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D1.8 Tools Interoperability and Service Registry

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


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    "description": "<p>The objective of EXCELERATE Deliverable 1.8, as stated in the original proposal, was to&nbsp;analyse the data format-usage landscape of tools registered the ELIXIR Tools and Data&nbsp;Services Registry (bio.tools) to provide a basis for targeted software developments to&nbsp;improve interoperability of registered tools. We originally foresaw those developments to&nbsp;be facilitated via a &ldquo;Matchmaking Service mechanism&rdquo; possibly including conversion of&nbsp;tools to use common formats, and development of format converter software where&nbsp;needed. Whilst such specific developments are laudable, it is now obvious that significant&nbsp;progress depends on the bioinformatics community at large, and requires vastly greater&nbsp;capacity than WP1 has at its disposal.</p>\n\n<p>Instead, we took a much more targeted approach, focussing - as an exemplar - upon the&nbsp;systematic curation of tools for proteomics data analysis, and subsequent exploitation of&nbsp;the annotations for automated workflow composition. The work addresses the challenge&nbsp;of tool interoperability and is a major stride in delivering a practical &ldquo;Matchmaking Service&nbsp;mechanism&rdquo;. The work is described in two articles:</p>\n\n<p>\u25cf Tsiamis, V., Ienasescu, H., Palmblad, M. Schw&auml;mmle, V. and Ison J. Community&nbsp;curation&nbsp;of&nbsp;software&nbsp;tools&nbsp;as&nbsp;illustrated&nbsp;for&nbsp;mass&nbsp;spectrometry&nbsp;based&nbsp;proteomics&nbsp;In&nbsp;preparation&uml;see https://tinyurl.com/proteomics-tools&nbsp;</p>\n\n<p>Palmblad, M., Lamprecht, A., Ison, J. and Schw&auml;mmle, V. (2018). Automated&nbsp;workflow&nbsp;composition&nbsp;in&nbsp;mass&nbsp;spectrometry&nbsp;based&nbsp;proteomics&nbsp;Accepted for&nbsp;publication in Bioinformatics&nbsp;</p>\n\n<p>The first article (Tsiamis et&dagger;al&dagger;.) describes a systematic approach towards the&nbsp;comprehensive coverage in bio.tools of the prevalent tools for proteomics data analysis,&nbsp;including expert curation of many tools to a high standard including consistent annotation&nbsp;of data formats and operation using the EDAM ontology. The second (Palmblad et&nbsp;al)&nbsp;explores automated workflow composition from the tool semantic annotation, and&nbsp;provides a toolkit to support researchers in identifying, comparing and benchmarking&nbsp;multiple workflows from individual bioinformatics tools.</p>\n\n<p>For this deliverable report, we link to and summarise the publications in press. The&nbsp;project files and workflows are freely available:</p>\n\n<p>\u25cf https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Co&nbsp;mposition</p>", 
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        "title": "ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.", 
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        "name": "Palmblad, Magnus"
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