{"id":"https://openalex.org/W2531566782","doi":"https://doi.org/10.1186/s13040-016-0110-8","title":"FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies","display_name":"FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies","publication_year":2016,"publication_date":"2016-10-10","ids":{"openalex":"https://openalex.org/W2531566782","doi":"https://doi.org/10.1186/s13040-016-0110-8","mag":"2531566782","pmid":"https://pubmed.ncbi.nlm.nih.gov/27777627"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-016-0110-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0110-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0110-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0110-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019398706","display_name":"Guangming Xing","orcid":"https://orcid.org/0000-0002-1234-5247"},"institutions":[{"id":"https://openalex.org/I94339441","display_name":"Western Kentucky University","ror":"https://ror.org/0446vnd56","country_code":"US","type":"education","lineage":["https://openalex.org/I94339441"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guangming Xing","raw_affiliation_strings":["Department of Computer Science, Western Kentucky University, Bowling Green, 42101 KY USA","Department of Computer Science, Western Kentucky University, Bowling Green, 42101, KY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Kentucky University, Bowling Green, 42101 KY USA","institution_ids":["https://openalex.org/I94339441"]},{"raw_affiliation_string":"Department of Computer Science, Western Kentucky University, Bowling Green, 42101, KY, USA","institution_ids":["https://openalex.org/I94339441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392487","display_name":"Guo\u2010Qiang Zhang","orcid":"https://orcid.org/0000-0002-3663-1109"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guo-Qiang Zhang","raw_affiliation_strings":["Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536 KY USA","Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536, KY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536 KY USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536, KY, USA","institution_ids":["https://openalex.org/I143302722"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049834185","display_name":"Licong Cui","orcid":"https://orcid.org/0000-0001-5549-8780"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Licong Cui","raw_affiliation_strings":["Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536 KY USA ; Department of Computer Science, University of Kentucky, Lexington, 40506 KY USA","Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536, KY, USA"],"raw_orcid":"https://orcid.org/0000-0001-5549-8780","affiliations":[{"raw_affiliation_string":"Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536 KY USA ; Department of Computer Science, University of Kentucky, Lexington, 40506 KY USA","institution_ids":["https://openalex.org/I143302722"]},{"raw_affiliation_string":"Institute of Biomedical Informatics, University of Kentucky, Lexington, 40536, KY, USA","institution_ids":["https://openalex.org/I143302722"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019398706"],"corresponding_institution_ids":["https://openalex.org/I94339441"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2186,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.80865705,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"9","issue":"1","first_page":"31","last_page":"31"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9355000257492065,"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":0.9355000257492065,"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":0.04179999977350235,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.010499999858438969,"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":0.7524620294570923},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6785871982574463},{"id":"https://openalex.org/keywords/snomed-ct","display_name":"SNOMED CT","score":0.6147876977920532},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.5717901587486267},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5625881552696228},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5215242505073547},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48420217633247375},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.4695014953613281},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4608132243156433},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.441888689994812},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4211363196372986},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.22789093852043152},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.22412893176078796},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.2091379165649414},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10268807411193848}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7524620294570923},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6785871982574463},{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.6147876977920532},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.5717901587486267},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5625881552696228},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5215242505073547},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48420217633247375},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.4695014953613281},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4608132243156433},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.441888689994812},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4211363196372986},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.22789093852043152},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.22412893176078796},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2091379165649414},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10268807411193848},{"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},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-016-0110-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0110-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0110-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:27777627","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27777627","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":"BioData mining","raw_type":null},{"id":"pmh:oai:uknowledge.uky.edu:bmi_facpub-1001","is_oa":true,"landing_page_url":"https://uknowledge.uky.edu/bmi_facpub/2","pdf_url":null,"source":{"id":"https://openalex.org/S4306402622","display_name":"UKnowledge (University of Kentucky)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I143302722","host_organization_name":"University of Kentucky","host_organization_lineage":["https://openalex.org/I143302722"],"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":"Institute of Biomedical Informatics Faculty Publications","raw_type":"text"},{"id":"pmh:oai:europepmc.org:4024247","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5057496","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"}],"best_oa_location":{"id":"doi:10.1186/s13040-016-0110-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0110-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0110-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G442359647","display_name":null,"funder_award_id":"UL1TR000117","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6095080147","display_name":null,"funder_award_id":"UL1TR000117","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"}],"funders":[{"id":"https://openalex.org/F4320311307","display_name":"Western Kentucky University","ror":"https://ror.org/0446vnd56"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2531566782.pdf","grobid_xml":"https://content.openalex.org/works/W2531566782.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W46109541","https://openalex.org/W145466531","https://openalex.org/W174626886","https://openalex.org/W1034019924","https://openalex.org/W1456257443","https://openalex.org/W1496540677","https://openalex.org/W1527927437","https://openalex.org/W1540874816","https://openalex.org/W2030103067","https://openalex.org/W2033406996","https://openalex.org/W2042820337","https://openalex.org/W2060948468","https://openalex.org/W2087204000","https://openalex.org/W2111715483","https://openalex.org/W2111831827","https://openalex.org/W2139144616","https://openalex.org/W2145900192","https://openalex.org/W2150387423","https://openalex.org/W2156997379","https://openalex.org/W2159583324","https://openalex.org/W2159946338","https://openalex.org/W2162181203","https://openalex.org/W2162684758","https://openalex.org/W2188545607","https://openalex.org/W2394650573","https://openalex.org/W2401811235","https://openalex.org/W2402498766","https://openalex.org/W2404369708","https://openalex.org/W2411864871","https://openalex.org/W2418920503","https://openalex.org/W2565311449"],"related_works":["https://openalex.org/W2400033706","https://openalex.org/W2507623806","https://openalex.org/W2127299687","https://openalex.org/W149627178","https://openalex.org/W22148886","https://openalex.org/W4206428734","https://openalex.org/W152870918","https://openalex.org/W1794266373","https://openalex.org/W2365397974","https://openalex.org/W2357882026"],"abstract_inverted_index":{"Redundant":[0,100],"hierarchical":[1,127],"relations":[2,52,128,166,187,257],"refer":[3],"to":[4,13,39,239],"such":[5,70],"patterns":[6],"as":[7,67,71],"two":[8,168],"paths":[9],"from":[10],"one":[11,15,18,27],"concept":[12],"another,":[14],"with":[16,23,118],"length":[17,24],"(direct)":[19],"and":[20,49,79,83,90,149,178,183,197,224],"the":[21,43,56,63,72,112,138,144,147,170,191,214,242],"other":[22],"greater":[25],"than":[26],"(indirect).":[28],"Each":[29],"redundant":[30,51,126,164,185,229,256],"relation":[31],"represents":[32],"a":[33,88,152,217,248],"possibly":[34],"unintended":[35],"defect":[36],"that":[37],"needs":[38],"be":[40],"corrected":[41],"in":[42,129,132,154,167,174,190,213,258],"ontology":[44,81],"quality":[45,104,263],"assurance":[46,105],"process.":[47],"Detecting":[48],"eliminating":[50],"would":[53],"help":[54],"improve":[55],"results":[57],"of":[58,74,99,115,124,140,146,162,169,194,200,221,244],"all":[59,125,163],"methods":[60],"relying":[61],"on":[62,208],"relevant":[64],"ontological":[65,108,130,172,260],"systems":[66,173,261],"knowledge":[68],"source,":[69],"computation":[73],"semantic":[75],"distance":[76],"between":[77],"concepts":[78],"for":[80,103,121,253,262],"matching":[82],"alignment.":[84],"This":[85],"paper":[86],"introduces":[87],"novel":[89],"scalable":[91],"approach,":[92],"called":[93],"FEDRR":[94,110,207,246],"\u2013":[95,102],"Fast,":[96],"Exhaustive":[97],"Detection":[98],"Relations":[101],"work":[106],"during":[107],"evolution.":[109],"combines":[111],"algorithm":[113],"ideas":[114],"Dynamic":[116],"Programming":[117],"Topological":[119],"Sort,":[120],"exhaustive":[122,160],"mining":[123],"hierarchies,":[131],"O(c\u00b7|V|+|E|)":[133],"time,":[134],"where":[135],"|V|":[136],"is":[137,143,151],"number":[139,145],"concepts,":[141],"|E|":[142],"relations,":[148],"c":[150],"constant":[153],"practice.":[155],"Using":[156],"FEDRR,":[157],"we":[158],"performed":[159,206],"search":[161],"is-a":[165,186,230],"largest":[171],"biomedicine:":[175],"SNOMED":[176,195],"CT":[177,196],"Gene":[179],"Ontology":[180],"(GO).":[181],"372":[182],"1609":[184],"were":[188],"found":[189],"2015-09-01":[192],"version":[193,199],"2015-05-01":[198],"GO,":[201],"respectively.":[202],"We":[203],"have":[204,235],"also":[205,236],"over":[209],"190":[210],"source":[211],"vocabularies":[212],"UMLS":[215],"-":[216],"large":[218,259],"integrated":[219],"repository":[220],"biomedical":[222],"ontologies,":[223],"identified":[225],"six":[226],"sources":[227],"containing":[228],"relations.":[231],"Randomly":[232],"generated":[233],"ontologies":[234],"been":[237],"used":[238],"further":[240],"validate":[241],"efficiency":[243],"FEDRR.":[245],"provides":[247],"generally":[249],"applicable,":[250],"effective":[251],"tool":[252],"systematic":[254],"detecting":[255],"improvement.":[264]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
