{"id":"https://openalex.org/W6910718406","doi":"https://doi.org/10.48550/arxiv.2204.04263","title":"BioRED: A Rich Biomedical Relation Extraction Dataset","display_name":"BioRED: A Rich Biomedical Relation Extraction Dataset","publication_year":2022,"publication_date":"2022-04-08","ids":{"openalex":"https://openalex.org/W6910718406","doi":"https://doi.org/10.48550/arxiv.2204.04263"},"language":"en","primary_location":{"id":"doi:10.48550/arxiv.2204.04263","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2204.04263","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article-journal"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2204.04263","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Luo, Ling","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luo, Ling","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Lai, Po-Ting","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lai, Po-Ting","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Wei, Chih-Hsuan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wei, Chih-Hsuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Arighi, Cecilia N","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Arighi, Cecilia N","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Lu, Zhiyong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lu, Zhiyong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"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":true,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9501000046730042,"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":0.9501000046730042,"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":0.03579999879002571,"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":0.0013000000035390258,"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/benchmarking","display_name":"Benchmarking","score":0.7311000227928162},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.7035999894142151},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.6866999864578247},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5662999749183655},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5291000008583069},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5185999870300293},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.47040000557899475},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.46970000863075256}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7925999760627747},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7311000227928162},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.7035999894142151},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.6866999864578247},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5662999749183655},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5291000008583069},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5284000039100647},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5185999870300293},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5011000037193298},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48030000925064087},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.47040000557899475},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.46970000863075256},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4438000023365021},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.43050000071525574},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4162999987602234},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3544999957084656},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.3540000021457672},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.34700000286102295},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3260999917984009},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.2955999970436096},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.29330000281333923},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.2824999988079071},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2653000056743622}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2204.04263","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2204.04263","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article-journal"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2204.04263","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2204.04263","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5464090704917908,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Automated":[0],"relation":[1,86,106],"extraction":[2],"(RE)":[3],"from":[4],"biomedical":[5,74],"literature":[6],"is":[7,168],"critical":[8],"for":[9,26,171,173,207],"many":[10],"downstream":[11],"text":[12],"mining":[13],"applications":[14],"in":[15,51],"both":[16],"research":[17],"and":[18,65,85,125,146,203,212],"real-world":[19],"settings.":[20],"However,":[21],"most":[22],"existing":[23,137,154],"benchmarking":[24,135],"datasets":[25],"bio-medical":[27],"RE":[28,49,66,75,147,175,205],"only":[29],"focus":[30],"on":[31,95,143,160],"relations":[32,181],"of":[33,48,98,132,165,183,199],"a":[34,72,96,110,191],"single":[35],"type":[36],"(e.g.,":[37,81,88],"protein-protein":[38],"interactions)":[39],"at":[40,91,218],"the":[41,46,92,130,144,161,174,197],"sentence":[42],"level,":[43,94],"greatly":[44],"limiting":[45],"development":[47,198],"systems":[50,206],"biomedicine.":[52,208],"In":[53],"this":[54],"work,":[55],"we":[56,69,103],"first":[57],"review":[58],"commonly":[59],"used":[60],"named":[61],"entity":[62,79],"recognition":[63],"(NER)":[64],"datasets.":[67],"Then":[68],"present":[70],"BioRED,":[71],"first-of-its-kind":[73],"corpus":[76],"with":[77],"multiple":[78],"types":[80],"gene/protein,":[82],"disease,":[83],"chemical)":[84],"pairs":[87],"gene-disease;":[89],"chemical-chemical)":[90],"document":[93],"set":[97],"600":[99],"PubMed":[100],"abstracts.":[101],"Further,":[102],"label":[104],"each":[105],"as":[107],"describing":[108],"either":[109],"novel":[111,124,180],"finding":[112],"or":[113],"previously":[114],"known":[115],"background":[116,126],"knowledge,":[117],"enabling":[118],"automated":[119],"algorithms":[120],"to":[121],"differentiate":[122],"between":[123],"information.":[127],"We":[128],"assess":[129],"utility":[131],"BioRED":[133,210],"by":[134],"several":[136],"state-of-the-art":[138],"methods,":[139],"including":[140],"BERT-based":[141],"models,":[142],"NER":[145,162],"tasks.":[148],"Our":[149,185],"results":[150],"show":[151],"that":[152,189],"while":[153],"approaches":[155],"can":[156,194],"reach":[157],"high":[158],"performance":[159],"task":[163],"(F-score":[164,182],"89.3%),":[166],"there":[167],"much":[169],"room":[170],"improvement":[172],"task,":[176],"especially":[177],"when":[178],"extracting":[179],"47.7%).":[184],"experiments":[186],"also":[187],"demonstrate":[188],"such":[190],"rich":[192],"dataset":[193,211],"successfully":[195],"facilitate":[196],"more":[200],"accurate,":[201],"efficient,":[202],"robust":[204],"The":[209],"annotation":[213],"guideline":[214],"are":[215],"freely":[216],"available":[217],"https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.":[219]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
