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  <doc>
    <id>8449</id>
    <completedYear/>
    <publishedYear>2021</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>5854</issue>
    <volume>12</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A proteomics sample metadata representation for multiomics integration and big data analysis</title>
    <abstract language="eng">The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.</abstract>
    <parentTitle language="eng">Nature Communications</parentTitle>
    <identifier type="doi">https://doi.org/10.1038/s41467-021-26111-3</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2021-09-16</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <author>Chengxin Dai</author>
    <submitter>Julianus Pfeuffer</submitter>
    <author>Anja Füllgrabe</author>
    <author>Julianus Pfeuffer</author>
    <author>Elizaveta M. Solovyeva</author>
    <author>Jingwen Deng</author>
    <author>Pablo Moreno</author>
    <author>Selvakumar Kamatchinathan</author>
    <author>Deepti Jaiswal Kundu</author>
    <author>Nancy George</author>
    <author>Silvie Fexovy</author>
    <author>Björn Grüning</author>
    <author>Melanie Christine Föll</author>
    <author>Johannes Griss</author>
    <author>Marc Vaudel</author>
    <author>Enrique Audain</author>
    <author>Marie Locard-Paulet</author>
    <author>Michael Turewicz</author>
    <author>Martin Eisenacher</author>
    <author>Julian Uszkoreit</author>
    <author>Tim Van Den Bossche</author>
    <author>Veit Schwämmle</author>
    <author>Henry Webel</author>
    <author>Stefan Schulze</author>
    <author>David Bouyssié</author>
    <author>Savita Jayaram</author>
    <author>Vinay Kumar Duggineni</author>
    <author>Patroklos Samaras</author>
    <author>Mathias Wilhelm</author>
    <author>Meena Choi</author>
    <author>Mingxun Wang</author>
    <author>Oliver Kohlbacher</author>
    <author>Alvis Brazma</author>
    <author>Irene Papatheodorou</author>
    <author>Nuno Bandeira</author>
    <author>Eric W. Deutsch</author>
    <author>Juan Antonio Vizcaíno</author>
    <author>Mingze Bai</author>
    <author>Timo Sachsenberg</author>
    <author>Lev I. Levitsky</author>
    <author>Yasset Perez-Riverol</author>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
</export-example>
