September 30, 2013 Report Open Access

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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  <identifier identifierType="DOI">10.5281/zenodo.3970778</identifier>
  <creators>
    <creator>
      <creatorName>Kristina Hettne</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Marco Roos</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Eleni Mina</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Eelke van de Horst</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Harish Dharuri</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Mark Thompson</creatorName>
      <affiliation>Leiden University Medical Centre (LUMC)</affiliation>
    </creator>
    <creator>
      <creatorName>Don Cruickshank</creatorName>
      <affiliation>University of Oxford</affiliation>
    </creator>
    <creator>
      <creatorName>Stian Soiland-Reyes</creatorName>
      <affiliation>University of Manchester</affiliation>
    </creator>
    <creator>
      <creatorName>Sander van Boom</creatorName>
      <affiliation>University of Applied Sciences Leiden</affiliation>
    </creator>
  </creators>
  <titles>
    <title>D6.3v3: Genome Wide Association Study Workflows v3</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2013</publicationYear>
  <subjects>
    <subject>Huntington's Disease</subject>
    <subject>Research Objects</subject>
    <subject>Metabolic Syndrome</subject>
    <subject>GWAS</subject>
    <subject>epiGenetics</subject>
    <subject>workflows</subject>
    <subject>research object</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2013-09-30</date>
  </dates>
  <resourceType resourceTypeGeneral="Report"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">http://web.archive.org/web/20151004031737/http://repo.wf4ever-project.org/dlibra/docmetadata?id=oai:repo.wf4ever-project.org:52</alternateIdentifier>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3970778</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3967615</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ro</relatedIdentifier>
  </relatedIdentifiers>
  <version>Wf4ever/2010/D6.3v3/v1.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/3.0/legalcode">Creative Commons Attribution 3.0 Unported</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
    <description descriptionType="Other">Wf4Ever Deliverable 
Identifier: oai:repo.wf4ever-project.org:52</description>
    <description descriptionType="Other">{"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"]}</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/270192/">270192</awardNumber>
      <awardTitle>Advanced Workflow Preservation Technologies for Enhanced Science</awardTitle>
    </fundingReference>
  </fundingReferences>
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