{"id":"https://openalex.org/W2114134510","doi":"https://doi.org/10.1186/1758-2946-6-24","title":"The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration","display_name":"The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration","publication_year":2014,"publication_date":"2014-05-13","ids":{"openalex":"https://openalex.org/W2114134510","doi":"https://doi.org/10.1186/1758-2946-6-24","mag":"2114134510"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-6-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-24","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-24","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-24","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027676813","display_name":"Antonino Fiannaca","orcid":"https://orcid.org/0000-0002-0114-4984"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Antonino Fiannaca","raw_affiliation_strings":["ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","ICAR-CNR, National Research Council of Italy, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052997301","display_name":"Massimo La Rosa","orcid":"https://orcid.org/0000-0001-6718-7269"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimo La Rosa","raw_affiliation_strings":["ICAR-CNR, National Research Council of Italy, via P. Castellino, 111, 80131, Napoli, Italy","ICAR-CNR, National Research Council of Italy, Napoli, Italy"],"affiliations":[{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, via P. Castellino, 111, 80131, Napoli, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Napoli, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007549483","display_name":"Giuseppe Di Fatta","orcid":"https://orcid.org/0000-0003-3096-2844"},"institutions":[{"id":"https://openalex.org/I71052956","display_name":"University of Reading","ror":"https://ror.org/05v62cm79","country_code":"GB","type":"education","lineage":["https://openalex.org/I71052956"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Giuseppe Di Fatta","raw_affiliation_strings":["School of Systems Engineering, University of Reading, RG6 6AX, Reading, UK","[Sch. of Syst. Eng., Univ. of Reading, Reading, UK]"],"affiliations":[{"raw_affiliation_string":"School of Systems Engineering, University of Reading, RG6 6AX, Reading, UK","institution_ids":["https://openalex.org/I71052956"]},{"raw_affiliation_string":"[Sch. of Syst. Eng., Univ. of Reading, Reading, UK]","institution_ids":["https://openalex.org/I71052956"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046377602","display_name":"Salvatore Gaglio","orcid":"https://orcid.org/0000-0002-5480-2100"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Salvatore Gaglio","raw_affiliation_strings":["ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","ICAR-CNR, National Research Council of Italy, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011731694","display_name":"Riccardo Rizzo","orcid":"https://orcid.org/0000-0001-5007-6925"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Riccardo Rizzo","raw_affiliation_strings":["ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","ICAR-CNR, National Research Council of Italy, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015541058","display_name":"Alfonso Urso","orcid":"https://orcid.org/0000-0003-3018-1458"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfonso Urso","raw_affiliation_strings":["ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","ICAR-CNR, National Research Council of Italy, Palermo, Italy"],"affiliations":[{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"ICAR-CNR, National Research Council of Italy, Palermo, Italy","institution_ids":["https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5027676813"],"corresponding_institution_ids":["https://openalex.org/I4210155236"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.2441,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.86217417,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"6","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9843000173568726,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9843000173568726,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9824000000953674,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9764999747276306,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8120765686035156},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7961032390594482},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7816239595413208},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7236629724502563},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7030752301216125},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5751627683639526},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.526671826839447},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4887516498565674},{"id":"https://openalex.org/keywords/data-exploration","display_name":"Data exploration","score":0.43686532974243164},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.43562930822372437},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.4235469698905945},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3615388870239258},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24451029300689697},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23651519417762756},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2094523012638092}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8120765686035156},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7961032390594482},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7816239595413208},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7236629724502563},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7030752301216125},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5751627683639526},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.526671826839447},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4887516498565674},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.43686532974243164},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.43562930822372437},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.4235469698905945},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3615388870239258},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24451029300689697},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23651519417762756},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2094523012638092},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-6-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-24","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-24","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:centaur.reading.ac.uk:39802","is_oa":false,"landing_page_url":"https://centaur.reading.ac.uk/view/creators/90000558.html>,","pdf_url":null,"source":{"id":"https://openalex.org/S4306402273","display_name":"CentAUR (University of Reading)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71052956","host_organization_name":"University of Reading","host_organization_lineage":["https://openalex.org/I71052956"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:europepmc.org:3009560","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4036106","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unipa.it:10447/96964","is_oa":false,"landing_page_url":"http://hdl.handle.net/10447/96964","pdf_url":null,"source":{"id":"https://openalex.org/S4306401065","display_name":"Nova Science Publishers (Nova Science Publishers, Inc.)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-6-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-24","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-24","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114134510.pdf","grobid_xml":"https://content.openalex.org/works/W2114134510.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1175789168","https://openalex.org/W1527722524","https://openalex.org/W1532781897","https://openalex.org/W1543248120","https://openalex.org/W1679913846","https://openalex.org/W1976892175","https://openalex.org/W2013434113","https://openalex.org/W2027128310","https://openalex.org/W2078688255","https://openalex.org/W2114940395","https://openalex.org/W2116105292","https://openalex.org/W2127432713","https://openalex.org/W2133990480","https://openalex.org/W2140157849","https://openalex.org/W2160406798","https://openalex.org/W2168480393","https://openalex.org/W2169178437","https://openalex.org/W2169599226","https://openalex.org/W2288927223","https://openalex.org/W2489445523","https://openalex.org/W2492158267","https://openalex.org/W2514612524","https://openalex.org/W2914889379","https://openalex.org/W4213332169","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W372138008","https://openalex.org/W2887634402","https://openalex.org/W4237581822","https://openalex.org/W4386968677","https://openalex.org/W3145315517","https://openalex.org/W1970758373","https://openalex.org/W2741978288","https://openalex.org/W4231395176","https://openalex.org/W4226145910","https://openalex.org/W1843301239"],"abstract_inverted_index":{"In":[0],"many":[1],"experimental":[2],"pipelines,":[3],"clustering":[4,47,83,214],"of":[5,42,84,98,124,143,149,151,156,173,188,224],"multidimensional":[6,144],"biological":[7,86,225],"datasets":[8],"is":[9,20,27,54,112,120,159],"used":[10,28],"to":[11,29,56,166,206],"detect":[12],"hidden":[13],"structures":[14],"in":[15,37,50,62,108],"unlabelled":[16],"input":[17,100],"data.":[18],"Taverna":[19,52,72,181],"a":[21,58,71,90,162,182,195,201],"popular":[22,183],"workflow":[23],"management":[24],"system":[25],"that":[26,81,138],"design":[30],"and":[31,35,48,64,88,102,146,171,176,212],"execute":[32],"scientific":[33,60,189],"workflows":[34],"aid":[36],"silico":[38],"experimentation.":[39],"The":[40,105,131,154,169],"availability":[41],"fast":[43],"unsupervised":[44],"methods":[45],"for":[46,95,185,220],"visualization":[49,97],"the":[51,74,96,99,109,125,140,147,157,186,221],"platform":[53],"important":[55],"support":[57],"data-driven":[59,202],"discovery":[61,204],"complex":[63],"explorative":[65,222],"bioinformatics":[66],"applications.":[67],"This":[68,192],"work":[69,193],"presents":[70,194],"plugin,":[73,197],"Biological":[75],"Data":[76],"Interactive":[77],"Clustering":[78],"Explorer":[79],"(BioDICE),":[80],"performs":[82],"high-dimensional":[85],"data":[87,101,145,190],"provides":[89,209],"nonlinear,":[91],"topology":[92],"preserving":[93],"projection":[94],"their":[103],"similarities.":[104],"core":[106],"algorithm":[107],"BioDICE":[110,208],"plugin":[111,132,158],"Fast":[113],"Learning":[114],"Self":[115,126],"Organizing":[116,127],"Map":[117,128],"(FLSOM),":[118],"which":[119,199,216],"an":[121,134,210],"improved":[122],"variant":[123],"(SOM)":[129],"algorithm.":[130],"generates":[133],"interactive":[135],"2D":[136],"map":[137],"allows":[139],"visual":[141],"exploration":[142],"identification":[148],"groups":[150],"similar":[152],"objects.":[153],"effectiveness":[155],"demonstrated":[160],"on":[161],"case":[163],"study":[164],"related":[165],"chemical":[167],"compounds.":[168],"number":[170],"variety":[172],"available":[174],"tools":[175],"its":[177],"extensibility":[178],"have":[179],"made":[180],"choice":[184],"development":[187],"workflows.":[191],"novel":[196],"BioDICE,":[198],"adds":[200],"knowledge":[203],"component":[205],"Taverna.":[207],"effective":[211],"powerful":[213],"tool,":[215],"can":[217],"be":[218],"adopted":[219],"analysis":[223],"datasets.":[226]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
