{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T05:52:36Z","timestamp":1747806756319,"version":"3.37.0"},"reference-count":29,"publisher":"Wiley","issue":"16","license":[{"start":{"date-parts":[[2009,7,8]],"date-time":"2009-07-08T00:00:00Z","timestamp":1247011200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Concurrency and Computation"],"published-print":{"date-parts":[[2009,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Automation in science is increasingly marked by the use of workflow technology. The<jats:italic>sharing<\/jats:italic>of workflows through repositories supports the verifiability, reproducibility and extensibility of computational experiments. However, the subsequent<jats:italic>discovery<\/jats:italic>of workflows remains a challenge, both from a sociological and technological viewpoint. Based on a survey with participants from 19 laboratories, we investigate the current practices in workflow sharing, re\u2010use and discovery among life scientists chiefly using the Taverna workflow management system. To address their perceived lack of effective workflow discovery tools, we go on to develop benchmarks for the evaluation of discovery tools, drawing on a series of practical exercises. We demonstrate the value of the benchmarks on two tools: one using graph matching and the other relying on text clustering. Copyright \u00a9 2009 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/cpe.1447","type":"journal-article","created":{"date-parts":[[2009,7,10]],"date-time":"2009-07-10T00:37:16Z","timestamp":1247186236000},"page":"2052-2069","source":"Crossref","is-referenced-by-count":6,"title":["Benchmarking workflow discovery: a case study from bioinformatics"],"prefix":"10.1002","volume":"21","author":[{"given":"Antoon","family":"Goderis","sequence":"first","affiliation":[]},{"given":"Paul","family":"Fisher","sequence":"additional","affiliation":[]},{"given":"Andrew","family":"Gibson","sequence":"additional","affiliation":[]},{"given":"Franck","family":"Tanoh","sequence":"additional","affiliation":[]},{"given":"Katy","family":"Wolstencroft","sequence":"additional","affiliation":[]},{"given":"David","family":"De Roure","sequence":"additional","affiliation":[]},{"given":"Carole","family":"Goble","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2009,7,8]]},"reference":[{"doi-asserted-by":"publisher","key":"e_1_2_10_2_2","DOI":"10.1109\/MC.2007.421"},{"issue":"10","key":"e_1_2_10_3_2","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1002\/cpe.993","article-title":"Taverna: Lessons in creating a workflow environment for the life sciences","volume":"18","author":"Oinn T","year":"2005","journal-title":"Concurrency and Computation: Practice and Experience"},{"doi-asserted-by":"crossref","unstructured":"De RoureD GobleC StevensR.Designing the myExperiment virtual research environment for the social sharing of workflows. Third IEEE International Conference on e\u2010Science and Grid Computing Bangalore India 10\u201313 December 2007;603\u2013610.","key":"e_1_2_10_4_2","DOI":"10.1109\/E-SCIENCE.2007.29"},{"doi-asserted-by":"publisher","key":"e_1_2_10_5_2","DOI":"10.1002\/cpe.1050"},{"unstructured":"MiersD HarmonP HallC. The 2007 BPM suites report. Available at:http:\/\/www.bptrends.com[1 April2009].","key":"e_1_2_10_6_2"},{"doi-asserted-by":"publisher","key":"e_1_2_10_7_2","DOI":"10.1016\/j.future.2008.06.014"},{"doi-asserted-by":"publisher","key":"e_1_2_10_8_2","DOI":"10.4018\/jwsr.2008100102"},{"unstructured":"GoderisA.Workflow re\u2010use and discovery in bioinformatics. PhD Thesis School of Computer Science The University of Manchester 2008.","key":"e_1_2_10_9_2"},{"doi-asserted-by":"publisher","key":"e_1_2_10_10_2","DOI":"10.1109\/TVCG.2007.70584"},{"doi-asserted-by":"crossref","unstructured":"ZhaoY WildeM FosterI.Applying the virtual data provenance model. International Provenance and Annotation Workshop (IPAW) Chicago U.S.A. 3\u20135 May 2006.","key":"e_1_2_10_11_2","DOI":"10.1007\/11890850_16"},{"doi-asserted-by":"publisher","key":"e_1_2_10_12_2","DOI":"10.1007\/11914853_15"},{"doi-asserted-by":"publisher","key":"e_1_2_10_13_2","DOI":"10.1007\/3-540-48005-6_9"},{"doi-asserted-by":"crossref","unstructured":"KieferC BernsteinA LeeHJ KleinM StockerM.Semantic process retrieval with iSPARQL. European Semantic Web Conference (ESWC) Innsbruck Austria 2007;609\u2013623.","key":"e_1_2_10_14_2","DOI":"10.1007\/978-3-540-72667-8_43"},{"doi-asserted-by":"publisher","key":"e_1_2_10_15_2","DOI":"10.1142\/S0218843003000711"},{"doi-asserted-by":"crossref","unstructured":"MahlekoB WombacherA.Indexing business processes based on annotated finite state automata. ICWS Chicago U.S.A. 2006;303\u2013311.","key":"e_1_2_10_16_2","DOI":"10.1109\/ICWS.2006.74"},{"doi-asserted-by":"publisher","key":"e_1_2_10_17_2","DOI":"10.3233\/MGS-2007-3306"},{"doi-asserted-by":"publisher","key":"e_1_2_10_18_2","DOI":"10.1504\/IJWGS.2005.007545"},{"doi-asserted-by":"crossref","unstructured":"KimJ GilY RatnakarV.Semantic metadata generation for large scientific workflows. International Semantic Web Conference (ISWC) Athens U.S.A. 5\u20139 November 2006.","key":"e_1_2_10_19_2","DOI":"10.1007\/11926078_26"},{"doi-asserted-by":"publisher","key":"e_1_2_10_20_2","DOI":"10.1145\/1035167.1035183"},{"doi-asserted-by":"publisher","key":"e_1_2_10_21_2","DOI":"10.1007\/s00778-003-0101-5"},{"key":"e_1_2_10_22_2","first-page":"97","volume-title":"INLG","author":"Reiter E","year":"2002"},{"unstructured":"KaramanisN.Entity coherence for descriptive text structuring. PhD Thesis School of Informatics University of Edinburgh 2003.","key":"e_1_2_10_23_2"},{"key":"e_1_2_10_24_2","first-page":"757","volume-title":"MIT Encyclopedia of the Cognitive Sciences","author":"Goldstone RL","year":"2001"},{"volume-title":"Nonparametric Statistics for the Behavioral Sciences","year":"1988","author":"Siegel S","key":"e_1_2_10_25_2"},{"doi-asserted-by":"crossref","unstructured":"DongX HalevyA MadhavanJ NemesE ZhangJ.Similarity search for web services. Proceedings of the 30th VLDB Conference Toronto Canada 2004.","key":"e_1_2_10_26_2","DOI":"10.1016\/B978-012088469-8.50035-8"},{"doi-asserted-by":"publisher","key":"e_1_2_10_27_2","DOI":"10.1002\/cpe.1231"},{"doi-asserted-by":"publisher","key":"e_1_2_10_28_2","DOI":"10.1145\/130844.130856"},{"doi-asserted-by":"crossref","unstructured":"BernsteinA KaufmannE BrkiC KleinM.How similar is it? Towards personalized similarity measures in ontologies. Seventh Internationale Tagung Wirtschaftsinformatik February2005.","key":"e_1_2_10_29_2","DOI":"10.1007\/3-7908-1624-8_71"},{"doi-asserted-by":"crossref","unstructured":"WombacherA.Evaluation of technical measures for workflow similarity based on a pilot study. CoopIS Montpellier France 1\u20133 November2006.","key":"e_1_2_10_30_2","DOI":"10.1007\/11914853_16"}],"container-title":["Concurrency and Computation: Practice and Experience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fcpe.1447","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpe.1447","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T21:36:41Z","timestamp":1739223401000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/cpe.1447"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,8]]},"references-count":29,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2009,11]]}},"alternative-id":["10.1002\/cpe.1447"],"URL":"https:\/\/doi.org\/10.1002\/cpe.1447","archive":["Portico"],"relation":{},"ISSN":["1532-0626","1532-0634"],"issn-type":[{"type":"print","value":"1532-0626"},{"type":"electronic","value":"1532-0634"}],"subject":[],"published":{"date-parts":[[2009,7,8]]}}}