D1.8 Tools Interoperability And Service Registry

The objective of EXCELERATE Deliverable 1.8, as stated in the original proposal, was toanalyse the data format-usage landscape of tools registered the ELIXIR Tools and DataServices Registry (bio.tools) to provide a basis for targeted software developments toimprove interoperability of registered tools. We originally foresaw those developments tobe facilitated via a “Matchmaking Service mechanism” possibly including conversion oftools to use common formats, and development of format converter software whereneeded. Whilst such specific developments are laudable, it is now obvious that significantprogress depends on the bioinformatics community at large, and requires vastly greatercapacity than WP1 has at its disposal. Instead, we took a much more targeted approach, focussing - as an exemplar - upon thesystematic curation of tools for proteomics data analysis, and subsequent exploitation ofthe annotations for automated workflow composition. The work addresses the challengeof tool interoperability and is a major stride in delivering a practical “Matchmaking Servicemechanism”. The work is described in two articles: ● Tsiamis, V., Ienasescu, H., Palmblad, M. Schwämmle, V. and Ison J. CommunitycurationofsoftwaretoolsasillustratedformassspectrometrybasedproteomicsInpreparation¨see https://tinyurl.com/proteomics-tools Palmblad, M., Lamprecht, A., Ison, J. and Schwämmle, V. (2018). AutomatedworkflowcompositioninmassspectrometrybasedproteomicsAccepted forpublication in Bioinformatics The first article (Tsiamis et†al†.) describes a systematic approach towards thecomprehensive coverage in bio.tools of the prevalent tools for proteomics data analysis,including expert curation of many tools to a high standard including consistent annotationof data formats and operation using the EDAM ontology. The second (Palmblad etal)explores automated workflow composition from the tool semantic annotation, andprovides a toolkit to support researchers in identifying, comparing and benchmarkingmultiple workflows from individual bioinformatics tools. For this deliverable report, we link to and summarise the publications in press. Theproject files and workflows are freely available: ● https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition