JSynCC: Jena Synthetic Clinical Corpus

This is the software to create the corpus JSynCC 2.0, the second version of Jena Synthetic Clinical Corpus (April 2026).

Before Usage: Request Content of Corpus

• Subscribe the following text books as PDF files and load them into the given directories:

  • 01: "Operationsberichte Orthopädie und Unfallchirurgie", Author / Editor: Siekmann, H., Irlenbusch, L., Klima, S., Publisher: Springer-Verlag, Edition: 2. Auflage, DOI: 10.1007/978-3-662-48881-2.
    • → store sources under source: books/01-Operationsberichte-Orthopaedie-und-Unfallchirurgie/978-3-662-48881-2.pdf
  • 02: "Operationsberichte Orthopädie: mit speziellen unfallchirurgisch-orthopädischen Eingriffen", Author / Editor: Siekmann, H., Klima, S., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-642-20790-7.
    • → store sources under source: books/02-Operationsberichte-Orthopaedie/978-3-642-20790-7.pdf
  • 03: "Operationsberichte Unfallchirurgie", Author / Editor: Siekmann, H., Irlenbusch, L., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-642-20784-6.
    • → store sources under source: books/03-Operationsberichte-Unfallchirurgie/978-3-642-20784-6.pdf
  • 04: "Operationsberichte für Einsteiger-Chirurgie: Operation vorbereiten—Bericht diktieren", Author / Editor: Hagen, M., Publisher: Georg-Thieme-Verlag, Edition: -, DOI: 10.1055/b-002-39790.
    • → store sources under source: books/04-Operationsberichte-fuer-Einsteiger/pdf
  • 05: "Fallbeispiele Notfallmedizin: Einprägsam-spannend-mit Lerneffekt", Author / Editor: Wenzel, V., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-47232-3.
    • → store sources under source: books/05-Fallbeispiele-Notfallmedizin/978-3-662-47232-3.pdf
  • 06: "Fallbuch Chirurgie: 140 Fälle aktiv bearbeiten", Author / Editor: Eisoldt, S., Publisher: Georg-Thieme-Verlag, Edition: 5., unveränderte Auflage, DOI: 10.1055/b-004-140674.
    • → store sources under source: books/06-Fallbuch-Chirurgie
  • 07: "Komplikationen in der Anästhesie", Author / Editor: Hübler, M., Koch, T., Publisher: Springer-Verlag, Edition: 3., überarbeitete Auflage, DOI: 10.1007/978-3-662-43440-6.
    • → store sources under source: books/07-Komplikationen-in-der-Anaesthesie/978-3-662-43440-6.pdf
  • 08: "Basiswissen Medizin des Alterns und des alten Menschen", Author / Editor: Zeyfang, A., Denkinger, M., Hagg-Grün, U., Publisher: Springer-Verlag, Edition: 2., überarbeitete Auflage, DOI: 10.1007/978-3-642-28905-7.
    • → store sources under source: books/08-Basiswissen Medizin-des-Alterns-und-des-alten-Menschen/978-3-642-28905-7.pdf
  • 09: "Praxis der Intensivmedizin", Author / Editor: Wilhelm, W., Publisher: Springer-Verlag, Edition: 2., aktualisierte und erweiterte Auflage, DOI: 10.1007/978-3-642-34433-6.
    • → store sources under source: books/09-Praxis-der-Intensivmedizin/978-3-642-34433-6.pdf
  • 10: "Patienten aus fremden Kulturen im Notarzt- und Rettungsdienst: Fallbeispiele und Praxistipps", Author / Editor: Machado, C., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-642-34869-3.
    • → store sources under source: books/10-Patienten-aus-fremden-Kulturen-im-Notarzt-und-Rettungsdienst-Fallbeispiele-und-Praxistipps/978-3-642-34869-3.pdf
  • 11: "Fallbeispiele Augenheilkunde", Author / Editor: Thiel, M.A., Bernauer, W., Schüpfer, M.Z., Schmid, M.K., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-642-42219-5.
    • → store sources under source: books/11-Fallbeispiele-Augenheilkunde/978-3-642-42219-5.pdf
  • 12: "Patientenorientierte Beratung in der Pflege Leitfäden und Fallbeispiele", Author / Editor: von Reibnitz, C., Sonntag, K., Strackbein, D., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-53028-3.
    • → store sources under source: books/12-Patientenorientierte-Beratung-in-der-Pflege/978-3-662-53028-3.pdf
  • 13: "Polyneuropathie", Author / Editor: Zifko, U., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-53871-5.
    • → store sources under source: books/13-Polyneuropathie/978-3-662-53871-5.pdf
  • 14: "Rheumatologie aus der Praxis: Ein Kurzlehrbuch der entzündlichen Gelenkerkrankungen mit Fallbeispielen", Author / Editor: Puchner, R. (Eds.), Publisher: Springer-Verlag, Edition: Zweite, überarbeitete und erweiterte Auflage, DOI: 10.1007/978-3-7091-1044-7.
    • → store sources under source: books/14-Rheumatologie-aus-der-Praxis/978-3-7091-1044-7.txt
  • 15: "Pädiatrie", Author / Editor: Speer, C.P., Gahr, M., Publisher: Springer-Verlag, Edition: 4., überarbeitete Auflage, DOI: 10.1007/978-3-642-34269-1.
    • → store sources under source: books/15-Pädiatrie/978-3-642-34269-1.pdf
  • 16: "Fallbuch Innere Medizin", Author / Editor: Hellmich, B., Publisher: Georg-Thieme-Verlag, Edition: 5., vollständig überarbeitete Auflage, DOI: 10.1055/b-0037-142744.
    • → store sources under source: books/16-Fallbuch-Innere-Medizin
  • 17: "Manual Jungenmedizin", Author / Editor: Stier, B., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-658-17323-4.
    • → store sources under source: books/17-Manual-Jungenmedizin/978-3-658-17323-4.pdf
  • 18: "Kindernotfälle im Rettungsdienst", Author / Editor: Flake, F., Steinichen, F., Publisher: Springer-Verlag, Edition: 5., aktualisierte Auflage, DOI: 10.1007/978-3-662-49305-2.
    • → store sources under source: books/18-Kindernotfälle-im-Rettungsdienst/978-3-662-49305-2.pdf
  • 19: "Basiswissen Radiologie: Nuklearmedizin und Strahlentherapie", Author / Editor: Kahl-Scholz, M., Vockelmann, C. (Eds.), Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-54278-1.
    • → store sources under source: books/19-Basiswissen-Radiologie/978-3-662-54278-1.pdf
  • 20: "Der klinisch-infektiologische Fall", Author / Editor: Geiss, H.K., Jacobs, E., Mack, D., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-540-69847-0.
    • → store sources under source: books/20-Der-klinisch-infektiologische-Fall/978-3-540-69847-0.pdf
  • 21: "Basiswissen Humangenetik", Author / Editor: Schaaf, C., Zschocke, J., Publisher: Springer-Verlag, Edition: 2., überarbeitete Auflage, DOI: 10.1007/978-3-642-28907-1.
    • → store sources under source: books/21-Basiswissen-Humangenetik/978-3-642-28907-1.pdf
  • 22: "Sportkardiologie", Author / Editor: Niebauer, J., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-43711-7
    • → store sources under source: books/22-Sportkardiologie/978-3-662-43711-7.pdf
  • 23: "Allgemeine und Spezielle Pathologie", Author / Editor: Riede, U.-N., Werner, M., Publisher: Springer-Verlag, Edition: 2., überarbeitete Auflage, DOI: 10.1007/978-3-662-48725-9.
    • → store sources under source: books/23-Allgemeine-und-Spezielle-Pathologie/2017_Book_AllgemeineUndSpeziellePatholog.pdf
  • 24: "Akutes Abdomen im Kindes-und Jugendalter", Author / Editor: Mayr, J., Fasching, G., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-55995-6.
    • → store sources under source: books/24-Akutes-Abdomen-im-Kindes-und-Jugendalter/2018_Book_AkutesAbdomenImKindes-UndJugen.pdf
  • 25: "Operationsberichte Allgemein-, Viszeral-, Gefäß- und Thoraxchirurgie", Author / Editor: Richter, O., Uhlmann, D., Publisher: Springer-Verlag, Edition: 2. Auflage, DOI: 10.1007/978-3-662-57283-2.
    • → store sources under source: books/25-Operationsberichte-Allgemein-Viszeral-Gefaeß-und-Thoraxchirurgie/2018_Book_OperationsberichteAllgemein-Vi.pdf
  • 26: "Nichtorganische Schlafstörungen", Author / Editor: Marx, C., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-50272-3.
    • → store sources under source: books/26-Nichtorganische-Schlafstörungen/2016_Book_NichtorganischeSchlafstörungen.pdf
  • 27: "Grundlegendes zur Allgemeinmedizin. Basiswissen Allgemeinmedizin", Author / Editor: Riedl, B., Peter W., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-53480-9.
    • → store sources under source: books/27-Basiswissen-Allgemein-Medizin/2017_Book_BasiswissenAllgemeinmedizin.pdf
  • 28: "Basiswissen Gynäkologie und Geburtshilfe", Author / Editor: Lasch, L., Fillenberg S., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-52809-9.
    • → store sources under source: books/28-Basiswissen-Gynäkologie/2017_Book_BasiswissenGynäkologieUndGebur.pdf
  • 29: "Ambulanzprotokolle Chirurgische Notfälle", Author / Editor: Siekmann, H., Publisher: Springer-Verlag, Edition: -, DOI: 10.1007/978-3-662-57651-9.
    • → store sources under source: books/29-Ambulanzprotokolle/2019_Book_AmbulanzprotokolleChirurgische.pdf
  • 30: "PubMed German Case Abstract",
    • Install Entres API from https://www.ncbi.nlm.nih.gov/books/NBK179288/
    • Open a terminal and run esearch -db pubmed -query "Case Reports[Publication Type] AND GER[LA]" | efetch -format xml > allGermanPubMedCaseAbstracts_JSynCC.xml
    • Wait some minutes!
    • JSynCC contains not all German PubMed Case Abstracts, only from this list.
    • → store sources under source: books/30-PubMed-Abstracts/allGermanPubMedCaseAbstracts_JSynCC.xml

Installation and Run

• Install Java and Maven and the packes from pom.xml

• The metadata of the named sources is stored under BookProperties.json. This file is adjusted by storage changes of the source files!

• This code works under Linux. The command-line tools pdftotext and pdftohtml are required. (It was run under Ubuntu.)

• Usage:

  • 'Main' file: BookReader.java
  • Open a terminal and run
    • mvn clean package
    • mvn exec:java -Dexec.mainClass="de.julielab.germanclinicaltext.readbooks.BookReader"
    • The full run needs around one hour.

Output of Corpus

Output is stored under directory output with some subdirectories:

• misc: contains different text outputs:

  • per every subcorpus one file with the extracted data
  • per every subcorpus one file with the extracted data in the mode of detected sentences
  • jsyncc-text.txt: text of full corpus in one file
  • jsyncc-tokens.txt: all tokens of full corpus

• txt: a folder with extracted single txt-files, it is named by an identifier of the original resource and the JSynCC internal document type. E.g.: Flake2016PediatricEmergencies-1-CaseDescription is extracted from "Kindernotfälle im Rettungsdienst" (Flake, F., Steinichen, F.; 2016) and part of the CaseDescription subcorpus.

• sentences: a folder with extracted single txt-files, one line contains one sentences, estimated by JCoRe pipelines, schema of names is extended with framed-sent

• tokens: a folder with extracted single txt-files, one line contains one tokens, estimated by JCoRe pipelines, schema of names is extended with framed-token

• stats: contains files with statistics of JSynCC 2.0's subcorpora and single files, statistics of sentences, tokens and types count by JCoRe pipelines.

• xml:

  • corpus.xml: XML file with corpus data, text and file names
  • output/xml/jsyncc-annotations.xml: XML file with annotations of sentences
  • md5Hex_checkSums.xml: File of md5 check sums for every extraced txt file.

• plots

  • some plots with corpus statistics created by scripts from python_scripts/stats/

Annotations

• JSynCC 2.0 is annotated
  • Sentences wise definition of Hl7-CDA section header definition
    • Annotation Rules
    • It is derived from: Christina Lohr, Stephanie Luther, Franz Matthies, Luise Modersohn, Danny Ammon, Kutaiba Saleh, Andreas G. Henkel, Michael Kiehntopf, and Udo Hahn: CDA-Compliant Section Annotation of German-Language Discharge Summaries: Guideline Development, Annotation Campaign, Section Classification. In: AMIA Annual Symposium Proceedings 2018, San Francisco, USA, Nov 3-7. [PMCID: PMC6371337]
    • Orig. Annotation Rules https://zenodo.org/records/7707756
    • Annotation files without textdata
    • Python-Skript to rebuild the annotations from JSynCC's output
  • Clinical entities & PII entities
    • Annotation Rules
    • It is derived from:
      • Tobias Kolditz, Christina Lohr, Johannes Hellrich, Luise Modersohn, Boris Betz, Michael Kiehntopf, Udo Hahn: Annotating German Clinical Documents for De-Identification (MedInfo 2019 Aug 25-30 Lyon France) [PMID:31437914] [DOI:10.3233/SHTI190212]
      • Christina Lohr, Luise Modersohn, Johannes Hellrich, Tobias Kolditz, Udo Hahn: An Evolutionary Approach to the of Discharge Summaries. In: Studies in Health Technology and Informatics, Vol. 270: Digital Personalized Health and Medicine - Proceedings of MIE 2020 [PMID: 32570340][DOI:10.3233/SHTI200116]
      • Orig. Annotation Rules:
        • https://zenodo.org/records/7707882
        • https://zenodo.org/records/7707917
      • Annotation files without textdata / offets
      • Python-Skript to rebuild the annotations from JSynCC's output

Some Python scripts

• python_scripts/stats/: contains some scripts to visualizing statistics of content of JSynCC

JSynCC 2.0 : Statistics

subcorpus	Documents	Sentences	Tokens	Types	Characters
OperativeReport	608	30.153	325.569	24.243	2.285.295
CaseDescription	264	11.761	185.385	24.958	1.167.095
CaseReport	600	6.353	105.369	16.208	692.122
ReportEmergency	153	6.021	50.606	8.560	351.160
Discussion	124	1.452	34.903	8.575	241.054
PubMedCaseAbstract	363	2.850	46.852	11.382	354.399
(Full) JSynCC 2.0	2.112	58.590	748.684	62.651	5.091.125

Licence

• MIT License: commercial use, modification, distribution, private use, no liability, no warranty.

About JSynCC 1 (2018)

• Code and documentation: https://github.com/julielab/jsyncc

• Look into the proceedings of LREC 2018:

  Christina Lohr,Sven Buechel and Udo Hahn: Sharing Copies of Synthetic Clinical Corpora without Physical Distribution — A Case Study to Get Around IPRs and Privacy Constraints Featuring the German JSYNCC Corpus

   @InProceedings{LOHR18.701,
     author = {Christina Lohr,Sven Buechel and Udo Hahn},
     title = {Sharing Copies of Synthetic Clinical Corpora without Physical Distribution — A Case Study to Get Around IPRs and Privacy Constraints Featuring the German JSYNCC Corpus},
     booktitle = {Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018)},
     year = {2018},
     month = {may},
     date = {7-12},
     publisher = {European Language Resources Association (ELRA)},
     isbn = {979-10-95546-00-9}
     }
  

About Version 1.1 (02/2020)

• During a expansion we revised all classes of the original JSynCC. We have new counts of the corpus:

  • Books: 10
  • Text Documents: 903
  • Sentences: 29476
  • Tokens: 368389