Nanopublications

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f1000research.54159.1 type Article assertion.
author-list _1 0000-0003-1953-5606 assertion.
author-list _2 0000-0002-5865-8994 assertion.
author-list _3 0000-0001-6666-1520 assertion.
author-list _4 0000-0002-9708-6722 assertion.
author-list _5 0000-0003-4647-3877 assertion.
0000-0002-1267-0234 name "Tobias Kuhn" assertion.
0000-0001-8465-8341 name "Yolanda Gil" assertion.
0000-0001-9842-9718 name "Stian Soiland-Reyes" assertion.
0000-0003-1219-2137 name "Carole Goble" assertion.
0000-0002-7552-1009 name "Hervé Ménager" assertion.
0000-0003-0183-6910 name "Paul Groth" assertion.
0000-0002-0309-604X name "Salvador Capella-Gutierrez" assertion.
04dkp9463 name "University of Amsterdam, Amsterdam, Netherlands" assertion.
0000-0002-1279-5133 name "Katherine Wolstencroft" assertion.
00rbjv475 name "Netherlands eScience Center, Amsterdam, Netherlands" assertion.
05xvt9f17 name "Leiden University Medical Center, Leiden, Netherlands" assertion.
027bh9e22 name "Leiden University, Leiden, Netherlands" assertion.
0000-0002-9984-2720 name "Robin A. Richardson" assertion.
0000-0001-6811-9196 name "Alireza Khanteymoori" assertion.
ammar-ben-hadj-amor name "Ammar Ben Hadj Amor" assertion.
0000-0003-1953-5606 name "Anna-Lena Lamprecht" assertion.
0000-0003-0373-9372 name "Aswin Verhoeven" assertion.
0000-0003-4004-6479 name "Christopher J. O. Baker" assertion.
0000-0003-1781-5508 name "Hailiang Mei" assertion.
0000-0001-9727-2544 name "Hans Ienasescu" assertion.
0000-0002-2196-0305 name "Ilkay Altintas" assertion.
0000-0001-6666-1520 name "Jon Ison" assertion.
0000-0002-5865-8994 name "Magnus Palmblad" assertion.
0000-0002-1509-4981 name "Matúš Kalaš" assertion.
0000-0002-2961-9670 name "Michael R. Crusoe" assertion.
0000-0003-4647-3877 name "Mohammad Sadnan Al Manir" assertion.
0000-0002-6899-4262 name "Paulos Charonyktakis" assertion.
0000-0003-0984-0973 name "Pratik Jagtap" assertion.
0000-0002-6038-9025 name "Robert Stevens" assertion.
0000-0002-7187-4683 name "Steffen Möller" assertion.
0000-0002-9609-9505 name "Suzan Verberne" assertion.
szoke-szaniszlo name "Szoke Szaniszlo" assertion.
0000-0001-6801-2559 name "Timothy J. Griffin" assertion.
0000-0002-0097-1056 name "Vedran Kasalica" assertion.
0000-0002-9708-6722 name "Veit Schwämmle" assertion.
0000-0002-9370-4677 name "Vincent Robert" assertion.
008xxew50 name "Vrije Universiteit Amsterdam, Amsterdam, Netherlands" assertion.
0168r3w48 name "University of California San Diego, La Jolla, United States" assertion.
03taz7m60 name "University of Southern California, Los Angeles, United States" assertion.
05sd8tv96 name "Barcelona Supercomputing Center, Barcelona, Spain" assertion.
0495fxg12 name "Institut Pasteur, Paris, France" assertion.
03zga2b32 name "University of Bergen, Bergen, Norway" assertion.
0245cg223 name "University of Freiburg, Freiburg, Germany" assertion.
05nkf0n29 name "University of New Brunswick, Saint John, Canada" assertion.
03yrrjy16 name "University of Southern Denmark, Odense, Denmark" assertion.
04pp8hn57 name "Utrecht University, Utrecht, Netherlands" assertion.
04dm1cm79 name "Rostock University Medical Center, Rostock, Germany" assertion.
027m9bs27 name "University of Manchester, Manchester, United Kingdom" assertion.
045f7pv37 name "Institut Français de Bioinformatique, Évry, France" assertion.
04qtj9h94 name "Technical University of Denmark, Kongens Lyngby, Denmark" assertion.
030a5r161 name "Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands" assertion.
017zqws13 name "University of Minnesota, Minneapolis, United States" assertion.
0153tk833 name "University of Virginia, Charlottesville, United States" assertion.
f1000research.54159.1 title "Perspectives on automated composition of workflows in the life sciences" assertion.
2046-1402 title "F1000Research" assertion.
f1000research.54159.1 date "2021-09-07" assertion.
author-list _10 0000-0002-6899-4262 assertion.
author-list _6 0000-0002-2196-0305 assertion.
author-list _7 0000-0003-4004-6479 assertion.
author-list _8 ammar-ben-hadj-amor assertion.
author-list _9 0000-0002-0309-604X assertion.
f1000research.54159.1 isPartOf 2046-1402 assertion.
f1000research.54159.1 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." assertion.
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