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D6.3v3: Genome Wide Association Study Workflows v3

Kristina Hettne; Marco Roos; Eleni Mina; Eelke van de Horst; Harish Dharuri; Mark Thompson; Don Cruickshank; Stian Soiland-Reyes; Sander van Boom


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    "references": [
      "Jelier R et al., Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol. 2008;9(6):R96.", 
      "Illig T et. al., A genome-wide perspective of genetic variation in human metabolism. Nature Genetics 2010, 42(2):137-41.", 
      "Hettne KM et al., Rewriting and suppressing UMLS terms for improved biomedical term identification. J Biomed Semantics. 2010 Mar 31;1(1):5.", 
      "Gardiner-Garden M and Frommer M, CpG Islands in Vertebrate Genomes. Journal of Molecular Biology 196, no. 2 (July 20, 1987): 261\u2013282.", 
      "Ernst J et al., Mapping and Analysis of Chromatin State Dynamics in Nine Human Cell Types.  Nature 473, no. 7345 (March 23, 2011): 43\u201349.", 
      "Hettne KM et al., Structuring research methods and data with the Research Object model: genomics workflows as a case study. Submitted to the Journal of Biomedical Semantics", 
      "Dharuri H et al., Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles. Submitted to BMC Genomics", 
      "Mina E et al., Hypotheses for epigenetic mechanisms in Huntington's Disease exposed by an e-Science approach. In preparation"
    ], 
    "keywords": [
      "Huntington's Disease", 
      "Research Objects", 
      "Metabolic Syndrome", 
      "GWAS", 
      "epiGenetics", 
      "workflows", 
      "research object"
    ], 
    "publication_date": "2013-09-30", 
    "creators": [
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Kristina Hettne"
      }, 
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Marco Roos"
      }, 
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Eleni Mina"
      }, 
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Eelke van de Horst"
      }, 
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Harish Dharuri"
      }, 
      {
        "affiliation": "Leiden University Medical Centre (LUMC)", 
        "name": "Mark Thompson"
      }, 
      {
        "affiliation": "University of Oxford", 
        "name": "Don Cruickshank"
      }, 
      {
        "affiliation": "University of Manchester", 
        "name": "Stian Soiland-Reyes"
      }, 
      {
        "affiliation": "University of Applied Sciences Leiden", 
        "name": "Sander van Boom"
      }
    ], 
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    "description": "<p>This document describes the workflows developed during phase III of the project at the <em>Human Genetics Department</em> of the <em>Leiden University Medical Centre</em> (HG-LUMC) for interpreting results from <em>genome-wide association</em> (GWA) studies and for gene expression data related to <em>Huntington&rsquo;s disease</em>.</p>\n\n<p>The main goal of this deliverable is to produce <strong>workflows</strong>. At the same time, we applied the <em>tooling</em> and <em>best practices</em> that are emerging from the project to aggregate the workflow and associated material as a preserved &ldquo;<strong>Research Object</strong>&rdquo; (RO).</p>\n\n<p>A detailed description about the state of the current tooling can be found in <em>D1.4v2</em>. Workflows form a crucial part of the data to populate the RO models and software in <em>Wf4Ever</em>, and the HG-LUMC is committed to producing good quality workflows that can be preserved.</p>\n\n<p>Finally, we characterize the workflows according to current state of workflow preservation and archived them according to the project tooling.</p>"
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