{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T03:26:39Z","timestamp":1772853999032,"version":"3.50.1"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T00:00:00Z","timestamp":1770854400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:00:00Z","timestamp":1772755200000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"DOI":"10.1186\/s13326-025-00339-0","type":"journal-article","created":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T09:18:35Z","timestamp":1770887915000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A practical and nuanced framework for entity linking evaluation"],"prefix":"10.1186","volume":"17","author":[{"given":"Fuqi","family":"Xu","sequence":"first","affiliation":[]},{"given":"Goran","family":"Nenadic","sequence":"additional","affiliation":[]},{"given":"Robert","family":"Stevens","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2026,2,12]]},"reference":[{"key":"339_CR1","doi-asserted-by":"crossref","unstructured":"Albertoni R, Camossi E, De Martino M, Giannini F, Monti M. Semantic granularity for the semantic web. In OTM Confederated International Conferences on the Move to Meaningful Internet Systems. Springer; 2006, pp. 1863\u201372.","DOI":"10.1007\/11915072_93"},{"key":"339_CR2","volume-title":"Web ontology language: OWL","author":"G Antoniou","year":"2009","unstructured":"Antoniou G, van Harmelen F. Web ontology language: OWL. Springer; 2009."},{"key":"339_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-7-267","volume":"7","author":"AG Castro","year":"2006","unstructured":"Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone S-A. The use of concept maps during knowledge elicitation in ontology development processes\u2013the nutrigenomics use case. BMC Bioinf. 2006;7:1\u201314.","journal-title":"BMC Bioinf"},{"key":"339_CR4","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1007\/978-3-031-11039-9_17","volume-title":"Terminology, ontology and their implementations","author":"S de Coronado","year":"2023","unstructured":"de Coronado S, Remennik L, Elkin PL. National Cancer Institute thesaurus (NCIt). In Terminology, Ontology and their Implementations. Springer; 2023. p. 395\u2013441."},{"key":"339_CR5","doi-asserted-by":"crossref","unstructured":"French E, McInnes BT. An overview of biomedical entity linking throughout the years. J Biomed Inf. 2023;137(104252).","DOI":"10.1016\/j.jbi.2022.104252"},{"key":"339_CR6","doi-asserted-by":"crossref","unstructured":"Garda S, Leser U. BELHD: improving biomedical entity linking with homonym disambiguation. Bioinformatics, page btae, 2024;474.","DOI":"10.1093\/bioinformatics\/btae474"},{"key":"339_CR7","doi-asserted-by":"crossref","unstructured":"Garda S, Weber-Genzel L, Martin R, Leser U. BELB: a biomedical entity linking benchmark. Bioinformatics. 2023;39(11):btad698.","DOI":"10.1093\/bioinformatics\/btad698"},{"key":"339_CR8","unstructured":"Gupta G, Rastegarpanah B, Iyer A, Rubin J, Kenthapadi K. Measuring distributional shifts in text: the advantage of language model-based embeddings. arXiv preprint arXiv:2312.02337, 2023."},{"key":"339_CR9","unstructured":"Hoehndorf R. Version of MeSH - RH-MESH ontology. http:\/\/phenomebrowser.net\/ontologies\/mesh\/https:\/\/bioportal.bioontology.org\/ontologies\/RH-MESH. Accessed 11 Nov 2024."},{"key":"339_CR10","doi-asserted-by":"crossref","unstructured":"Jin D, Sisman B, Wei H, Dong XL, Koutra D. Deep transfer learning for multi-source entity linkage via domain adaptation. arXiv preprint arXiv:2110.14509, 2021.","DOI":"10.14778\/3494124.3494131"},{"key":"339_CR11","unstructured":"Jonquet C, Shah NH, Youn CH, Musen MA, Callendar C, Storey M-A. NCBO annotator: semantic annotation of biomedical data. In ISWC 2009-8th International Semantic Web Conference, Poster and Demo Session. CEUR Workshop Proceedings. 2009;171."},{"key":"339_CR12","first-page":"101","volume-title":"MEDINFO 2021: One world, one health\u2013global partnership for digital innovation","author":"H Kang","year":"2022","unstructured":"Kang H, Park H. Mapping korean national health insurance reimbursement claim codes for therapeutic and surgical procedures to SNOMED-CT to facilitate data reuse. In MEDINFO 2021: one world, one health\u2013global partnership for digital innovation. IOS Press; 2022. pp. 101\u201305."},{"key":"339_CR13","doi-asserted-by":"crossref","unstructured":"Kartchner D, Deng J, Lohiya S, Kopparthi T, Bathala P, Domingo-Fern\u00e1ndez D, Mitchell CS. A comprehensive evaluation of biomedical entity linking models. In Proceedings of the Conference on Empirical Methods in Natural Language Processing. NIH Public Access; 2023, p. 14462.","DOI":"10.18653\/v1\/2023.emnlp-main.893"},{"key":"339_CR14","unstructured":"DMIS Lab. BioSyn: biomedical entity representations with synonym marginalization. GitHub repository. 2020. https:\/\/github.com\/dmis-lab\/BioSyn."},{"key":"339_CR15","doi-asserted-by":"crossref","unstructured":"Leaman R, Islamaj R, Adams V, Alliheedi MA, Rafael Almeida J, Antunes R, Bevan R, Chang Y-C, Erdengasileng A, Hodgskiss M, et al. Chemical identification and indexing in full-text articles: an overview of the nlm-chem track at biocreative vii. Database. 2023, 2023:baad005.","DOI":"10.1093\/database\/baad005"},{"key":"339_CR16","doi-asserted-by":"crossref","unstructured":"Leaman R, Zhiyong L. TaggerOne: joint named entity recognition and normalization with semi-markov models. Bioinformatics. 2016;32(18):2839\u201346.","DOI":"10.1093\/bioinformatics\/btw343"},{"key":"339_CR17","doi-asserted-by":"crossref","unstructured":"Jiao L, Sun Y, Johnson RJ, Sciaky D, Wei C-H, Leaman R, Davis AP, Mattingly CJ, Wiegers TC, Zhiyong L. Biocreative v cdr task corpus: a resource for chemical disease relation extraction. Database. 2016;2016:baw068.","DOI":"10.1093\/database\/baw068"},{"key":"339_CR18","unstructured":"Carolyn E Lipscomb. Medical subject headings (MeSH). Bulletin Med Library Assoc. 2000;88(3):265."},{"key":"339_CR19","doi-asserted-by":"crossref","unstructured":"Opitz J. A closer look at classification evaluation metrics and a critical reflection of common evaluation practice. Trans Assoc Comput Linguist. 2024;12:820\u201336.","DOI":"10.1162\/tacl_a_00675"},{"key":"339_CR20","doi-asserted-by":"crossref","unstructured":"Rani GJJ, Gladis D, Mammen JJ. SNOMED CT annotation for improved pathological decisions in breast cancer domain. Int J Recent Technol Eng. 2019;8(3):8400\u201306.","DOI":"10.35940\/ijrte.C6519.098319"},{"key":"339_CR21","doi-asserted-by":"crossref","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25(11):1251\u201355.","DOI":"10.1038\/nbt1346"},{"key":"339_CR22","doi-asserted-by":"crossref","unstructured":"Sung M, Jeon H, Lee J, Kang J. Biomedical entity representations with synonym marginalization. arXiv preprint arXiv:2005.00239, 2020.","DOI":"10.18653\/v1\/2020.acl-main.335"},{"key":"339_CR23","doi-asserted-by":"crossref","unstructured":"Tutubalina E, Kadurin A, Miftahutdinov Z. Fair evaluation in concept normalization: a large-scale comparative analysis for BERT-Based models. In Proceedings of the 28th International Conference on Computational Linguistics. 2020, pp. 6710\u201316.","DOI":"10.18653\/v1\/2020.coling-main.588"},{"key":"339_CR24","unstructured":"Van Erp M, Mendes P, Paulheim H, Ilievski F, Plu J, Rizzo G, Waitelonis J. Evaluating entity linking: an analysis of current benchmark datasets and a roadmap for doing a better job. In Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC\u201916). 2016, pp. 4373\u201379."},{"issue":"W1","key":"339_CR25","doi-asserted-by":"publisher","first-page":"W587","DOI":"10.1093\/nar\/gkz389","volume":"47","author":"C-H Wei","year":"2019","unstructured":"Wei C-H, Allot A, Leaman R, Zhiyong L. PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res. 2019;47(W1):W587\u201393.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"339_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1145\/1993036.1993039","volume":"29","author":"X Yan","year":"2011","unstructured":"Yan X, Lau RY, Song D, Xue L, Jian M. Toward a semantic granularity model for domain-specific information retrieval. ACM Trans On Inf Syst (TOIS). 2011;29(3):1\u201346.","journal-title":"ACM Trans On Inf Syst (TOIS)"},{"key":"339_CR27","doi-asserted-by":"crossref","unstructured":"Zhang S, Cheng H, Vashishth S, Wong C, Xiao J, Liu X, Naumann T, Gao J, Poon H. Knowledge-rich self-supervision for biomedical entity linking. arXiv:2112.07887, 2022.","DOI":"10.18653\/v1\/2022.findings-emnlp.61"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-025-00339-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-025-00339-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-025-00339-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T15:12:10Z","timestamp":1772809930000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13326-025-00339-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,12]]},"references-count":27,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["339"],"URL":"https:\/\/doi.org\/10.1186\/s13326-025-00339-0","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,12]]},"assertion":[{"value":"22 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 February 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"5"}}