{"id":"https://openalex.org/W2160926845","doi":"https://doi.org/10.1186/2041-1480-5-32","title":"BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data","display_name":"BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data","publication_year":2014,"publication_date":"2014-07-10","ids":{"openalex":"https://openalex.org/W2160926845","doi":"https://doi.org/10.1186/2041-1480-5-32","mag":"2160926845","pmid":"https://pubmed.ncbi.nlm.nih.gov/25089180"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-5-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-32","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-32","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-32","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076695031","display_name":"Hongyan Wu","orcid":"https://orcid.org/0000-0002-6887-2548"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hongyan Wu","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]},{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073025090","display_name":"Toyofumi Fujiwara","orcid":"https://orcid.org/0000-0002-0170-9172"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Toyofumi Fujiwara","raw_affiliation_strings":["INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan","INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo, 136-8637, Japan"],"affiliations":[{"raw_affiliation_string":"INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan","institution_ids":[]},{"raw_affiliation_string":"INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo, 136-8637, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063942302","display_name":"Yasunori Yamamoto","orcid":"https://orcid.org/0000-0002-6943-6887"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasunori Yamamoto","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]},{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078283120","display_name":"Jerven Bolleman","orcid":"https://orcid.org/0000-0002-7449-1266"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jerven Bolleman","raw_affiliation_strings":["Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland","Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211, Geneva, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Swiss-Prot group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211, Geneva, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001958215","display_name":"Atsuko Yamaguchi","orcid":"https://orcid.org/0000-0001-7538-5337"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Atsuko Yamaguchi","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]},{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5076695031"],"corresponding_institution_ids":["https://openalex.org/I4210158934"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":9.5371,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.97779749,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"32","last_page":"32"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9919999837875366,"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":0.9919999837875366,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.989300012588501,"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":0.9891999959945679,"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/computer-science","display_name":"Computer science","score":0.823067307472229},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6979295015335083},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.644578218460083},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.6413960456848145},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.6151079535484314},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5796334743499756},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5350948572158813},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.483078271150589},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.4480467736721039},{"id":"https://openalex.org/keywords/data-management","display_name":"Data management","score":0.4276618957519531},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.41636693477630615},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3114638924598694},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.289864182472229},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.22653838992118835},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1293720006942749}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.823067307472229},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6979295015335083},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.644578218460083},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.6413960456848145},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.6151079535484314},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5796334743499756},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5350948572158813},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.483078271150589},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.4480467736721039},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.4276618957519531},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.41636693477630615},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3114638924598694},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.289864182472229},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.22653838992118835},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1293720006942749},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/2041-1480-5-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-32","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-32","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:25089180","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25089180","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4118313","is_oa":true,"landing_page_url":"http://doi.org/10.1186/2041-1480-5-32","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-5-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-5-32","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-5-32","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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 Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320335238","display_name":"Staatssekretariat f\u00fcr Bildung, Forschung und Innovation","ror":"https://ror.org/01kw63t33"},{"id":"https://openalex.org/F4320338078","display_name":"National Bioscience Database Center","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160926845.pdf","grobid_xml":"https://content.openalex.org/works/W2160926845.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W182745451","https://openalex.org/W1495014783","https://openalex.org/W1578906473","https://openalex.org/W1969142598","https://openalex.org/W1989009626","https://openalex.org/W1992674717","https://openalex.org/W1993597101","https://openalex.org/W2020541351","https://openalex.org/W2026203102","https://openalex.org/W2052522161","https://openalex.org/W2076213621","https://openalex.org/W2098405885","https://openalex.org/W2103539617","https://openalex.org/W2113582899","https://openalex.org/W2117190895","https://openalex.org/W2123280311","https://openalex.org/W2127451705","https://openalex.org/W2138807684","https://openalex.org/W2141056051","https://openalex.org/W2161811833","https://openalex.org/W2168301896","https://openalex.org/W2168708922","https://openalex.org/W2169049983","https://openalex.org/W2171681733","https://openalex.org/W2274895364","https://openalex.org/W2293694195","https://openalex.org/W2404210823","https://openalex.org/W2605068739","https://openalex.org/W2794878800","https://openalex.org/W2953113902","https://openalex.org/W4212920271","https://openalex.org/W4229743141","https://openalex.org/W4232154957","https://openalex.org/W4238312772","https://openalex.org/W4239696231","https://openalex.org/W4248441758","https://openalex.org/W4254899372","https://openalex.org/W4255855797"],"related_works":["https://openalex.org/W2615202182","https://openalex.org/W4206665951","https://openalex.org/W2529794967","https://openalex.org/W2904139343","https://openalex.org/W2604011835","https://openalex.org/W3139465322","https://openalex.org/W2484233589","https://openalex.org/W2528203718","https://openalex.org/W4241483715","https://openalex.org/W2768092701"],"abstract_inverted_index":{"Our":[0],"paper":[1],"shows":[2,104,130],"that":[3,51],"with":[4,43,88],"appropriate":[5],"configuration":[6],"Virtuoso":[7,61,78],"and":[8,17,55,60,101,113],"OWLIM-SE":[9,38,59],"can":[10],"satisfy":[11],"the":[12,32,92],"basic":[13],"requirements":[14],"to":[15],"load":[16],"query":[18],"biological":[19],"data":[20,49,74,86,127],"less":[21,97],"than":[22,98],"8":[23],"billion":[24,77],"or":[25,125],"so":[26],"on":[27,84],"a":[28,115,131],"single":[29],"node,":[30],"for":[31,41,121],"simultaneous":[33],"access":[34],"of":[35,94,133],"64":[36],"clients.":[37],"performs":[39,82],"best":[40],"databases":[42],"approximately":[44],"11":[45],"million":[46,54,57,124],"triples;":[47],"For":[48,73],"sets":[50,87],"contain":[52],"94":[53],"590":[56],"triples,":[58],"perform":[62],"best.":[63,80],"They":[64],"do":[65],"not":[66],"show":[67],"overwhelming":[68],"advantage":[69],"over":[70,75],"each":[71],"other;":[72],"4":[76],"works":[79],"4store":[81],"well":[83],"small":[85],"limited":[89],"features":[90],"when":[91],"number":[93],"triples":[95],"is":[96,107,114],"100":[99],"million,":[100],"our":[102],"test":[103],"its":[105],"scalability":[106],"poor;":[108],"Bigdata":[109],"demonstrates":[110],"average":[111],"performance":[112],"good":[116],"open":[117],"source":[118],"triple":[119],"store":[120],"middle-sized":[122],"(500":[123],"so)":[126],"set;":[128],"Mulgara":[129],"little":[132],"fragility.":[134]},"counts_by_year":[{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}
