Christina Lohr

About Christina Lohr:

  • since 2023: Research Assistant at IMISE of Leipzig University

  • 2016 - 2022: Research Assistant at JULIE Lab of Friedrich Schiller University Jena

  • 2015 - 2016: Research Assistant at Chemnitz University of Technology, Chair Media Informatics and Chair Practical Computer Science

  • 2007 - 2015: Student Assistant at Klinikum Chemnitz (Klinik für Allgemein- und Viszeralchirurgie)

  • 2012 - 2015: Studies of Computer Science at Chemnitz University of Technology (Master of Science)

  • 2007 - 2012: Studies of Applied Computer Science at Chemnitz University of Technology (Bachelor of Science)

  • Twitter: chlor89

  • Github: chlor

  • ResearcheGate: https://www.researchgate.net/profile/Christina-Lohr-2

  • Google Scholar: https://scholar.google.com/citations?user=NEyGC4AAAAAJ

LHA ID: 852PCVY5YC-8

Location:  Germany

ORCID: https://orcid.org/0000-0001-9889-162X

Joined: 16th Dec 2020

Expertise: Not specified

Tools: spaCy, Python

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Related items

SMITH - Smart Medical Information Technology for Healthcare

Medical data routinely generated in everyday clinical practice is processed and made available to medical research in a standardized form. Patients benefit from reliable research results, more precise diagnoses and better treatments. In order to link data from care and research, the participating university hospitals in Aachen, Bonn, Essen, Halle, Hamburg, Jena and Leipzig have established sustainable Data Integration Centers. The network partners Ruhr University Bochum, the Düsseldorf University ...

Programme: MII - Medical Informatics Initiative

Public web page: https://www.smith.care/

Start date: 1st Jan 2018

Methodical Use Case PheP - NLP
Methodical Use Case PheP

One of the challenges of Phenotypingt is that too little clinical information is available as machine-readable data sets. Admission letters, findings and operating room reports in particular contain valuable information such as diagnoses, medications, side effects and laboratory data that can only be extracted using methods of natural language processing and semantic text analysis methods. Natural Language Processing (NLP) is used to process documents from the Hospital Information System (HIS). ...

Submitter: Frank A. Meineke

Studies: No Studies

Resources: No Resources

GRASCCO — The First Publicly Shareable, Multiply-Alienated German Clinical Text Corpus
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We describe the creation of GRASCCO, a novel German-language corpus composed of some 60 clinical documents with more than.43,000 tokens. GRASCCO is a synthetic corpus resulting from a series of alienation … steps to obfuscate privacy-sensitive information contained in real clinical documents, the true origin of all GRASCCO texts. Therefore, it is publicly shareable without any legal restrictions We also explore whether this corpus still represents common clinical language use by comparison with a real (non-shareable) clinical corpus we developed as a contribution to the Medical Informatics Initiative in Germany (MII) within the SMITH consortium. We find evidence that such a claim can indeed be made.

Editor:

Date Published: 17th Aug 2022

Publication Type: InProceedings

GRASCCO — the first publicly shareable, multiply-alienated German clinical text corpus
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We describe the creation of GRASCCO, a novel German-language corpus composed of some 60 clinical documents with more than.43,000 tokens. GRASCCO is a synthetic corpus resulting from a series of alienation … steps to obfuscate privacy-sensitive information contained in real clinical documents, the true origin of all GRASCCO texts. Therefore, it is publicly shareable without any legal restrictions We also explore whether this corpus still represents common clinical language use by comparison with a real (non-shareable) clinical corpus we developed as a contribution to the Medical Informatics Initiative in Germany (MII) within the SMITH consortium. We find evidence that such a claim can indeed be made.

Authors: Luise Modersohn, Stefan Schulz, Christina Lohr, Udo Hahn

Date Published: 1st Aug 2022

Publication Type: InCollection

GGPONC 2.0 — The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

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.

Editor: 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

Date Published: 19th Jun 2022

Publication Type: Journal article

Pseudonymization of PHI Items in German Clinical Reports
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We describe the adaptation of a non-clinical pseudonymization system, originally developed for a German email corpus, for clinical use. This tool replaces previously identified Protected Health Information … (PHI) items as carriers of privacy-sensitive information (original names for people, organizations, places, etc.) with semantic type-conformant, yet, fictitious surrogates. We evaluate the generated substitutes for grammatical correctness, semantic and medical plausibility and find particularly low numbers of error instances (less than 1%) on all of these dimensions.

Editor:

Date Published: 27th May 2021

Publication Type: Journal article

Pseudonymization of PHI items in German clinical reports
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We describe the adaptation of a non-clinical pseudonymization system, originally developed for a German email corpus, for clinical use. This tool replaces previously identified Protected Health Information … (PHI) items as carriers of privacy-sensitive information (original names for people, organizations, places, etc.) with semantic type-conformant, yet, fictitious surrogates. We evaluate the generated substitutes for grammatical correctness, semantic and medical plausibility and find particularly low numbers of error instances (less than 1%) on all of these dimensions.

Authors: Christina Lohr, Elisabeth Eder, Udo Hahn

Date Published: 1st May 2021

Publication Type: InCollection

An Evolutionary Approach to the Annotation of Discharge Summaries.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to … their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Authors: C. Lohr, L. Modersohn, J. Hellrich, T. Kolditz, U. Hahn

Date Published: 16th Jun 2020

Publication Type: InProceedings

An evolutionary approach to the annotation of discharge summaries
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to … their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Authors: Christina Lohr, Luise Modersohn, Johannes Hellrich, Tobias Kolditz, Udo Hahn

Date Published: 1st Jun 2020

Publication Type: Journal article

Annotating German Clinical Documents for De-Identification.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We devised annotation guidelines for the de-identification of German clinical documents and assembled a corpus of 1,106 discharge summaries and transfer letters with 44K annotated protected health … information (PHI) items. After three iteration rounds, our annotation team finally reached an inter-annotator agreement of 0.96 on the instance level and 0.97 on the token level of annotation (averaged pair-wise F1 score). To establish a baseline for automatic de-identification on our corpus, we trained a recurrent neural network (RNN) and achieved F1 scores greater than 0.9 on most major PHI categories.

Authors: T. Kolditz, C. Lohr, J. Hellrich, L. Modersohn, B. Betz, M. Kiehntopf, U. Hahn

Date Published: 21st Aug 2019

Publication Type: InProceedings

3000PA-Towards a National Reference Corpus of German Clinical Language
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We introduce 3000PA, a clinical document corpus composed of 3,000 EPRs from three different clinical sites, which will serve as the backbone of a national reference language resource for German clinical … NLP. We outline its design principles, results from a medication annotation campaign and the evaluation of a first medication information extraction prototype using a subset of 3000PA.

Authors: U. Hahn, F. Matthies, C. Lohr, Markus Löffler

Date Published: 24th Apr 2018

Publication Type: InProceedings

GraSCCo - Graz Synthetic Clinical text Corpus
SMITH - Smart Medical Information Technology for Healthcare
No description specified

Creator: Christina Lohr

Submitter: Christina Lohr

MII - Medical Informatics Initiative

The medical informatics initiative was created to close the gap between research and healthcare. All of Germany’s university hospitals have joined forces with research institutions, businesses, health insurers, and patient advocacy groups to create a framework that harnesses research findings to the direct benefit of patients. The German Federal Ministry of Education and Research (BMBF) is investing around 160 million euros in the programme through 2021. The digitisation of medicine is creating ...

Projects: Methodical Use Case PheP, SMITH - Smart Medical Information Technology for Healthcare, POLAR - Polypharmacy, Drug Interactions, Risks

Web page: https://www.medizininformatik-initiative.de/en

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