{"id":"https://openalex.org/W2044330111","doi":"https://doi.org/10.1142/s1793351x14500032","title":"Enabling Ontology Based Semantic Queries in Biomedical Database Systems","display_name":"Enabling Ontology Based Semantic Queries in Biomedical Database Systems","publication_year":2014,"publication_date":"2014-03-01","ids":{"openalex":"https://openalex.org/W2044330111","doi":"https://doi.org/10.1142/s1793351x14500032","mag":"2044330111","pmid":"https://pubmed.ncbi.nlm.nih.gov/25541585"},"language":"en","primary_location":{"id":"doi:10.1142/s1793351x14500032","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s1793351x14500032","pdf_url":null,"source":{"id":"https://openalex.org/S4210201727","display_name":"International Journal of Semantic Computing","issn_l":"1793-351X","issn":["1793-351X","1793-7108"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Semantic Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083941550","display_name":"Shuai Zheng","orcid":"https://orcid.org/0000-0002-8090-9278"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuai Zheng","raw_affiliation_strings":["Department of Mathematics and Computer Science, Emory University Atlanta, Georgia, USA","Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Emory University Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100704639","display_name":"Fusheng Wang","orcid":"https://orcid.org/0000-0002-9369-9361"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fusheng Wang","raw_affiliation_strings":["Department of Biomedical Informatics, Emory University Atlanta, Georgia, USA","Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Emory University Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101476502","display_name":"James J. Lu","orcid":"https://orcid.org/0000-0001-7888-7412"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Lu","raw_affiliation_strings":["Department of Mathematics and Computer Science, Emory University Atlanta, Georgia, USA","Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Emory University Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I150468666"],"apc_list":null,"apc_paid":null,"fwci":0.5584,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.66275883,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"08","issue":"01","first_page":"67","last_page":"83"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9986000061035156,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9819999933242798,"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":0.8965651988983154},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6568889617919922},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5897043347358704},{"id":"https://openalex.org/keywords/semantic-query","display_name":"Semantic query","score":0.5712493062019348},{"id":"https://openalex.org/keywords/sparql","display_name":"SPARQL","score":0.5375401973724365},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4773845076560974},{"id":"https://openalex.org/keywords/query-language","display_name":"Query language","score":0.4596201479434967},{"id":"https://openalex.org/keywords/query-optimization","display_name":"Query optimization","score":0.4510471522808075},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.4266185462474823},{"id":"https://openalex.org/keywords/view","display_name":"View","score":0.4189606308937073},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3236009478569031},{"id":"https://openalex.org/keywords/web-search-query","display_name":"Web search query","score":0.3036285638809204},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.2119370698928833},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.19694259762763977},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.11405274271965027}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8965651988983154},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6568889617919922},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5897043347358704},{"id":"https://openalex.org/C2778816267","wikidata":"https://www.wikidata.org/wiki/Q21015578","display_name":"Semantic query","level":4,"score":0.5712493062019348},{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.5375401973724365},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4773845076560974},{"id":"https://openalex.org/C192028432","wikidata":"https://www.wikidata.org/wiki/Q845739","display_name":"Query language","level":2,"score":0.4596201479434967},{"id":"https://openalex.org/C157692150","wikidata":"https://www.wikidata.org/wiki/Q2919848","display_name":"Query optimization","level":2,"score":0.4510471522808075},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.4266185462474823},{"id":"https://openalex.org/C54239708","wikidata":"https://www.wikidata.org/wiki/Q1329910","display_name":"View","level":3,"score":0.4189606308937073},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3236009478569031},{"id":"https://openalex.org/C164120249","wikidata":"https://www.wikidata.org/wiki/Q995982","display_name":"Web search query","level":3,"score":0.3036285638809204},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.2119370698928833},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.19694259762763977},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.11405274271965027},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1142/s1793351x14500032","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s1793351x14500032","pdf_url":null,"source":{"id":"https://openalex.org/S4210201727","display_name":"International Journal of Semantic Computing","issn_l":"1793-351X","issn":["1793-351X","1793-7108"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Semantic Computing","raw_type":"journal-article"},{"id":"pmid:25541585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25541585","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":"International journal of semantic computing","raw_type":null},{"id":"pmh:oai:europepmc.org:3240726","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4275106","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1980356736","display_name":null,"funder_award_id":"UL1 RR025008","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G3275434493","display_name":null,"funder_award_id":"R01 LM009239","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6032214852","display_name":null,"funder_award_id":"HHSN261200800001E","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2811659","https://openalex.org/W1537351552","https://openalex.org/W1581156986","https://openalex.org/W1804396726","https://openalex.org/W1993456074","https://openalex.org/W2014485346","https://openalex.org/W2077284797","https://openalex.org/W2091729411","https://openalex.org/W2092023749","https://openalex.org/W2103260426","https://openalex.org/W2123152121","https://openalex.org/W2131660156","https://openalex.org/W2140480784","https://openalex.org/W4210894999","https://openalex.org/W4231091991"],"related_works":["https://openalex.org/W1821144310","https://openalex.org/W3193425175","https://openalex.org/W2614542053","https://openalex.org/W2494918970","https://openalex.org/W1574546694","https://openalex.org/W1528266144","https://openalex.org/W2036832324","https://openalex.org/W4287661590","https://openalex.org/W3088315510","https://openalex.org/W3095095169"],"abstract_inverted_index":{"There":[0],"is":[1,122],"a":[2,29,56,152,166],"lack":[3],"of":[4,154,200,207],"tools":[5],"to":[6,27,39,90,116,125],"ease":[7],"the":[8,45,69,83,91,135,197,204,208],"integration":[9],"and":[10,35,64,67,109,160,177,186,190,203],"ontology":[11,23,33,72,156],"based":[12,157],"semantic":[13,41,57,62,95,158,201],"queries":[14,42,70,96,202],"in":[15,44,82,101],"biomedical":[16,182],"databases,":[17],"which":[18,143],"are":[19,80],"often":[20],"annotated":[21,37],"with":[22,47,165,179],"concepts.":[24],"We":[25,53,132],"aim":[26],"provide":[28],"middle":[30],"layer":[31],"between":[32],"repositories":[34],"semantically":[36],"databases":[38,46],"support":[40,126],"directly":[43,99],"expressive":[48],"standard":[49,102],"database":[50,84,92,103,167,183],"query":[51,58,65,104,118],"languages.":[52],"have":[54,133,161],"developed":[55],"engine":[59],"that":[60],"provides":[61,113],"reasoning":[63],"processing,":[66],"translates":[68],"into":[71],"repository":[73],"operations":[74,159],"on":[75],"NCBO":[76],"BioPortal.":[77,149],"Semantic":[78],"operators":[79],"implemented":[81,134],"as":[85,107,138],"user":[86],"defined":[87],"functions":[88],"extended":[89],"engine,":[93],"thus":[94],"can":[97],"be":[98],"specified":[100],"languages":[105],"such":[106],"SQL":[108],"XQuery.":[110],"The":[111,120,172],"system":[112,121,136,169,173],"caching":[114],"management":[115,168],"boosts":[117],"performance.":[119],"highly":[123],"adaptable":[124],"different":[127],"ontologies":[128,146],"through":[129],"easy":[130],"customizations.":[131],"DBOntoLink":[137,150],"an":[139,180],"open":[140],"source":[141],"software,":[142],"supports":[144,151],"major":[145],"hosted":[147],"at":[148],"set":[153],"common":[155],"them":[162],"fully":[163],"integrated":[164],"IBM":[170],"DB2.":[171],"has":[174],"been":[175],"deployed":[176],"evaluated":[178],"existing":[181],"for":[184],"managing":[185],"querying":[187],"image":[188],"annotations":[189],"markups":[191],"(AIM).":[192],"Our":[193],"performance":[194],"study":[195],"demonstrates":[196],"high":[198,205],"expressiveness":[199],"efficiency":[206],"queries.":[209]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
