Project deliverable Open Access

D1.8 Tools Interoperability and Service Registry

Palmblad, Magnus; Lamprecht, Anna-Lena; Schwämmle, Veit; Ison, Jon


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  <identifier identifierType="DOI">10.5281/zenodo.1456766</identifier>
  <creators>
    <creator>
      <creatorName>Palmblad, Magnus</creatorName>
      <givenName>Magnus</givenName>
      <familyName>Palmblad</familyName>
      <affiliation>DTU</affiliation>
    </creator>
    <creator>
      <creatorName>Lamprecht, Anna-Lena</creatorName>
      <givenName>Anna-Lena</givenName>
      <familyName>Lamprecht</familyName>
      <affiliation>DTU</affiliation>
    </creator>
    <creator>
      <creatorName>Schwämmle, Veit</creatorName>
      <givenName>Veit</givenName>
      <familyName>Schwämmle</familyName>
      <affiliation>DTU</affiliation>
    </creator>
    <creator>
      <creatorName>Ison, Jon</creatorName>
      <givenName>Jon</givenName>
      <familyName>Ison</familyName>
      <affiliation>DTU</affiliation>
    </creator>
  </creators>
  <titles>
    <title>D1.8 Tools Interoperability and Service Registry</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <dates>
    <date dateType="Issued">2018-10-11</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Project deliverable</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1456766</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1456765</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The objective of EXCELERATE Deliverable 1.8, as stated in the original proposal, was to&amp;nbsp;analyse the data format-usage landscape of tools registered the ELIXIR Tools and Data&amp;nbsp;Services Registry (bio.tools) to provide a basis for targeted software developments to&amp;nbsp;improve interoperability of registered tools. We originally foresaw those developments to&amp;nbsp;be facilitated via a &amp;ldquo;Matchmaking Service mechanism&amp;rdquo; possibly including conversion of&amp;nbsp;tools to use common formats, and development of format converter software where&amp;nbsp;needed. Whilst such specific developments are laudable, it is now obvious that significant&amp;nbsp;progress depends on the bioinformatics community at large, and requires vastly greater&amp;nbsp;capacity than WP1 has at its disposal.&lt;/p&gt;

&lt;p&gt;Instead, we took a much more targeted approach, focussing - as an exemplar - upon the&amp;nbsp;systematic curation of tools for proteomics data analysis, and subsequent exploitation of&amp;nbsp;the annotations for automated workflow composition. The work addresses the challenge&amp;nbsp;of tool interoperability and is a major stride in delivering a practical &amp;ldquo;Matchmaking Service&amp;nbsp;mechanism&amp;rdquo;. The work is described in two articles:&lt;/p&gt;

&lt;p&gt;● Tsiamis, V., Ienasescu, H., Palmblad, M. Schw&amp;auml;mmle, V. and Ison J. Community&amp;nbsp;curation&amp;nbsp;of&amp;nbsp;software&amp;nbsp;tools&amp;nbsp;as&amp;nbsp;illustrated&amp;nbsp;for&amp;nbsp;mass&amp;nbsp;spectrometry&amp;nbsp;based&amp;nbsp;proteomics&amp;nbsp;In&amp;nbsp;preparation&amp;uml;see https://tinyurl.com/proteomics-tools&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Palmblad, M., Lamprecht, A., Ison, J. and Schw&amp;auml;mmle, V. (2018). Automated&amp;nbsp;workflow&amp;nbsp;composition&amp;nbsp;in&amp;nbsp;mass&amp;nbsp;spectrometry&amp;nbsp;based&amp;nbsp;proteomics&amp;nbsp;Accepted for&amp;nbsp;publication in Bioinformatics&amp;nbsp;&lt;/p&gt;

&lt;p&gt;The first article (Tsiamis et&amp;dagger;al&amp;dagger;.) describes a systematic approach towards the&amp;nbsp;comprehensive coverage in bio.tools of the prevalent tools for proteomics data analysis,&amp;nbsp;including expert curation of many tools to a high standard including consistent annotation&amp;nbsp;of data formats and operation using the EDAM ontology. The second (Palmblad et&amp;nbsp;al)&amp;nbsp;explores automated workflow composition from the tool semantic annotation, and&amp;nbsp;provides a toolkit to support researchers in identifying, comparing and benchmarking&amp;nbsp;multiple workflows from individual bioinformatics tools.&lt;/p&gt;

&lt;p&gt;For this deliverable report, we link to and summarise the publications in press. The&amp;nbsp;project files and workflows are freely available:&lt;/p&gt;

&lt;p&gt;● https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Co&amp;nbsp;mposition&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/676559/">676559</awardNumber>
      <awardTitle>ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.</awardTitle>
    </fundingReference>
  </fundingReferences>
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