{"id":"https://openalex.org/W2955703013","doi":"https://doi.org/10.1162/dint_a_00033","title":"FAIR Computational Workflows","display_name":"FAIR Computational Workflows","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W2955703013","doi":"https://doi.org/10.1162/dint_a_00033","mag":"2955703013"},"language":"en","primary_location":{"id":"doi:10.1162/dint_a_00033","is_oa":true,"landing_page_url":"https://doi.org/10.1162/dint_a_00033","pdf_url":"https://direct.mit.edu/dint/article-pdf/2/1-2/108/1893377/dint_a_00033.pdf","source":{"id":"https://openalex.org/S4210186383","display_name":"Data Intelligence","issn_l":"2096-7004","issn":["2096-7004","2641-435X"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315718","host_organization_name":"The MIT Press","host_organization_lineage":["https://openalex.org/P4310315718"],"host_organization_lineage_names":["The MIT Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://direct.mit.edu/dint/article-pdf/2/1-2/108/1893377/dint_a_00033.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027899893","display_name":"Carole Goble","orcid":"https://orcid.org/0000-0003-1219-2137"},"institutions":[{"id":"https://openalex.org/I2800081431","display_name":"British Academy","ror":"https://ror.org/0302b4677","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800081431"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Carole Goble","raw_affiliation_strings":["Department of Computer Science, The University of Manchester, Oxford Road,                         Manchester M13 9PL, UK","knowledge management and the Semantic Web","new models of scholarship for data-intensive science. Carole has served on numerous committees and currently serves in the G7 Open Science Working Group as the UK expert. In 2008 she was awarded the Microsoft Jim Gray e-Science award for contributions to e-Science and in 2010 was elected a Fellow of the Royal Academy of Engineering. In 2014 she was awarded the Commander of the Order of the British Empire for services to Science","Department of Computer Science, The University of Manchester, Oxford Road,\n Manchester M13 9PL, UK","social, virtual environments","software engineering for scientific software","Carole Goble is Professor of Computer Science at The University of Manchester. Over the past 25 years Carole has pursued research interests in the acceleration of FAIR scientific innovation through: distributed computing, workflows and automation"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Manchester, Oxford Road,                         Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"knowledge management and the Semantic Web","institution_ids":[]},{"raw_affiliation_string":"new models of scholarship for data-intensive science. Carole has served on numerous committees and currently serves in the G7 Open Science Working Group as the UK expert. In 2008 she was awarded the Microsoft Jim Gray e-Science award for contributions to e-Science and in 2010 was elected a Fellow of the Royal Academy of Engineering. In 2014 she was awarded the Commander of the Order of the British Empire for services to Science","institution_ids":["https://openalex.org/I2800081431"]},{"raw_affiliation_string":"Department of Computer Science, The University of Manchester, Oxford Road,\n Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"social, virtual environments","institution_ids":[]},{"raw_affiliation_string":"software engineering for scientific software","institution_ids":[]},{"raw_affiliation_string":"Carole Goble is Professor of Computer Science at The University of Manchester. Over the past 25 years Carole has pursued research interests in the acceleration of FAIR scientific innovation through: distributed computing, workflows and automation","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067733747","display_name":"Sarah Cohen\u2010Boulakia","orcid":"https://orcid.org/0000-0002-7439-1441"},"institutions":[{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210165492","display_name":"Samaritan Health Services","ror":"https://ror.org/05scg1q91","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210165492"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Sarah Cohen-Boulakia","raw_affiliation_strings":["Laboratoire de Recherche en Informatique, CNRS, Universit\u00e9                         Paris-Saclay, Batiment 650, Universit\u00e9 Paris-Sud, 91405 ORSAY Cedex,                         France","Sarah Cohen-Boulakia is a full Professor at the Laboratoire de Recherche en Informatique at Universite Paris-Sud. She holds a PhD in Computer Science and a Habilitation from the same university. She has been working for fifteen years in multi-disciplinary groups involving computer scientists and biologists of various domains. She spent two years as a postdoctoral researcher at the University of Pennsylvania, USA and 18 months at the Institute of Computational Biology (IBC) of Montpellier, France. Dr. Cohen-Boulakia's research interests include provenance and design of scientific workflows, reproducibility of scientific experiments, integration, querying and ranking in the context of biological and biomedical databases. She currently co-animates a National working group on reproducibility of scientific experiments and she is involved in the European Research Infrastructure ELIXIR ()"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Recherche en Informatique, CNRS, Universit\u00e9                         Paris-Saclay, Batiment 650, Universit\u00e9 Paris-Sud, 91405 ORSAY Cedex,                         France","institution_ids":["https://openalex.org/I4210144804","https://openalex.org/I277688954","https://openalex.org/I102197404","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Sarah Cohen-Boulakia is a full Professor at the Laboratoire de Recherche en Informatique at Universite Paris-Sud. She holds a PhD in Computer Science and a Habilitation from the same university. She has been working for fifteen years in multi-disciplinary groups involving computer scientists and biologists of various domains. She spent two years as a postdoctoral researcher at the University of Pennsylvania, USA and 18 months at the Institute of Computational Biology (IBC) of Montpellier, France. Dr. Cohen-Boulakia's research interests include provenance and design of scientific workflows, reproducibility of scientific experiments, integration, querying and ranking in the context of biological and biomedical databases. She currently co-animates a National working group on reproducibility of scientific experiments and she is involved in the European Research Infrastructure ELIXIR ()","institution_ids":["https://openalex.org/I4210165492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029941394","display_name":"Stian Soiland\u2010Reyes","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4210093580","display_name":"The Nature Conservancy","ror":"https://ror.org/00gcd8h55","country_code":"CO","type":"nonprofit","lineage":["https://openalex.org/I4210093580"]},{"id":"https://openalex.org/I59746437","display_name":"Open University of Cyprus","ror":"https://ror.org/033sm2k57","country_code":"CY","type":"education","lineage":["https://openalex.org/I59746437"]}],"countries":["CO","CY","GB"],"is_corresponding":false,"raw_author_name":"Stian Soiland-Reyes","raw_affiliation_strings":["Common Workflow Language project, Software Freedom Conservancy, Inc. 137                         Montague St STE 380, NY 11201-3548, USA","Department of Computer Science, The University of Manchester, Oxford Road,                         Manchester M13 9PL, UK","Common Workflow Language project, Software Freedom Conservancy, Inc. 137\n Montague St STE 380, NY 11201-3548, USA","Department of Computer Science, The University of Manchester, Oxford Road,\n Manchester M13 9PL, UK","Stian Soiland-Reyes is a Technical Architect in the eScience Lab, based in the Department of Computer Science at The University of Manchester. Since 2006 he has worked as a software engineer and researcher focusing on reproducibility, scientific workflows, interoperability, linked data, metadata and open science. He is a persistent advocate of Open Scholarly Communication, and is on the leadership team of the Common Workflow Language and on the Project Management Committee of several open source projects at the Apache Software Foundation. He co-created the Research Object model, contributed to the W3C provenance model PROV-O and multiple Linked Data initiatives. He is co-chair of the Research Object Crate team"],"affiliations":[{"raw_affiliation_string":"Common Workflow Language project, Software Freedom Conservancy, Inc. 137                         Montague St STE 380, NY 11201-3548, USA","institution_ids":["https://openalex.org/I4210093580"]},{"raw_affiliation_string":"Department of Computer Science, The University of Manchester, Oxford Road,                         Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Common Workflow Language project, Software Freedom Conservancy, Inc. 137\n Montague St STE 380, NY 11201-3548, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, The University of Manchester, Oxford Road,\n Manchester M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Stian Soiland-Reyes is a Technical Architect in the eScience Lab, based in the Department of Computer Science at The University of Manchester. Since 2006 he has worked as a software engineer and researcher focusing on reproducibility, scientific workflows, interoperability, linked data, metadata and open science. He is a persistent advocate of Open Scholarly Communication, and is on the leadership team of the Common Workflow Language and on the Project Management Committee of several open source projects at the Apache Software Foundation. He co-created the Research Object model, contributed to the W3C provenance model PROV-O and multiple Linked Data initiatives. He is co-chair of the Research Object Crate team","institution_ids":["https://openalex.org/I59746437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033224077","display_name":"Daniel Garijo","orcid":"https://orcid.org/0000-0003-0454-7145"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I1295297804","display_name":"Ciena (United States)","ror":"https://ror.org/05w425588","country_code":"US","type":"company","lineage":["https://openalex.org/I1295297804"]},{"id":"https://openalex.org/I2801204180","display_name":"Marina Del Rey Hospital","ror":"https://ror.org/05wqyfz02","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801204180"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Garijo","raw_affiliation_strings":["Information Sciences Institute, University of Southern California, Marina                         Del Rey CA 90292, USA","Information Sciences Institute, University of Southern California, Marina\n Del Rey CA 90292, USA","Daniel Garijo is a computer scientist at the Information Sciences Institute of the University of Southern California. His research activities focus on e-Science and the Semantic Web, specifically on how to increase the understandability of software and scientific workflows using their associated provenance, metadata and intermediate results. Daniel was a member of the W3C Provenance Working Group to develop a standard for provenance on the Web, and he is currently collaborating with domain scientists to ease the description and composition of software in environmental and social sciences"],"affiliations":[{"raw_affiliation_string":"Information Sciences Institute, University of Southern California, Marina                         Del Rey CA 90292, USA","institution_ids":["https://openalex.org/I2801204180"]},{"raw_affiliation_string":"Information Sciences Institute, University of Southern California, Marina\n Del Rey CA 90292, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Daniel Garijo is a computer scientist at the Information Sciences Institute of the University of Southern California. His research activities focus on e-Science and the Semantic Web, specifically on how to increase the understandability of software and scientific workflows using their associated provenance, metadata and intermediate results. Daniel was a member of the W3C Provenance Working Group to develop a standard for provenance on the Web, and he is currently collaborating with domain scientists to ease the description and composition of software in environmental and social sciences","institution_ids":["https://openalex.org/I1295297804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040878653","display_name":"Yolanda Gil","orcid":"https://orcid.org/0000-0001-8465-8341"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I2801204180","display_name":"Marina Del Rey Hospital","ror":"https://ror.org/05wqyfz02","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801204180"]},{"id":"https://openalex.org/I4210105785","display_name":"Intelligent Systems Research (United States)","ror":"https://ror.org/01reevc91","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105785"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yolanda Gil","raw_affiliation_strings":["Information Sciences Institute, University of Southern California, Marina                         Del Rey CA 90292, USA","Information Sciences Institute, University of Southern California, Marina\n Del Rey CA 90292, USA","Yolanda Gil is Director of Knowledge Technologies and Associate Division Director at the Information Sciences Institute of the University of Southern California, and Research Professor in Computer Science and in Spatial Sciences. She is also Associate Director of Interdisciplinary Programs in Data Science at USC. She received her M.S. and PhD degrees in Computer Science from Carnegie Mellon University, with a focus on artificial intelligence. Her research is on intelligent interfaces for knowledge capture and discovery, which she investigates in a variety of projects concerning knowledge-based planning and problem solving, information analysis and assessment of trust, semantic annotation and metadata, and community-wide development of knowledge bases. Dr. Gil collaborates with scientists in different domains on semantic workflows and metadata capture, social knowledge collection, computer-mediated collaboration, and automated discovery. She initiated and chaired the W3C Provenance Group that led to a community standard in this area. Dr. Gil is a Fellow of the Association for Computing Machinery (ACM), and Past Chair of its Special Interest Group in Artificial Intelligence. She is also a Fellow of the Association for the Advancement of Artificial Intelligence (AAAI), and was elected as its 24th President in 2016"],"affiliations":[{"raw_affiliation_string":"Information Sciences Institute, University of Southern California, Marina                         Del Rey CA 90292, USA","institution_ids":["https://openalex.org/I2801204180"]},{"raw_affiliation_string":"Information Sciences Institute, University of Southern California, Marina\n Del Rey CA 90292, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Yolanda Gil is Director of Knowledge Technologies and Associate Division Director at the Information Sciences Institute of the University of Southern California, and Research Professor in Computer Science and in Spatial Sciences. She is also Associate Director of Interdisciplinary Programs in Data Science at USC. She received her M.S. and PhD degrees in Computer Science from Carnegie Mellon University, with a focus on artificial intelligence. Her research is on intelligent interfaces for knowledge capture and discovery, which she investigates in a variety of projects concerning knowledge-based planning and problem solving, information analysis and assessment of trust, semantic annotation and metadata, and community-wide development of knowledge bases. Dr. Gil collaborates with scientists in different domains on semantic workflows and metadata capture, social knowledge collection, computer-mediated collaboration, and automated discovery. She initiated and chaired the W3C Provenance Group that led to a community standard in this area. Dr. Gil is a Fellow of the Association for Computing Machinery (ACM), and Past Chair of its Special Interest Group in Artificial Intelligence. She is also a Fellow of the Association for the Advancement of Artificial Intelligence (AAAI), and was elected as its 24th President in 2016","institution_ids":["https://openalex.org/I4210105785"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020288899","display_name":"Michael R. Crusoe","orcid":"https://orcid.org/0000-0002-2961-9670"},"institutions":[{"id":"https://openalex.org/I16718484","display_name":"Hess (United States)","ror":"https://ror.org/00zbk1w77","country_code":"US","type":"company","lineage":["https://openalex.org/I16718484"]},{"id":"https://openalex.org/I4210093580","display_name":"The Nature Conservancy","ror":"https://ror.org/00gcd8h55","country_code":"CO","type":"nonprofit","lineage":["https://openalex.org/I4210093580"]}],"countries":["CO","US"],"is_corresponding":false,"raw_author_name":"Michael R. Crusoe","raw_affiliation_strings":["Common Workflow Language project, Software Freedom Conservancy, Inc. 137                         Montague St STE 380, NY 11201-3548, USA","Common Workflow Language project, Software Freedom Conservancy, Inc. 137\n Montague St STE 380, NY 11201-3548, USA","Michael R. Crusoe is one of the co-founders of the Common Workflow Language project and the CWL Project Lead. His facilitation, technical contributions, and training on behalf of CWL draw from his time as the former lead developer of C. Titus Brown's k-h-mer project, his previous career as a sysadmin and programmer, and his experiences in various Free and Open Source Software communities. This is not Michael's first time working on a standards project as he was the technical author of the International Labour Organization's Seafarers' Identity Card (2003) standard which is in force and ratified by 32 countries. Currently based in Berlin, Germany","Michael has been living in Europe for the last 4 years where he has enjoyed partnering with ELIXIR, ASTRON, and the EOSCPilot to build collaborations across the continent and across the world"],"affiliations":[{"raw_affiliation_string":"Common Workflow Language project, Software Freedom Conservancy, Inc. 137                         Montague St STE 380, NY 11201-3548, USA","institution_ids":["https://openalex.org/I4210093580"]},{"raw_affiliation_string":"Common Workflow Language project, Software Freedom Conservancy, Inc. 137\n Montague St STE 380, NY 11201-3548, USA","institution_ids":[]},{"raw_affiliation_string":"Michael R. Crusoe is one of the co-founders of the Common Workflow Language project and the CWL Project Lead. His facilitation, technical contributions, and training on behalf of CWL draw from his time as the former lead developer of C. Titus Brown's k-h-mer project, his previous career as a sysadmin and programmer, and his experiences in various Free and Open Source Software communities. This is not Michael's first time working on a standards project as he was the technical author of the International Labour Organization's Seafarers' Identity Card (2003) standard which is in force and ratified by 32 countries. Currently based in Berlin, Germany","institution_ids":[]},{"raw_affiliation_string":"Michael has been living in Europe for the last 4 years where he has enjoyed partnering with ELIXIR, ASTRON, and the EOSCPilot to build collaborations across the continent and across the world","institution_ids":["https://openalex.org/I16718484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085643207","display_name":"Kristian Peters","orcid":"https://orcid.org/0000-0002-4321-0257"},"institutions":[{"id":"https://openalex.org/I4210110463","display_name":"Leibniz Institute of Plant Biochemistry","ror":"https://ror.org/01mzk5576","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210110463"]},{"id":"https://openalex.org/I4210156829","display_name":"Research Network (United States)","ror":"https://ror.org/04tgjxk96","country_code":"US","type":"company","lineage":["https://openalex.org/I4210156829"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Kristian Peters","raw_affiliation_strings":["Leibniz Institute of Plant Biochemistry (IPB Halle), Department of                         Biochemistry of Plant Interactions, Weinberg 3, 06120 Halle (Saale),                         Germany","Kristian Peters is currently working at the Leibniz Institute of Plant Biochemistry. He is part of the Germany network of bioinformatic infrastructures (de.NBI) and is a member of the GoFAIR metabolomics implementation network and the societies NBS and BLAM e.V. which focus on bryophyte biology and ecology. As he has studied both Information Technology and Biology his research focus is mainly on interdisciplinarity and integrating the research fields biochemistry, bioinformatics and ecology. His expertise in data integration covers a wide range of topics, including cloud e-infrastructures, statistics, machine learning, chemical ecology and ecometabolomics, targeted and untargeted metabolomics, plant and vegetation ecology, bryophyte biology, macro- and microscopy and climate change biology. His current research activities focus on the integrative data analysis and characterisation of compound classes of rare species in ecological contexts, creating scientific computational workflows for use cases in ecometabolomics and biomedicine, promoting the reproducibility and interoperability of software tools and the adoption of standardized research objects and formats","Leibniz Institute of Plant Biochemistry (IPB Halle), Department of\n Biochemistry of Plant Interactions, Weinberg 3, 06120 Halle (Saale),\n Germany"],"affiliations":[{"raw_affiliation_string":"Leibniz Institute of Plant Biochemistry (IPB Halle), Department of                         Biochemistry of Plant Interactions, Weinberg 3, 06120 Halle (Saale),                         Germany","institution_ids":["https://openalex.org/I4210110463"]},{"raw_affiliation_string":"Kristian Peters is currently working at the Leibniz Institute of Plant Biochemistry. He is part of the Germany network of bioinformatic infrastructures (de.NBI) and is a member of the GoFAIR metabolomics implementation network and the societies NBS and BLAM e.V. which focus on bryophyte biology and ecology. As he has studied both Information Technology and Biology his research focus is mainly on interdisciplinarity and integrating the research fields biochemistry, bioinformatics and ecology. His expertise in data integration covers a wide range of topics, including cloud e-infrastructures, statistics, machine learning, chemical ecology and ecometabolomics, targeted and untargeted metabolomics, plant and vegetation ecology, bryophyte biology, macro- and microscopy and climate change biology. His current research activities focus on the integrative data analysis and characterisation of compound classes of rare species in ecological contexts, creating scientific computational workflows for use cases in ecometabolomics and biomedicine, promoting the reproducibility and interoperability of software tools and the adoption of standardized research objects and formats","institution_ids":["https://openalex.org/I4210156829"]},{"raw_affiliation_string":"Leibniz Institute of Plant Biochemistry (IPB Halle), Department of\n Biochemistry of Plant Interactions, Weinberg 3, 06120 Halle (Saale),\n Germany","institution_ids":["https://openalex.org/I4210110463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049157539","display_name":"Daniel Schober","orcid":"https://orcid.org/0000-0001-8014-6648"},"institutions":[{"id":"https://openalex.org/I4210110463","display_name":"Leibniz Institute of Plant 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