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
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nam##2200000uu#4500</leader> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Jelier R et al., Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol. 2008;9(6):R96.</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Illig T et. al., A genome-wide perspective of genetic variation in human metabolism. Nature Genetics 2010, 42(2):137-41.</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Hettne KM et al., Rewriting and suppressing UMLS terms for improved biomedical term identification. J Biomed Semantics. 2010 Mar 31;1(1):5.</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Gardiner-Garden M and Frommer M, CpG Islands in Vertebrate Genomes. Journal of Molecular Biology 196, no. 2 (July 20, 1987): 261–282.</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Ernst J et al., Mapping and Analysis of Chromatin State Dynamics in Nine Human Cell Types. Nature 473, no. 7345 (March 23, 2011): 43–49.</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">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</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Dharuri H et al., Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles. Submitted to BMC Genomics</subfield> </datafield> <datafield tag="999" ind1="C" ind2="5"> <subfield code="x">Mina E et al., Hypotheses for epigenetic mechanisms in Huntington's Disease exposed by an e-Science approach. In preparation</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">Huntington's Disease</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">Research Objects</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">Metabolic Syndrome</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">GWAS</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">epiGenetics</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">workflows</subfield> </datafield> <datafield tag="653" ind1=" " ind2=" "> <subfield code="a">research object</subfield> </datafield> <controlfield tag="005">20200803125922.0</controlfield> <datafield tag="500" ind1=" " ind2=" "> <subfield code="a">Wf4Ever Deliverable Identifier: oai:repo.wf4ever-project.org:52</subfield> </datafield> <controlfield tag="001">3970778</controlfield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Marco Roos</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Eleni Mina</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Eelke van de Horst</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Harish Dharuri</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Mark Thompson</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">University of Oxford</subfield> <subfield code="a">Don Cruickshank</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">University of Manchester</subfield> <subfield code="a">Stian Soiland-Reyes</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">University of Applied Sciences Leiden</subfield> <subfield code="a">Sander van Boom</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">777728</subfield> <subfield code="z">md5:796b364e9d50acfa4038616c6302218d</subfield> <subfield code="u">https://zenodo.org/record/3970778/files/D6.3v3_v1.0.doc</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">776126</subfield> <subfield code="z">md5:390f9987ca0fdb37dda5c5873c766e7a</subfield> <subfield code="u">https://zenodo.org/record/3970778/files/D6.3v3_v1.0.pdf</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2013-09-30</subfield> </datafield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="p">openaire</subfield> <subfield code="p">user-ro</subfield> <subfield code="o">oai:zenodo.org:3970778</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="u">Leiden University Medical Centre (LUMC)</subfield> <subfield code="a">Kristina Hettne</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">D6.3v3: Genome Wide Association Study Workflows v3</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">user-ro</subfield> </datafield> <datafield tag="536" ind1=" " ind2=" "> <subfield code="c">270192</subfield> <subfield code="a">Advanced Workflow Preservation Technologies for Enhanced Science</subfield> </datafield> <datafield tag="540" ind1=" " ind2=" "> <subfield code="u">https://creativecommons.org/licenses/by/3.0/legalcode</subfield> <subfield code="a">Creative Commons Attribution 3.0 Unported</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a"><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> <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> <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> <p>Finally, we characterize the workflows according to current state of workflow preservation and archived them according to the project tooling.</p></subfield> </datafield> <datafield tag="773" ind1=" " ind2=" "> <subfield code="n">doi</subfield> <subfield code="i">isVersionOf</subfield> <subfield code="a">10.5281/zenodo.3967615</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.5281/zenodo.3970778</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="q">alternateidentifier</subfield> <subfield code="a">http://web.archive.org/web/20151004031737/http://repo.wf4ever-project.org/dlibra/docmetadata?id=oai:repo.wf4ever-project.org:52</subfield> <subfield code="2">url</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">publication</subfield> <subfield code="b">report</subfield> </datafield> </record>
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