{"id":"https://openalex.org/W1986612502","doi":"https://doi.org/10.1109/bibm.2013.6732546","title":"Sesame: A new bioinformatics semantic workflow design system","display_name":"Sesame: A new bioinformatics semantic workflow design system","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W1986612502","doi":"https://doi.org/10.1109/bibm.2013.6732546","mag":"1986612502"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2013.6732546","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732546","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100388592","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0001-9890-1365"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lu Zhang","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009073023","display_name":"Yunsheng Wang","orcid":"https://orcid.org/0000-0001-5003-4434"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]},{"id":"https://openalex.org/I52180223","display_name":"Hunan Agricultural University","ror":"https://ror.org/01dzed356","country_code":"CN","type":"education","lineage":["https://openalex.org/I52180223"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yunsheng Wang","raw_affiliation_strings":["College of Plant Protection, Hunan Agricultural University, Changsha, China","School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"College of Plant Protection, Hunan Agricultural University, Changsha, China","institution_ids":["https://openalex.org/I52180223"]},{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108111002","display_name":"Pengfei Xuan","orcid":null},"institutions":[{"id":"https://openalex.org/I52180223","display_name":"Hunan Agricultural University","ror":"https://ror.org/01dzed356","country_code":"CN","type":"education","lineage":["https://openalex.org/I52180223"]},{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Pengfei Xuan","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Coll. of Plant Protection, Hunan Agric. Univ., Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Coll. of Plant Protection, Hunan Agric. Univ., Changsha, China","institution_ids":["https://openalex.org/I52180223"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042882312","display_name":"Alexander Duvall","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Duvall","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053172769","display_name":"Jonathan J. Lowe","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Lowe","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003295463","display_name":"Yanyan Wang","orcid":"https://orcid.org/0000-0003-4333-015X"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]},{"id":"https://openalex.org/I52180223","display_name":"Hunan Agricultural University","ror":"https://ror.org/01dzed356","country_code":"CN","type":"education","lineage":["https://openalex.org/I52180223"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yanyan Wang","raw_affiliation_strings":["College of Plant Protection, Hunan Agricultural University, Changsha, China","School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"College of Plant Protection, Hunan Agricultural University, Changsha, China","institution_ids":["https://openalex.org/I52180223"]},{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103012712","display_name":"Arvind Subramanian","orcid":"https://orcid.org/0000-0001-8795-9895"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arvind Subramanian","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047296304","display_name":"Pradip K. Srimani","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pradip K Srimani","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100683466","display_name":"Feng Luo","orcid":"https://orcid.org/0000-0002-4813-2403"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feng Luo","raw_affiliation_strings":["School of Computing, Clemson University, SC, USA","Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Computing, Clemson University, SC, USA","institution_ids":["https://openalex.org/I8078737"]},{"raw_affiliation_string":"Sch. of Comput., Clemson Univ., Clemson, SC, USA#TAB#","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002481364","display_name":"Yongping Duan","orcid":"https://orcid.org/0000-0003-1775-1479"},"institutions":[{"id":"https://openalex.org/I4210155113","display_name":"U.S. Horticultural Research Laboratory","ror":"https://ror.org/04a4m2h70","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210122704","https://openalex.org/I4210155113"]},{"id":"https://openalex.org/I1312222531","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongping Duan","raw_affiliation_strings":["Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, FL, USA","Agric. Res. Service, U.S. Horticultural Res. Lab., Fort Pierce, FL, USA"],"affiliations":[{"raw_affiliation_string":"Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, FL, USA","institution_ids":["https://openalex.org/I4210155113","https://openalex.org/I1312222531"]},{"raw_affiliation_string":"Agric. Res. Service, U.S. Horticultural Res. Lab., Fort Pierce, FL, USA","institution_ids":["https://openalex.org/I4210155113"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5100388592"],"corresponding_institution_ids":["https://openalex.org/I8078737"],"apc_list":null,"apc_paid":null,"fwci":2.325,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.9107464,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"271","issue":null,"first_page":"504","last_page":"508"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9868000149726868,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8770151138305664},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.8159029483795166},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8048812747001648},{"id":"https://openalex.org/keywords/workflow-engine","display_name":"Workflow engine","score":0.5885536074638367},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.5425788164138794},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.531904935836792},{"id":"https://openalex.org/keywords/workflow-technology","display_name":"Workflow technology","score":0.5305289030075073},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4568222165107727},{"id":"https://openalex.org/keywords/windows-workflow-foundation","display_name":"Windows Workflow Foundation","score":0.4436764717102051},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2578933835029602},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1753133237361908}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8770151138305664},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.8159029483795166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8048812747001648},{"id":"https://openalex.org/C188220564","wikidata":"https://www.wikidata.org/wiki/Q3325097","display_name":"Workflow engine","level":3,"score":0.5885536074638367},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.5425788164138794},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.531904935836792},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.5305289030075073},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4568222165107727},{"id":"https://openalex.org/C163888707","wikidata":"https://www.wikidata.org/wiki/Q1154450","display_name":"Windows Workflow Foundation","level":4,"score":0.4436764717102051},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2578933835029602},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1753133237361908},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2013.6732546","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2013.6732546","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W67041390","https://openalex.org/W118013854","https://openalex.org/W181007914","https://openalex.org/W1484074565","https://openalex.org/W1499966647","https://openalex.org/W1529006120","https://openalex.org/W2068422180","https://openalex.org/W2077797310","https://openalex.org/W2083697678","https://openalex.org/W2103017472","https://openalex.org/W2117844868","https://openalex.org/W2122805915","https://openalex.org/W2123663722","https://openalex.org/W2131616418","https://openalex.org/W2132939942","https://openalex.org/W2136482257","https://openalex.org/W2168103533","https://openalex.org/W4252427272","https://openalex.org/W6602641671"],"related_works":["https://openalex.org/W2373541195","https://openalex.org/W2376410910","https://openalex.org/W2091596831","https://openalex.org/W2166163080","https://openalex.org/W291310304","https://openalex.org/W2374818432","https://openalex.org/W2365658322","https://openalex.org/W2379425324","https://openalex.org/W2028407054","https://openalex.org/W329008868"],"abstract_inverted_index":{"Biologists":[0,138],"have":[1,23,28,43,92],"become":[2,29],"increasingly":[3],"dependent":[4],"on":[5],"bioinformatics":[6,21,77,86,98],"tools":[7,22,53,66,99],"to":[8,46,117,134,173,179],"analyze":[9],"and":[10,17,26,31,36,100,103,167],"interpret":[11],"their":[12],"datasets.":[13],"The":[14],"number,":[15],"variety":[16],"complexity":[18],"of":[19,50,52,128,145,161],"these":[20],"increased":[24],"dramatically":[25],"they":[27],"more":[30,32],"computationally":[33],"complex,":[34],"expensive":[35],"resource":[37],"intensive.":[38],"Powerful":[39],"workflow":[40,63,88,109,123,147,151],"design":[41,89,110,148,152],"systems":[42],"been":[44,165],"developed":[45,83],"automate":[47],"the":[48,73,121,126,135,143],"execution":[49],"set":[51],"for":[54,97],"a":[55,60,76,85,94,158],"specific":[56],"task.":[57],"However,":[58],"designing":[59],"complex":[61,176],"executable":[62,119,150],"using":[64,112],"such":[65],"still":[67],"requires":[68],"considerable":[69],"computational":[70,154],"expertise":[71],"or":[72],"help":[74],"from":[75,142,149],"expert.":[78],"In":[79],"this":[80,113],"paper,":[81],"we":[82],"Sesame,":[84],"semantic":[87,108,122,146],"system.":[90],"We":[91],"designed":[93],"new":[95,114],"ontology":[96,106],"services":[101],"(OBTS)":[102],"proposed":[104],"an":[105,118],"driven":[107],"mechanism,":[111],"OBTS.":[115],"Compared":[116],"workflow,":[120],"is":[124],"at":[125],"level":[127],"biological":[129],"concepts":[130],"that":[131],"are":[132],"closer":[133],"scientific":[136,181],"research.":[137],"will":[139,170],"greatly":[140],"benefit":[141],"decoupling":[144],"with":[153],"implementation":[155],"details.":[156],"Currently,":[157],"prototype":[159],"version":[160],"Sesame":[162,169],"system":[163],"has":[164],"implemented":[166],"deployed.":[168],"allow":[171],"biologists":[172],"efficiently":[174],"perform":[175],"data":[177],"analysis":[178],"address":[180],"questions.":[182]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
