{"id":"https://openalex.org/W4362601037","doi":"https://doi.org/10.1093/bioinformatics/btad174","title":"K-RET: knowledgeable biomedical relation extraction system","display_name":"K-RET: knowledgeable biomedical relation extraction system","publication_year":2023,"publication_date":"2023-04-01","ids":{"openalex":"https://openalex.org/W4362601037","doi":"https://doi.org/10.1093/bioinformatics/btad174","pmid":"https://pubmed.ncbi.nlm.nih.gov/37018156"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad174","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/4/btad174/50015871/btad174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/4/btad174/50015871/btad174.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075883524","display_name":"Diana Sousa","orcid":"https://orcid.org/0000-0003-0597-9273"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Diana F Sousa","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa 1749-016, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-0597-9273","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa 1749-016, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014333753","display_name":"Francisco M. Couto","orcid":"https://orcid.org/0000-0003-0627-1496"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Francisco M Couto","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa 1749-016, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-0627-1496","affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa 1749-016, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5075883524"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.0352,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.8650447,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9606000185012817,"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":0.9606000185012817,"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/T10028","display_name":"Topic Modeling","score":0.028599999845027924,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.0012000000569969416,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.8075881004333496},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5876734256744385},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.5746260285377502},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3302115201950073},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2812332510948181},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16927465796470642},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15994426608085632},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.1487913429737091}],"concepts":[{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.8075881004333496},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5876734256744385},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.5746260285377502},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3302115201950073},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2812332510948181},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16927465796470642},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15994426608085632},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.1487913429737091}],"mesh":[{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad174","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/4/btad174/50015871/btad174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37018156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37018156","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10112952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10112952","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10112952/pdf/btad174.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1970408","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1970408","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad174","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad174","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/4/btad174/50015871/btad174.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1759428316","display_name":"LASIGE - Extreme Computing","funder_award_id":"UIDP/00408/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1831196592","display_name":null,"funder_award_id":"PTDC/CCIBIO/28685/2017","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G2089664753","display_name":"LASIGE - Extreme Computing","funder_award_id":"UIDB/00408/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5240966281","display_name":null,"funder_award_id":"UIDB/00408/2020 and UIDP/00408/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5454278309","display_name":null,"funder_award_id":"/2017","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320337197","display_name":"Nuclear Fuel Cycle and Supply Chain","ror":"https://ror.org/05tj7dm33"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4362601037.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2033377040","https://openalex.org/W2103017472","https://openalex.org/W2123112337","https://openalex.org/W2135192531","https://openalex.org/W2148282068","https://openalex.org/W2159583324","https://openalex.org/W2170189740","https://openalex.org/W2346452181","https://openalex.org/W2911489562","https://openalex.org/W2950595506","https://openalex.org/W3026298482","https://openalex.org/W3046375318","https://openalex.org/W3106811464","https://openalex.org/W3109027161","https://openalex.org/W3131198033","https://openalex.org/W3134169372","https://openalex.org/W3163457243","https://openalex.org/W3183495504","https://openalex.org/W3207974842","https://openalex.org/W3214608846","https://openalex.org/W4252974092","https://openalex.org/W4280590868","https://openalex.org/W4284959212"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4234874385","https://openalex.org/W2390279801","https://openalex.org/W2323648130","https://openalex.org/W2358668433","https://openalex.org/W2157140558","https://openalex.org/W2376932109","https://openalex.org/W2378782423","https://openalex.org/W2001405890","https://openalex.org/W2382290278"],"abstract_inverted_index":{"MOTIVATION:":[0],"Relation":[1],"extraction":[2],"(RE)":[3],"is":[4,26],"a":[5,23,27,57,97,173],"crucial":[6],"process":[7],"to":[8,18,120,168],"deal":[9],"with":[10,56,155],"the":[11,33,48,61,65,105,156,160],"amount":[12],"of":[13,50,71,114,175],"text":[14,28],"published":[15],"daily,":[16],"e.g.":[17],"find":[19],"missing":[20],"associations":[21],"in":[22,60,84,92,164,170],"database.":[24],"RE":[25,101],"mining":[29],"task":[30],"for":[31,104],"which":[32],"state-of-the-art":[34,42,149],"approaches":[35],"use":[36],"bidirectional":[37],"encoders,":[38],"namely,":[39],"BERT.":[40],"However,":[41],"performance":[43],"may":[44],"be":[45],"limited":[46],"by":[47,81,110,151],"lack":[49],"efficient":[51],"external":[52],"knowledge":[53,75,109],"injection":[54],"approaches,":[55],"larger":[58],"impact":[59],"biomedical":[62,72,88,100,142],"area":[63],"given":[64],"widespread":[66],"usage":[67],"and":[68,118,123,133,138],"high":[69],"quality":[70],"ontologies.":[73],"This":[74],"can":[76],"propel":[77],"these":[78],"systems":[79],"forward":[80],"aiding":[82],"them":[83],"predicting":[85],"more":[86],"explainable":[87],"associations.":[89],"With":[90],"this":[91],"mind,":[93],"we":[94],"developed":[95],"K-RET,":[96],"novel,":[98],"knowledgeable":[99],"system":[102],"that,":[103],"first":[106],"time,":[107],"injects":[108],"handling":[111,144],"different":[112,145],"types":[113],"associations,":[115],"multiple":[116],"sources":[117],"where":[119],"apply":[121],"it,":[122],"multi-token":[124],"entities.":[125,146],"RESULTS:":[126],"We":[127],"tested":[128],"K-RET":[129,147],"on":[130,153],"three":[131],"independent":[132],"open-access":[134],"corpora":[135],"(DDI,":[136],"BC5CDR,":[137],"PGR)":[139],"using":[140],"four":[141],"ontologies":[143],"improved":[148],"results":[150],"2.68%":[152],"average,":[154],"DDI":[157],"Corpus":[158],"yielding":[159],"most":[161],"significant":[162],"boost":[163],"performance,":[165],"from":[166],"79.30%":[167],"87.19%":[169],"F-measure,":[171],"representing":[172],"P-value":[174],"2.91\u00d710-12.":[176],"AVAILABILITY":[177],"AND":[178],"IMPLEMENTATION:":[179],"https://github.com/lasigeBioTM/K-RET.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
