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Sökning: WFRF:(Vihinen M) > (2015-2019)

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1.
  • Deans, Andrew R, et al. (författare)
  • Finding Our Way through Phenotypes.
  • 2015
  • Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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5.
  • Vihinen, Mauno, et al. (författare)
  • Human Variome Project Quality Assessment Criteria for Variation Databases.
  • 2016
  • Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 37:6, s. 549-549
  • Tidskriftsartikel (refereegranskat)abstract
    • Numerous databases containing information about DNA, RNA and protein variations are available. Gene-specific variant databases (locus specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. This article is protected by copyright. All rights reserved.
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