{"id":"https://openalex.org/W967886317","doi":"https://doi.org/10.1007/s10009-015-0392-z","title":"Using registries to integrate bioinformatics tools and services into workbench environments","display_name":"Using registries to integrate bioinformatics tools and services into workbench environments","publication_year":2015,"publication_date":"2015-07-24","ids":{"openalex":"https://openalex.org/W967886317","doi":"https://doi.org/10.1007/s10009-015-0392-z","mag":"967886317"},"language":"en","primary_location":{"id":"doi:10.1007/s10009-015-0392-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10009-015-0392-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10009-015-0392-z.pdf","source":{"id":"https://openalex.org/S122567160","display_name":"International Journal on Software Tools for Technology Transfer","issn_l":"1433-2779","issn":["1433-2779","1433-2787"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal on Software Tools for Technology Transfer","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10009-015-0392-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057666741","display_name":"Herv\u00e9 M\u00e9nager","orcid":"https://orcid.org/0000-0002-7552-1009"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Herv\u00e9 M\u00e9nager","raw_affiliation_strings":["Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I157536573"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007975575","display_name":"Mat\u00fa\u0161 Kala\u0161","orcid":"https://orcid.org/0000-0002-1509-4981"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Mat\u00fa\u0161 Kala\u0161","raw_affiliation_strings":["Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway","Computational Biology Unit, Dept of Informatics, University of Bergen, Bergen, Norway"],"affiliations":[{"raw_affiliation_string":"Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Computational Biology Unit, Dept of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016909243","display_name":"Kristoffer Rapacki","orcid":null},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Kristoffer Rapacki","raw_affiliation_strings":["Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800, Kongens Lyngby, Denmark","Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark 2800#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark 2800#TAB#","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080837511","display_name":"Jon Ison","orcid":"https://orcid.org/0000-0001-6666-1520"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jon Ison","raw_affiliation_strings":["Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800, Kongens Lyngby, Denmark","Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark 2800#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark 2800#TAB#","institution_ids":["https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057666741"],"corresponding_institution_ids":["https://openalex.org/I157536573"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":5.2294,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.95401156,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"6","first_page":"581","last_page":"586"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9993000030517578,"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":0.9993000030517578,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9853000044822693,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.9119491577148438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7646371722221375},{"id":"https://openalex.org/keywords/theory-of-computation","display_name":"Theory of computation","score":0.7238101959228516},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.49264389276504517},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.34323251247406006},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33288198709487915},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32417750358581543},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2195490598678589},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1969783902168274},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10035261511802673},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.06393185257911682}],"concepts":[{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.9119491577148438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7646371722221375},{"id":"https://openalex.org/C24858836","wikidata":"https://www.wikidata.org/wiki/Q844718","display_name":"Theory of computation","level":2,"score":0.7238101959228516},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.49264389276504517},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.34323251247406006},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33288198709487915},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32417750358581543},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2195490598678589},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1969783902168274},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10035261511802673},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.06393185257911682}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/s10009-015-0392-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10009-015-0392-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10009-015-0392-z.pdf","source":{"id":"https://openalex.org/S122567160","display_name":"International Journal on Software Tools for Technology Transfer","issn_l":"1433-2779","issn":["1433-2779","1433-2787"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal on Software Tools for Technology Transfer","raw_type":"journal-article"},{"id":"pmh:oai:bora.uib.no:1956/12836","is_oa":true,"landing_page_url":"https://hdl.handle.net/1956/12836","pdf_url":null,"source":{"id":"https://openalex.org/S4306400085","display_name":"Bergen Open Research Archive (BORA) (University of Bergen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4432739","host_organization_name":"University of Bergen","host_organization_lineage":["https://openalex.org/I4432739"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/b956035d-6346-415c-ad6e-01835fe8fa15","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/b956035d-6346-415c-ad6e-01835fe8fa15","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"M\u00e9nager , H , Kala\u0161 , M , Rapacki , K &amp; Ison , J 2016 , ' Using registries to integrate bioinformatics tools and services into workbench environments ' , International Journal on Software Tools for Technology Transfer , vol. 18 , no. 6 , pp. 581-586 . https://doi.org/10.1007/s10009-015-0392-z","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1007/s10009-015-0392-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10009-015-0392-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10009-015-0392-z.pdf","source":{"id":"https://openalex.org/S122567160","display_name":"International Journal on Software Tools for Technology Transfer","issn_l":"1433-2779","issn":["1433-2779","1433-2787"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal on Software Tools for Technology Transfer","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W967886317.pdf","grobid_xml":"https://content.openalex.org/works/W967886317.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1484019536","https://openalex.org/W1583240815","https://openalex.org/W1977859620","https://openalex.org/W1996423252","https://openalex.org/W1996902131","https://openalex.org/W2013434113","https://openalex.org/W2050320831","https://openalex.org/W2087404450","https://openalex.org/W2089572204","https://openalex.org/W2097464861","https://openalex.org/W2098466396","https://openalex.org/W2102883811","https://openalex.org/W2113182242","https://openalex.org/W2117306576","https://openalex.org/W2117724905","https://openalex.org/W2128880918","https://openalex.org/W2141541659","https://openalex.org/W2148300596","https://openalex.org/W2160943260","https://openalex.org/W2161427213","https://openalex.org/W2161645441","https://openalex.org/W2162094394","https://openalex.org/W2170654685","https://openalex.org/W2398401816","https://openalex.org/W2969954034","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W2050384624","https://openalex.org/W2166015079","https://openalex.org/W2776888796","https://openalex.org/W4241678738","https://openalex.org/W2048496244","https://openalex.org/W2513537424","https://openalex.org/W139548500","https://openalex.org/W1498799334"],"abstract_inverted_index":{"The":[0,82],"diversity":[1],"and":[2,14,31,36,53,65,72,75,79,87,91,97,111,115,152],"complexity":[3],"of":[4,51,102,136],"bioinformatics":[5,137],"resources":[6,138],"presents":[7],"significant":[8],"challenges":[9],"to":[10,34,59,76,89,108,118],"their":[11,144],"localisation,":[12],"deployment":[13],"use,":[15],"creating":[16],"a":[17,128,140],"need":[18],"for":[19],"reliable":[20],"systems":[21],"that":[22,131],"address":[23],"these":[24],"issues.":[25],"Meanwhile,":[26],"users":[27],"demand":[28],"increasingly":[29],"usable":[30],"integrated":[32,42],"ways":[33],"access":[35],"analyse":[37],"data,":[38],"especially":[39],"within":[40],"convenient,":[41],"\u201cworkbench\u201d":[43],"environments.":[44],"Resource":[45],"descriptions":[46,83],"are":[47,57,95],"the":[48,62,103,112,124,134,148],"core":[49],"element":[50],"registry":[52],"workbench":[54,141],"systems,":[55],"which":[56],"used":[58,117],"both":[60],"help":[61],"user":[63],"find":[64],"comprehend":[66],"available":[67],"software":[68,129],"tools,":[69],"data":[70,113],"resources,":[71],"Web":[73],"Services,":[74],"localise,":[77],"execute":[78],"combine":[80],"them.":[81],"are,":[84],"however,":[85],"hard":[86],"expensive":[88],"create":[90],"maintain,":[92],"because":[93],"they":[94],"volatile":[96],"require":[98],"an":[99],"exhaustive":[100],"knowledge":[101],"described":[104],"resource,":[105],"its":[106],"applicability":[107],"biological":[109],"research,":[110],"model":[114],"syntax":[116],"describe":[119],"it.":[120],"We":[121],"present":[122],"here":[123],"Workbench":[125],"Integration":[126],"Enabler,":[127],"component":[130],"will":[132],"ease":[133],"integration":[135],"in":[139],"environment,":[142],"using":[143],"description":[145],"provided":[146],"by":[147],"existing":[149],"ELIXIR":[150],"Tools":[151],"Data":[153],"Services":[154],"Registry.":[155]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
