{"id":"https://openalex.org/W2170936537","doi":"https://doi.org/10.1186/2041-1480-4-8","title":"Building Linked Open Data towards integration of biomedical scientific literature with DBpedia","display_name":"Building Linked Open Data towards integration of biomedical scientific literature with DBpedia","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2170936537","doi":"https://doi.org/10.1186/2041-1480-4-8","mag":"2170936537","pmid":"https://pubmed.ncbi.nlm.nih.gov/23497538"},"language":"en","primary_location":{"id":"doi:10.1186/2041-1480-4-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-8","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/10.1186/2041-1480-4-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063942302","display_name":"Yasunori Yamamoto","orcid":"https://orcid.org/0000-0002-6943-6887"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yasunori Yamamoto","raw_affiliation_strings":["Database Center for Life Science, Faculty of Engineering Bldg, 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan. yy@dbcls.rois.ac.jp","Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg, 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan. yy@dbcls.rois.ac.jp","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001958215","display_name":"Atsuko Yamaguchi","orcid":"https://orcid.org/0000-0001-7538-5337"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Atsuko Yamaguchi","raw_affiliation_strings":["Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan","Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109877761","display_name":"Akinori Yonezawa","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akinori Yonezawa","raw_affiliation_strings":["Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan","Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Database Center for Life Science, Faculty of Engineering Bldg. 12, The University of Tokyo, Bunkyo-ku, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063942302"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":1340,"currency":"USD","value_usd":1340},"apc_paid":{"value":1340,"currency":"USD","value_usd":1340},"fwci":1.1006,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.77361746,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"4","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9298999905586243,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9298999905586243,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.013700000010430813,"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/T14427","display_name":"Environmental Monitoring and Data Management","score":0.01360000018030405,"subfield":{"id":"https://openalex.org/subfields/1907","display_name":"Geology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8385292887687683},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.637735903263092},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.584030032157898},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5278677344322205},{"id":"https://openalex.org/keywords/synonym","display_name":"Synonym (taxonomy)","score":0.51711106300354},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.47714564204216003},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4383794367313385},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.42541009187698364}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8385292887687683},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.637735903263092},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.584030032157898},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5278677344322205},{"id":"https://openalex.org/C173483453","wikidata":"https://www.wikidata.org/wiki/Q1040689","display_name":"Synonym (taxonomy)","level":3,"score":0.51711106300354},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.47714564204216003},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4383794367313385},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.42541009187698364},{"id":"https://openalex.org/C157369684","wikidata":"https://www.wikidata.org/wiki/Q34740","display_name":"Genus","level":2,"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/2041-1480-4-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-8","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:23497538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23497538","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:europepmc.org:2623993","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3621846","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3621846","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3621846","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Biomed Semantics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/2041-1480-4-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2041-1480-4-8","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/2041-1480-4-8","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/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338078","display_name":"National Bioscience Database Center","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170936537.pdf","grobid_xml":"https://content.openalex.org/works/W2170936537.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W41404523","https://openalex.org/W1647671624","https://openalex.org/W1972793074","https://openalex.org/W1973726039","https://openalex.org/W2066102695","https://openalex.org/W2101906686","https://openalex.org/W2118658201","https://openalex.org/W2138807684","https://openalex.org/W2142787640","https://openalex.org/W2156467546","https://openalex.org/W2160845726"],"related_works":["https://openalex.org/W2776293731","https://openalex.org/W1723367271","https://openalex.org/W4211148702","https://openalex.org/W1780389289","https://openalex.org/W1607526536","https://openalex.org/W2127217276","https://openalex.org/W4239617640","https://openalex.org/W2130019778","https://openalex.org/W4293165842","https://openalex.org/W2779513816"],"abstract_inverted_index":{"BACKGROUND:":[0],"There":[1,311],"is":[2,146,179,312],"a":[3,18,71,122,150,168,176,189,204,247,313,355],"growing":[4],"need":[5],"for":[6,75,118,401],"efficient":[7],"and":[8,34,50,68,106,196,222,260,282,329,353,358,376,387,396],"integrated":[9],"access":[10],"to":[11,30,77,104,120,148,156,163,170,212,225,240,265,382,389],"databases":[12],"provided":[13],"by":[14,37,215,277],"diverse":[15,25],"institutions.":[16],"Using":[17],"linked":[19,32,380],"data":[20,26],"design":[21],"pattern":[22],"allows":[23],"the":[24,28,42,59,64,80,102,108,128,134,140,160,171,242,250,255,271,274,295,303,306,322,344,348,360,379,384],"on":[27],"Internet":[29],"be":[31],"effectively":[33],"accessed":[35],"efficiently":[36],"computers.":[38],"Previously,":[39],"we":[40,236,373],"developed":[41],"Allie":[43,69,161,195,341],"database,":[44],"which":[45,99,145,228],"stores":[46],"pairs":[47,187],"of":[48,66,82,136,153,181,185,192,273,288,305,325],"abbreviations":[49,109],"long":[51],"forms":[52],"(LFs,":[53],"or":[54],"expanded":[55],"forms)":[56],"used":[57,237,363],"in":[58,139,308,327,333,365,370],"life":[60,243],"sciences.":[61],"LFs":[62,117,162,211,262,307,326,364,392],"define":[63],"semantics":[65],"abbreviations,":[67],"provides":[70],"Web-based":[72],"search":[73],"service":[74,87],"researchers":[76],"look":[78],"up":[79],"LF":[81],"an":[83,286],"unfamiliar":[84],"abbreviation.":[85],"This":[86,174],"encounters":[88],"two":[89],"problems.":[90,173],"First,":[91],"it":[92],"does":[93],"not":[94],"display":[95],"each":[96],"LF's":[97],"definition,":[98],"could":[100],"help":[101,340],"user":[103],"disambiguate":[105],"learn":[107],"more":[110,368],"easily.":[111],"Furthermore,":[112],"there":[113],"are":[114,198,229,350],"too":[115],"many":[116],"us":[119],"prepare":[121],"full":[123],"dictionary":[124],"from":[125,302],"scratch.":[126],"On":[127],"other":[129],"hand,":[130],"DBpedia":[131,164,197,213,266,334,371,397],"has":[132],"made":[133],"contents":[135],"Wikipedia":[137],"available":[138],"Resource":[141],"Description":[142],"Framework":[143],"(RDF),":[144],"expected":[147],"contain":[149],"significant":[151],"number":[152],"entries":[154,165],"corresponding":[155],"LFs.":[157,346],"Therefore,":[158],"linking":[159],"may":[166],"present":[167],"solution":[169],"Allie's":[172],"requires":[175],"method":[177],"that":[178,209],"capable":[180],"matching":[182,276],"large":[183],"numbers":[184],"string":[186,275],"within":[188],"reasonable":[190],"period":[191],"time":[193],"because":[194,359],"frequently":[199,362],"updated.":[200],"RESULTS:":[201],"We":[202,268],"built":[203],"Linked":[205],"Open":[206],"Data":[207],"set":[208],"links":[210,264],"titles":[214],"applying":[216],"key":[217,251],"collision":[218,252],"methods":[219,253,349],"(i.e.,":[220],"fingerprint":[221],"n-gram":[223],"fingerprint)":[224],"their":[226,330],"literals,":[227],"simple":[230,352],"approximate":[231],"string-matching":[232],"methods.":[233],"In":[234,290],"addition,":[235,291],"UMLS":[238],"resources":[239,257],"normalise":[241],"science":[244],"terms.":[245],"As":[246],"result,":[248],"combining":[249],"with":[254],"domain-specific":[256],"performed":[258],"best,":[259],"44,027":[261],"have":[263],"titles.":[267,335],"manually":[269],"evaluated":[270],"accuracy":[272],"randomly":[278],"sampling":[279],"1200":[280],"LFs,":[281],"our":[283,292],"approach":[284],"achieved":[285],"F-measure":[287],"0.98.":[289],"experiments":[293],"revealed":[294],"following.":[296],"(1)":[297],"Performances":[298],"were":[299],"similar":[300],"independently":[301],"frequency":[304],"MEDLINE.":[309],"(2)":[310],"relationship":[314],"(r2":[315],"=":[316],"0.96,":[317],"P":[318],"<":[319],"0.01)":[320],"between":[321,393],"occurrence":[323],"frequencies":[324],"MEDLINE":[328,366],"presence":[331],"probabilities":[332],"CONCLUSIONS:":[336],"The":[337],"obtained":[338],"results":[339],"users":[342],"locate":[343],"correct":[345],"Because":[347],"computationally":[351],"yield":[354],"high":[356],"performance":[357],"most":[361],"appear":[367],"often":[369],"titles,":[372],"can":[374],"continually":[375],"reasonably":[377],"update":[378],"dataset":[381],"reflect":[383],"latest":[385],"publications":[386],"additions":[388],"DBpedia.":[390],"Joining":[391],"scientific":[394],"literature":[395],"enables":[398],"cross-resource":[399],"exploration":[400],"mutual":[402],"benefits.":[403]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
