{"id":"https://openalex.org/W7128736303","doi":"https://doi.org/10.1186/s13326-025-00339-0","title":"A practical and nuanced framework for entity linking evaluation","display_name":"A practical and nuanced framework for entity linking evaluation","publication_year":2026,"publication_date":"2026-02-12","ids":{"openalex":"https://openalex.org/W7128736303","doi":"https://doi.org/10.1186/s13326-025-00339-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/41680815"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-025-00339-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00339-0","pdf_url":null,"source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13326-025-00339-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113105080","display_name":"Fuqi Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fuqi Xu","raw_affiliation_strings":["Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005912060","display_name":"Goran Nenadi\u0107","orcid":"https://orcid.org/0000-0003-0795-5363"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Goran Nenadic","raw_affiliation_strings":["Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125719281","display_name":"Robert Stevens","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robert Stevens","raw_affiliation_strings":["Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK. robert.stevens@manchester.ac.uk"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, UK. robert.stevens@manchester.ac.uk","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5125719281"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":1190,"currency":"GBP","value_usd":1459},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.48083934,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","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":0.5019999742507935,"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":0.5019999742507935,"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":0.34209999442100525,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.07729999721050262,"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/entity-linking","display_name":"Entity linking","score":0.6082000136375427},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.5715000033378601},{"id":"https://openalex.org/keywords/named-entity","display_name":"Named entity","score":0.49729999899864197},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4952999949455261},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.47130000591278076},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.37070000171661377},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.362199991941452}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8831999897956848},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.6082000136375427},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.5715000033378601},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.49729999899864197},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4952999949455261},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.47130000591278076},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.44600000977516174},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4104999899864197},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3950999975204468},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39399999380111694},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.37070000171661377},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.362199991941452},{"id":"https://openalex.org/C100521375","wikidata":"https://www.wikidata.org/wiki/Q2015382","display_name":"Competence (human resources)","level":2,"score":0.3560999929904938},{"id":"https://openalex.org/C2778493491","wikidata":"https://www.wikidata.org/wiki/Q7449072","display_name":"Semantic matching","level":3,"score":0.3427000045776367},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.3043000102043152},{"id":"https://openalex.org/C110615152","wikidata":"https://www.wikidata.org/wiki/Q1469824","display_name":"Controlled vocabulary","level":2,"score":0.29260000586509705},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.27970001101493835},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.2743000090122223},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.2680000066757202},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.2632000148296356}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13326-025-00339-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00339-0","pdf_url":null,"source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:41680815","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41680815","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":"Journal of biomedical semantics","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/8d7a6bee-3e37-404b-8c24-ee62365a89f7","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/8d7a6bee-3e37-404b-8c24-ee62365a89f7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Xu, F, Nenadic, G & Stevens, R 2026, 'A practical and nuanced framework for entity linking evaluation', Journal of Biomedical Semantics, vol. 17, no. 1. https://doi.org/10.1186/s13326-025-00339-0","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:doaj.org/article:9bb9aad6cbab490ab248eb53e5134ab1","is_oa":true,"landing_page_url":"https://doaj.org/article/9bb9aad6cbab490ab248eb53e5134ab1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Biomedical Semantics, Vol 17, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12967008","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12967008/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Semantics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/8d7a6bee-3e37-404b-8c24-ee62365a89f7","is_oa":true,"landing_page_url":"https://link.springer.com/10.1186/s13326-025-00339-0","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Xu, F, Nenadic, G & Stevens, R 2026, 'A practical and nuanced framework for entity linking evaluation', Journal of Biomedical Semantics, vol. 17, no. 1. https://doi.org/10.1186/s13326-025-00339-0","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1186/s13326-025-00339-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-025-00339-0","pdf_url":null,"source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.7402107119560242}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1535019131","https://openalex.org/W1642891250","https://openalex.org/W2004319612","https://openalex.org/W2113142309","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2946690328","https://openalex.org/W3034229721","https://openalex.org/W3116070535","https://openalex.org/W4237293770","https://openalex.org/W4285338394","https://openalex.org/W4311903220","https://openalex.org/W4323519786","https://openalex.org/W4384915295","https://openalex.org/W4385574140","https://openalex.org/W4388775058","https://openalex.org/W4389519296","https://openalex.org/W4396242195","https://openalex.org/W4401103297"],"related_works":[],"abstract_inverted_index":{"Entity":[0],"linking":[1,17,32,122],"maps":[2],"textual":[3],"mentions":[4],"with":[5,99],"entities":[6],"in":[7],"vocabularies.":[8],"While":[9],"accuracy":[10],"is":[11],"the":[12,23,37,62,75,93,112],"primary":[13],"metric":[14],"for":[15,108,114],"entity":[16,31,88,109,121],"evaluation,":[18],"it":[19],"fails":[20],"to":[21,68],"capture":[22],"complexity":[24],"of":[25,40,79,95,120],"model":[26,53],"behaviour.":[27],"We":[28,73],"propose":[29],"an":[30],"evaluation":[33,97],"framework":[34,56,81],"that":[35],"clarifies":[36],"target":[38],"objects":[39],"metrics":[41,98],"calculation,":[42],"incorporates":[43],"term":[44],"hierarchy,":[45],"generates":[46],"performance":[47],"profiles,":[48],"and":[49,77,102,117],"summarises":[50],"them":[51],"as":[52],"characteristics.":[54],"The":[55],"emphasises":[57],"hierarchical":[58,105],"vocabulary":[59],"structures,":[60],"shifting":[61],"focus":[63],"from":[64],"text-level":[65],"label":[66],"matching":[67],"semantic":[69],"comparison":[70],"between":[71],"concepts.":[72],"illustrate":[74],"competence":[76],"utility":[78],"this":[80],"through":[82],"a":[83],"case":[84],"study":[85],"on":[86],"disease":[87],"linking.":[89],"Our":[90],"results":[91],"highlight":[92],"importance":[94],"aligning":[96],"application-specific":[100],"requirements,":[101],"provide":[103],"structured":[104],"error":[106],"analysis":[107],"linking,":[110],"paving":[111],"way":[113],"more":[115],"nuanced":[116],"practical":[118],"assessments":[119],"systems.":[123]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-02-13T00:00:00"}
