https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/Head https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/assertion https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/provenance https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/pubinfo https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/assertion http://id.crossref.org/issn/2046-1402 http://purl.org/dc/terms/title F1000Research https://doi.org/10.12688/f1000research.54159.1 http://purl.org/dc/terms/abstract Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future. https://doi.org/10.12688/f1000research.54159.1 http://purl.org/dc/terms/date 2021-09-07 https://doi.org/10.12688/f1000research.54159.1 http://purl.org/dc/terms/isPartOf http://id.crossref.org/issn/2046-1402 https://doi.org/10.12688/f1000research.54159.1 http://purl.org/dc/terms/title Perspectives on automated composition of workflows in the life sciences https://doi.org/10.12688/f1000research.54159.1 http://purl.org/ontology/bibo/authorList https://w3id.org/np/RAA73nc1zabSyHtZr6gupgsnlijzqcQYOJrXDJtK0V1kA/author-list https://doi.org/10.12688/f1000research.54159.1 http://purl.org/ontology/bibo/pageStart 897 https://doi.org/10.12688/f1000research.54159.1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://purl.org/spar/fabio/Article https://orcid.org/0000-0001-6666-1520 http://schema.org/affiliation https://ror.org/045f7pv37 https://orcid.org/0000-0001-6666-1520 http://xmlns.com/foaf/0.1/name Jon Ison https://orcid.org/0000-0001-6801-2559 http://schema.org/affiliation https://ror.org/017zqws13 https://orcid.org/0000-0001-6801-2559 http://xmlns.com/foaf/0.1/name Timothy J. 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Richardson https://orcid.org/0000-0003-0183-6910 http://schema.org/affiliation https://ror.org/04dkp9463 https://orcid.org/0000-0003-0183-6910 http://xmlns.com/foaf/0.1/name Paul Groth https://orcid.org/0000-0003-0373-9372 http://schema.org/affiliation https://ror.org/05xvt9f17 https://orcid.org/0000-0003-0373-9372 http://xmlns.com/foaf/0.1/name Aswin Verhoeven https://orcid.org/0000-0003-0984-0973 http://schema.org/affiliation https://ror.org/017zqws13 https://orcid.org/0000-0003-0984-0973 http://xmlns.com/foaf/0.1/name Pratik Jagtap https://orcid.org/0000-0003-1219-2137 http://schema.org/affiliation https://ror.org/027m9bs27 https://orcid.org/0000-0003-1219-2137 http://xmlns.com/foaf/0.1/name Carole Goble https://orcid.org/0000-0003-1781-5508 http://schema.org/affiliation https://ror.org/05xvt9f17 https://orcid.org/0000-0003-1781-5508 http://xmlns.com/foaf/0.1/name Hailiang Mei https://orcid.org/0000-0003-1953-5606 http://schema.org/affiliation https://ror.org/04pp8hn57 https://orcid.org/0000-0003-1953-5606 http://xmlns.com/foaf/0.1/name Anna-Lena Lamprecht https://orcid.org/0000-0003-4004-6479 http://schema.org/affiliation https://ror.org/05nkf0n29 https://orcid.org/0000-0003-4004-6479 http://xmlns.com/foaf/0.1/name Christopher J. 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Baker https://orcid.org/0000-0003-4647-3877 http://schema.org/affiliation https://ror.org/0153tk833 https://orcid.org/0000-0003-4647-3877 http://xmlns.com/foaf/0.1/name Mohammad Sadnan Al Manir https://ror.org/008xxew50 http://xmlns.com/foaf/0.1/name Vrije Universiteit Amsterdam, Amsterdam, Netherlands https://ror.org/00rbjv475 http://xmlns.com/foaf/0.1/name Netherlands eScience Center, Amsterdam, Netherlands https://ror.org/0153tk833 http://xmlns.com/foaf/0.1/name University of Virginia, Charlottesville, United States https://ror.org/0168r3w48 http://xmlns.com/foaf/0.1/name University of California San Diego, La Jolla, United States https://ror.org/017zqws13 http://xmlns.com/foaf/0.1/name University of Minnesota, Minneapolis, United States https://ror.org/0245cg223 http://xmlns.com/foaf/0.1/name University of Freiburg, Freiburg, Germany https://ror.org/027bh9e22 http://xmlns.com/foaf/0.1/name Leiden University, Leiden, Netherlands https://ror.org/027m9bs27 http://xmlns.com/foaf/0.1/name University of Manchester, Manchester, United Kingdom https://ror.org/030a5r161 http://xmlns.com/foaf/0.1/name Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands https://ror.org/03taz7m60 http://xmlns.com/foaf/0.1/name University of Southern California, Los Angeles, United States https://ror.org/03yrrjy16 http://xmlns.com/foaf/0.1/name University of Southern Denmark, Odense, Denmark https://ror.org/03zga2b32 http://xmlns.com/foaf/0.1/name University of Bergen, Bergen, Norway https://ror.org/045f7pv37 http://xmlns.com/foaf/0.1/name Institut Français de Bioinformatique, Évry, France https://ror.org/0495fxg12 http://xmlns.com/foaf/0.1/name Institut Pasteur, Paris, France https://ror.org/04dkp9463 http://xmlns.com/foaf/0.1/name University of Amsterdam, Amsterdam, Netherlands https://ror.org/04dm1cm79 http://xmlns.com/foaf/0.1/name Rostock University Medical Center, Rostock, Germany https://ror.org/04pp8hn57 http://xmlns.com/foaf/0.1/name Utrecht 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