Project deliverable Open Access

D1.8 Tools Interoperability and Service Registry

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


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    <subfield code="a">&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;</subfield>
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