A reference set of curated biomedical data and metadata from clinical case reports View Full Text


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Article Info

DATE

2018-11-20

AUTHORS

J. Harry Caufield, Yijiang Zhou, Anders O. Garlid, Shaun P. Setty, David A. Liem, Quan Cao, Jessica M. Lee, Sanjana Murali, Sarah Spendlove, Wei Wang, Li Zhang, Yizhou Sun, Alex Bui, Henning Hermjakob, Karol E. Watson, Peipei Ping

ABSTRACT

Clinical case reports (CCRs) provide an important means of sharing clinical experiences about atypical disease phenotypes and new therapies. However, published case reports contain largely unstructured and heterogeneous clinical data, posing a challenge to mining relevant information. Current indexing approaches generally concern document-level features and have not been specifically designed for CCRs. To address this disparity, we developed a standardized metadata template and identified text corresponding to medical concepts within 3,100 curated CCRs spanning 15 disease groups and more than 750 reports of rare diseases. We also prepared a subset of metadata on reports on selected mitochondrial diseases and assigned ICD-10 diagnostic codes to each. The resulting resource, Metadata Acquired from Clinical Case Reports (MACCRs), contains text associated with high-level clinical concepts, including demographics, disease presentation, treatments, and outcomes for each report. Our template and MACCR set render CCRs more findable, accessible, interoperable, and reusable (FAIR) while serving as valuable resources for key user groups, including researchers, physician investigators, clinicians, data scientists, and those shaping government policies for clinical trials. More... »

PAGES

180258

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/sdata.2018.258

    DOI

    http://dx.doi.org/10.1038/sdata.2018.258

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1110033193

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30457569


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    337 The NIH BD2K Center of Excellence in Biomedical Computing, University of California at Los Angeles, 90095, Los Angeles, CA, USA
    338 rdf:type schema:Organization
    339 grid-institutes:grid.225360.0 schema:alternateName Molecular Systems Cluster, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
    340 schema:name Molecular Systems Cluster, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
    341 The NIH BD2K Center of Excellence in Biomedical Computing, University of California at Los Angeles, 90095, Los Angeles, CA, USA
    342 rdf:type schema:Organization
     




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