{"id":"https://openalex.org/W4416254417","doi":"https://doi.org/10.48550/arxiv.2509.19057","title":"RELATE: Relation Extraction in Biomedical Abstracts with LLMs and Ontology Constraints","display_name":"RELATE: Relation Extraction in Biomedical Abstracts with LLMs and Ontology Constraints","publication_year":2025,"publication_date":"2025-09-23","ids":{"openalex":"https://openalex.org/W4416254417","doi":"https://doi.org/10.48550/arxiv.2509.19057"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2509.19057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2509.19057","pdf_url":"https://arxiv.org/pdf/2509.19057","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2509.19057","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114420098","display_name":"Olawumi Olasunkanmi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Olasunkanmi, Olawumi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Satusky, Mathew","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Satusky, Mathew","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051369513","display_name":"Hong Yi","orcid":"https://orcid.org/0000-0002-5699-1259"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yi, Hong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043972221","display_name":"Chris Bizon","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bizon, Chris","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055567952","display_name":"Harlin Lee","orcid":"https://orcid.org/0000-0001-6128-9942"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lee, Harlin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5072157766","display_name":"Stanley C. Ahalt","orcid":"https://orcid.org/0000-0002-8395-1279"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ahalt, Stanley","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.5936999917030334,"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":0.5936999917030334,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.12520000338554382,"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":0.10980000346899033,"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/ontology","display_name":"Ontology","score":0.5845000147819519},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5475000143051147},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5379999876022339},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5285000205039978},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.5090000033378601},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.4878000020980835},{"id":"https://openalex.org/keywords/negation","display_name":"Negation","score":0.4553000032901764},{"id":"https://openalex.org/keywords/predicate","display_name":"Predicate (mathematical logic)","score":0.45399999618530273},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.39879998564720154}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7073000073432922},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5845000147819519},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5475000143051147},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5379999876022339},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5285000205039978},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5138000249862671},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.5090000033378601},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.4878000020980835},{"id":"https://openalex.org/C2185349","wikidata":"https://www.wikidata.org/wiki/Q190558","display_name":"Negation","level":2,"score":0.4553000032901764},{"id":"https://openalex.org/C140146324","wikidata":"https://www.wikidata.org/wiki/Q1144319","display_name":"Predicate (mathematical logic)","level":2,"score":0.45399999618530273},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.39879998564720154},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.38659998774528503},{"id":"https://openalex.org/C2988080768","wikidata":"https://www.wikidata.org/wiki/Q7095057","display_name":"Semantic relation","level":3,"score":0.37610000371932983},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36550000309944153},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.35280001163482666},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.335099995136261},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3328999876976013},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.32910001277923584},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.32519999146461487},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.31299999356269836},{"id":"https://openalex.org/C234837","wikidata":"https://www.wikidata.org/wiki/Q1420493","display_name":"Conceptual graph","level":3,"score":0.29670000076293945},{"id":"https://openalex.org/C58166","wikidata":"https://www.wikidata.org/wiki/Q224821","display_name":"Fuzzy logic","level":2,"score":0.2770000100135803},{"id":"https://openalex.org/C2778820784","wikidata":"https://www.wikidata.org/wiki/Q1027508","display_name":"Ontology engineering","level":4,"score":0.2612000107765198},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2554999887943268},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2551000118255615},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2538999915122986},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.2538999915122986},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.25369998812675476},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.25279998779296875},{"id":"https://openalex.org/C10551718","wikidata":"https://www.wikidata.org/wiki/Q5227332","display_name":"Data pre-processing","level":2,"score":0.2515000104904175}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2509.19057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2509.19057","pdf_url":"https://arxiv.org/pdf/2509.19057","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"doi:10.48550/arxiv.2509.19057","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2509.19057","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2509.19057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2509.19057","pdf_url":"https://arxiv.org/pdf/2509.19057","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Biomedical":[0],"knowledge":[1],"graphs":[2],"(KGs)":[3],"are":[4],"vital":[5],"for":[6,128,146],"drug":[7],"discovery":[8],"and":[9,30,53,72,101,104,116],"clinical":[10],"decision":[11],"support":[12],"but":[13],"remain":[14],"incomplete.":[15],"Large":[16],"language":[17],"models":[18],"(LLMs)":[19],"excel":[20],"at":[21],"extracting":[22],"biomedical":[23,123,149],"relations,":[24],"yet":[25],"their":[26],"outputs":[27,87],"lack":[28],"standardization":[29],"alignment":[31],"with":[32,63,70,76,135],"ontologies,":[33],"limiting":[34],"KG":[35,129],"integration.":[36],"We":[37],"introduce":[38],"RELATE,":[39],"a":[40,141],"three-stage":[41],"pipeline":[42,58],"that":[43],"maps":[44],"LLM-extracted":[45],"relations":[46],"to":[47,88],"standardized":[48,152],"ontology":[49,61],"predicates":[50],"using":[51],"ChemProt":[52,94],"the":[54,93],"Biolink":[55],"Model.":[56],"The":[57],"includes:":[59],"(1)":[60],"preprocessing":[62],"predicate":[64],"embeddings,":[65],"(2)":[66],"similarity-based":[67],"retrieval":[68],"enhanced":[69],"SapBERT,":[71],"(3)":[73],"LLM-based":[74],"reranking":[75],"explicit":[77],"negation":[78],"handling.":[79],"This":[80],"approach":[81],"transforms":[82],"relation":[83],"extraction":[84],"from":[85],"free-text":[86],"structured,":[89],"ontology-constrained":[90],"representations.":[91],"On":[92],"benchmark,":[95],"RELATE":[96,120,139],"achieves":[97],"52%":[98],"exact":[99],"match":[100],"94%":[102],"accuracy@10,":[103],"in":[105],"2,400":[106],"HEAL":[107],"Project":[108],"abstracts,":[109],"it":[110],"effectively":[111],"rejects":[112],"irrelevant":[113],"associations":[114],"(0.4%)":[115],"identifies":[117],"negated":[118],"assertions.":[119],"captures":[121],"nuanced":[122],"relationships":[124],"while":[125],"ensuring":[126],"quality":[127],"augmentation.":[130],"By":[131],"combining":[132],"vector":[133],"search":[134],"contextual":[136],"LLM":[137],"reasoning,":[138],"provides":[140],"scalable,":[142],"semantically":[143],"accurate":[144],"framework":[145],"converting":[147],"unstructured":[148],"literature":[150],"into":[151],"KGs.":[153]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
