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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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    <dct:title>D6.3v3: Genome Wide Association Study Workflows v3</dct:title>
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    <dcat:keyword>Huntington's Disease</dcat:keyword>
    <dcat:keyword>Research Objects</dcat:keyword>
    <dcat:keyword>Metabolic Syndrome</dcat:keyword>
    <dcat:keyword>GWAS</dcat:keyword>
    <dcat:keyword>epiGenetics</dcat:keyword>
    <dcat:keyword>workflows</dcat:keyword>
    <dcat:keyword>research object</dcat:keyword>
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    <dct:description>&lt;p&gt;This document describes the workflows developed during phase III of the project at the &lt;em&gt;Human Genetics Department&lt;/em&gt; of the &lt;em&gt;Leiden University Medical Centre&lt;/em&gt; (HG-LUMC) for interpreting results from &lt;em&gt;genome-wide association&lt;/em&gt; (GWA) studies and for gene expression data related to &lt;em&gt;Huntington&amp;rsquo;s disease&lt;/em&gt;.&lt;/p&gt; &lt;p&gt;The main goal of this deliverable is to produce &lt;strong&gt;workflows&lt;/strong&gt;. At the same time, we applied the &lt;em&gt;tooling&lt;/em&gt; and &lt;em&gt;best practices&lt;/em&gt; that are emerging from the project to aggregate the workflow and associated material as a preserved &amp;ldquo;&lt;strong&gt;Research Object&lt;/strong&gt;&amp;rdquo; (RO).&lt;/p&gt; &lt;p&gt;A detailed description about the state of the current tooling can be found in &lt;em&gt;D1.4v2&lt;/em&gt;. Workflows form a crucial part of the data to populate the RO models and software in &lt;em&gt;Wf4Ever&lt;/em&gt;, and the HG-LUMC is committed to producing good quality workflows that can be preserved.&lt;/p&gt; &lt;p&gt;Finally, we characterize the workflows according to current state of workflow preservation and archived them according to the project tooling.&lt;/p&gt;</dct:description>
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    <dct:description>{"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"]}</dct:description>
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