{"id":"https://openalex.org/W2168301896","doi":"https://doi.org/10.1186/1471-2105-13-s1-s3","title":"Gauging triple stores with actual biological data","display_name":"Gauging triple stores with actual biological data","publication_year":2012,"publication_date":"2012-01-25","ids":{"openalex":"https://openalex.org/W2168301896","doi":"https://doi.org/10.1186/1471-2105-13-s1-s3","mag":"2168301896"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080056836","display_name":"Vladimir Mironov","orcid":"https://orcid.org/0000-0002-9454-5823"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Vladimir Mironov","raw_affiliation_strings":["Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070953656","display_name":"Nirmala Seethappan","orcid":null},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Nirmala Seethappan","raw_affiliation_strings":["Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","High Performance Computing, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","institution_ids":["https://openalex.org/I204778367"]},{"raw_affiliation_string":"High Performance Computing, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083985501","display_name":"Ward Blond\u00e9","orcid":"https://orcid.org/0000-0001-7624-4069"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Ward Blond\u00e9","raw_affiliation_strings":["Dept. Applied Mathematics, Biometrics and Process Control, Ghent University, Ghent, 9000, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Applied Mathematics, Biometrics and Process Control, Ghent University, Ghent, 9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059590876","display_name":"Erick Antezana","orcid":"https://orcid.org/0000-0002-2497-8236"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Erick Antezana","raw_affiliation_strings":["Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044293753","display_name":"Andrea Splendiani","orcid":"https://orcid.org/0000-0002-3201-9617"},"institutions":[{"id":"https://openalex.org/I2799553609","display_name":"Rothamsted Research","ror":"https://ror.org/0347fy350","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2799553609","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrea Splendiani","raw_affiliation_strings":["Dept. Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, AL5 2JQ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, AL5 2JQ, UK","institution_ids":["https://openalex.org/I2799553609"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077915624","display_name":"Martin Kuiper","orcid":"https://orcid.org/0000-0002-1171-9876"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Martin Kuiper","raw_affiliation_strings":["Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. Biology, Norwegian University for Science and Technology (NTNU), Trondheim, 7491, Norway","institution_ids":["https://openalex.org/I204778367"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077915624"],"corresponding_institution_ids":["https://openalex.org/I204778367"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":4.1488,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.94120292,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9984999895095825,"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":0.9901000261306763,"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/computer-science","display_name":"Computer science","score":0.5218602418899536},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4649805724620819},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4485258162021637},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.420803427696228},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41609811782836914},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3174031376838684},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.30121731758117676},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1472225785255432},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07091671228408813}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5218602418899536},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4649805724620819},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4485258162021637},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.420803427696228},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41609811782836914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3174031376838684},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30121731758117676},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1472225785255432},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07091671228408813},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:brage.bibsys.no:11250/2366703","is_oa":false,"landing_page_url":"http://hdl.handle.net/11250/2366703","pdf_url":null,"source":{"id":"https://openalex.org/S4306400255","display_name":"BIBSYS Brage (BIBSYS (Norway))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173212132","host_organization_name":"Vilnius University","host_organization_lineage":["https://openalex.org/I173212132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"13","raw_type":"Journal article"},{"id":"pmh:oai:archive.ugent.be:3072981","is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/3072981","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.rothamsted.ac.uk:8qq2z","is_oa":true,"landing_page_url":"https://dx.doi.org/10.1186/1471-2105-13-S1-S3","pdf_url":null,"source":{"id":"https://openalex.org/S4306402645","display_name":"Rothamsted Repository (Rothamsted Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799553609","host_organization_name":"Rothamsted Research","host_organization_lineage":["https://openalex.org/I2799553609"],"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":"conference-item"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s1-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2014059278","display_name":"From data to knowledge / the ONDEX System for integrating Life Sciences data sources","funder_award_id":"BB/F006039/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2633328597","display_name":null,"funder_award_id":"BB/F006039/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2168301896.pdf","grobid_xml":"https://content.openalex.org/works/W2168301896.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1593630595","https://openalex.org/W1972793074","https://openalex.org/W1988463271","https://openalex.org/W1989009626","https://openalex.org/W2052522161","https://openalex.org/W2061253631","https://openalex.org/W2103103282","https://openalex.org/W2113439138","https://openalex.org/W2129994470","https://openalex.org/W2160845726","https://openalex.org/W2163040665","https://openalex.org/W2165685472","https://openalex.org/W2169049983","https://openalex.org/W2274895364","https://openalex.org/W2612240612","https://openalex.org/W4239696231"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237","https://openalex.org/W2990314835","https://openalex.org/W2899267400","https://openalex.org/W2625471714"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Semantic":[2,22,46,90],"Web":[3,15,23,47,91],"technologies":[4,48,92],"have":[5,150],"been":[6],"developed":[7,128,342],"to":[8,26,117,133,244],"overcome":[9],"the":[10,13,29,33,42,45,50,106,135,153,179,183,188,221,249,254,260,301,309,332],"limitations":[11],"of":[12,36,41,44,108,111,120,131,137,155,215],"current":[14],"and":[16,172,187,201,235,257,281,295,318,325],"conventional":[17],"data":[18,30,180],"integration":[19],"solutions.":[20],"The":[21,89,190],"is":[24,49,62],"expected":[25],"link":[27],"all":[28,300],"present":[31],"on":[32,158],"Internet":[34],"instead":[35],"linking":[37],"just":[38],"documents.":[39],"One":[40],"foundations":[43],"knowledge":[51,139],"representation":[52],"language":[53,83],"Resource":[54],"Description":[55],"Framework":[56],"(RDF).":[57],"Knowledge":[58],"expressed":[59],"in":[60,65,248,253,259,272],"RDF":[61,72],"typically":[63],"stored":[64],"so-called":[66],"triple":[67,99,122,147,161,274],"stores":[68],"(also":[69],"known":[70],"as":[71,115,145,284],"stores),":[73],"from":[74],"which":[75],"it":[76,312],"can":[77],"be":[78,245,346],"retrieved":[79],"with":[80,279],"SPARQL,":[81],"a":[82,109,118,129,146,246,273,287,314,319],"designed":[84],"for":[85,299,343,349],"querying":[86],"RDF-based":[87],"models.":[88],"should":[93],"allow":[94],"federated":[95],"queries":[96,114,132,157,191,216,234,269,303,341],"over":[97],"multiple":[98],"stores.":[100],"In":[101],"this":[102],"paper":[103],"we":[104,127,192,202],"compare":[105],"efficiency":[107],"set":[110],"biologically":[112],"relevant":[113],"applied":[116],"number":[119],"different":[121,222],"store":[123,206,275],"implementations.":[124,335,351],"Results":[125],"Previously":[126],"library":[130],"guide":[134],"use":[136],"our":[138],"base":[140],"Cell":[141],"Cycle":[142],"Ontology":[143],"implemented":[144],"store.":[148],"We":[149,174,211],"now":[151],"compared":[152],"performance":[154,177,207,290],"these":[156],"five":[159],"non-commercial":[160],"stores:":[162,223],"OpenLink":[163],"Virtuoso":[164,258,344],"(Open-Source":[165],"Edition),":[166],"Jena":[167,169,323,326],"SDB,":[168],"TDB,":[170],"SwiftOWLIM":[171,242,280],"4Store.":[173,282],"examined":[175],"three":[176,213,334],"aspects:":[178],"uploading":[181],"time,":[182],"query":[184],"execution":[185],"time":[186,228,233,240,294,298],"scalability.":[189],"had":[193],"chosen":[194],"addressed":[195],"diverse":[196],"ontological":[197],"or":[198],"biological":[199],"questions,":[200],"found":[203],"that":[204,267,339],"individual":[205],"was":[208],"quite":[209],"query-specific.":[210],"identified":[212],"groups":[214],"displaying":[217],"similar":[218],"behaviour":[219],"across":[220],"1)":[224],"relatively":[225,237],"short":[226],"response":[227,232,239,297],"queries,":[229],"2)":[230],"moderate":[231],"3)":[236],"long":[238],"queries.":[241],"proved":[243],"winner":[247],"first":[250],"group,":[251],"4Store":[252],"second":[255],"one":[256],"third":[261],"one.":[262],"Conclusions":[263],"Our":[264,336],"analysis":[265,337],"showed":[266,313],"some":[268],"behaved":[270],"idiosyncratically,":[271],"specific":[276],"manner,":[277],"mainly":[278],"Virtuoso,":[283],"expected,":[285],"displayed":[286],"very":[288,315],"balanced":[289],"-":[291],"its":[292,296],"load":[293],"tested":[302],"were":[304,328],"better":[305],"than":[306,331],"average":[307],"among":[308],"selected":[310],"stores;":[311],"good":[316],"scalability":[317],"reasonable":[320],"run-to-run":[321],"reproducibility.":[322],"SDB":[324],"TDB":[327],"consistently":[329],"slower":[330],"other":[333,350],"demonstrated":[338],"most":[340],"could":[345],"successfully":[347],"used":[348]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
