

The data request needs to contain the following information:

  1. A signed DUA, signed by each data user individually.
  2. A group description including the requestor's (data user’s) name, affiliation, position and email address and website of the institution.
  3. A project description of the research purpose (max. 150 words)
  4. Name, affiliation, position, email address and signature of the responsible person to administer and manage the infrastructure on which CARDIO:de will be stored.

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