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958 Publications visible to you, out of a total of 958
Challenges and experiences extending the cBioPortal for cancer genomics to a molecular tumor board platform
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

In Molecular Tumor Boards (MTBs), therapy recommendations for cancer patients are discussed. To aid decision-making based on the patient’s molecular profile, the research platform cBioPortal was extended … based on users’ requirements. Additionally, a comprehensive dockerized workflow was developed to support the deployment of cBioPortal and connected services. In this work, we present the challenges and experiences of nearly two years of implementing and deploying an MTB platform based on cBioPortal and compare those to findings of a previous study.

Authors: Niklas Reimer, Philipp Unberath, Hauke Busch, Melanie Börries, Patrick Metzger, Arsenij Ustjanzew, Christopher Renner, Hans-Ulrich Prokosch, Jan Christoph

Date Published: 1st Nov 2021

Publication Type: InCollection

A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy.
Leipzig Melanoma Studies, oBIG - omics Bioinformatics for Health

Abstract (Expand)

Genetic splice variants have become of central interest in recent years, as they play an important role in different cancers. Little is known about splice variants in melanoma. Here, we analyzed a … genome-wide transcriptomic dataset of benign melanocytic nevi and primary melanomas (n = 80) for the expression of specific splice variants. Using kallisto, a map for differentially expressed splice variants in melanoma vs. benign melanocytic nevi was generated. Among the top genes with differentially expressed splice variants were Ras-related in brain 6B (RAB6B), a member of the RAS family of GTPases, Macrophage Scavenger Receptor 1 (MSR1), Collagen Type XI Alpha 2 Chain (COLL11A2), and LY6/PLAUR Domain Containing 1 (LYPD1). The Gene Ontology terms of differentially expressed splice variants showed no enrichment for functional gene sets of melanoma vs. nevus lesions, but between type 1 (pigmentation type) and type 2 (immune response type) melanocytic lesions. A number of genes such as Checkpoint Kinase 1 (CHEK1) showed an association of mutational patterns and occurrence of splice variants in melanoma. Moreover, mutations in genes of the splicing machinery were common in both benign nevi and melanomas, suggesting a common mechanism starting early in melanoma development. Mutations in some of these genes of the splicing machinery, such as Serine and Arginine Rich Splicing Factor A3 and B3 (SF3A3, SF3B3), were significantly enriched in melanomas as compared to benign nevi. Taken together, a map of splice variants in melanoma is presented that shows a multitude of differentially expressed splice genes between benign nevi and primary melanomas. The underlying mechanisms may involve mutations in genes of the splicing machinery.

Authors: S. Hakobyan, H. Loeffler-Wirth, A. Arakelyan, H. Binder, M. Kunz

Date Published: 2nd Jul 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.

Editor:

Date Published: 27th May 2021

Publication Type: Journal article

Ontological Modelling and Execution of Phenotypic Queries in the Leipzig Health Atlas.
LHA - Leipzig Health Atlas, Onto-Med Research Group, SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Sharing data is of great importance for research in medical sciences. It is the basis for reproducibility and reuse of already generated outcomes in new projects and in new contexts. FAIR data principles … are the basics for sharing data. The Leipzig Health Atlas (LHA) platform follows these principles and provides data, describing metadata, and models that have been implemented in novel software tools and are available as demonstrators. LHA reuses and extends three different major components that have been previously developed by other projects. The SEEK management platform is the foundation providing a repository for archiving, presenting and secure sharing a wide range of publication results, such as published reports, (bio)medical data as well as interactive models and tools. The LHA Data Portal manages study metadata and data allowing to search for data of interest. Finally, PhenoMan is an ontological framework for phenotype modelling. This paper describes the interrelation of these three components. In particular, we use the PhenoMan to, firstly, model and represent phenotypes within the LHA platform. Then, secondly, the ontological phenotype representation can be used to generate search queries that are executed by the LHA Data Portal. The PhenoMan generates the queries in a novel domain specific query language (SDQL), which is specific for data management systems based on CDISC ODM standard, such as the LHA Data Portal. Our approach was successfully applied to represent phenotypes in the Leipzig Health Atlas with the possibility to execute corresponding queries within the LHA Data Portal.

Authors: A. Uciteli, C. Beger, J. Wagner, A. Kiel, F. A. Meineke, S. Staubert, M. Lobe, R. Hansel, J. Schuster, T. Kirsten, H. Herre

Date Published: 24th May 2021

Publication Type: Journal article

Concept and implementation of data usage proposal process based on international standards in SMITH
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Accessing secondary-use healthcare data in Germany requires contracting with each organization that acts as a data provider. The SMITH Service Platform offers a central access point for scientists, … facilitating contracting as part of an integrated data use and access process with several Data Integration Centers (DIC) at once. Process support is realized by a central Business Process Engine (BPE), which manages process definition and process control, combined with a central IHE infrastructure. The use of IHE XDS and IHE XDW profiles enables the exchange of process instance information with multiple distributed visualization and user interaction tools for provided user tasks based on international standards. User task information include structured forms for submitting instructions and results as task input and output for the users, and are synchronized between the shared process instance and the BPE. A reference user interface is also provided with the SMITH Marketplace. In the future, further standardization efforts regarding the structured forms and the use of the IHE XDW profile should be pursued.

Authors: Marcel Klötgen, Eric Fiege, Salima Houta

Date Published: 1st May 2021

Publication Type: InCollection

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

Health Informatics learning objectives on an interoperable, collaborative platform
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Catalogues of learning objectives for Biomedical and Health Informatics are relevant prerequisites for systematic and effective qualification. Catalogue management needs to integrate different catalogues … and support collaborative revisioning. The Health Informatics Learning Objectives Navigator (HI-LONa) offers an open, interoperable platform based on Semantic Web Technology. At present HI-LONa contains 983 learning objectives of three relevant catalogues. HI-LONa successfully supported a multiprofessional consensus process.

Authors: Cord Spreckelsen, Ulrike Schemmann, Lo An Phan-Vogtmann, André Scherag, Alfred Winter, Birgit Schneider

Date Published: 1st May 2021

Publication Type: Journal article

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The Health Atlas - Local Data Hub/Leipzig is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research fields.

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