{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T16:51:20Z","timestamp":1780332680826,"version":"3.54.1"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T00:00:00Z","timestamp":1496793600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T00:00:00Z","timestamp":1496793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54 HG004028"],"award-info":[{"award-number":["U54 HG004028"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U54 AI117925"],"award-info":[{"award-number":["U54 AI117925"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["701771"],"award-info":[{"award-number":["701771"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-12-JS02-01001"],"award-info":[{"award-number":["ANR-12-JS02-01001"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s13326-017-0128-y","type":"journal-article","created":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T12:00:46Z","timestamp":1496836846000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":78,"title":["NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation"],"prefix":"10.1186","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9814-3258","authenticated-orcid":false,"given":"Marcos","family":"Mart\u00ednez-Romero","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clement","family":"Jonquet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin J.","family":"O\u2019Connor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Graybeal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Pazos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark A.","family":"Musen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,6,7]]},"reference":[{"key":"128_CR1","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1038\/nbt0604-773","volume":"22","author":"J Blake","year":"2004","unstructured":"Blake J. Bio-ontologies-fast and furious. Nat Biotechnol. 2004;22:773\u20134.","journal-title":"Nat Biotechnol"},{"key":"128_CR2","doi-asserted-by":"crossref","unstructured":"Bodenreider O, Stevens R. Bio-ontologies: Current trends and future directions. Brief Bioinform. 2006;7:256\u201374.","DOI":"10.1093\/bib\/bbl027"},{"key":"128_CR3","unstructured":"Whetzel PL, Noy N, Shah N, Alexander P, Dorf M, Fergerson R, Storey MA, Smith B, Chute C, Musen M: BioPortal: Ontologies and integrated data resources at the click of a mouse. In CEUR Workshop Proceedings. Volume 833; 2011:292\u2013293"},{"key":"128_CR4","doi-asserted-by":"crossref","unstructured":"Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011;39(Suppl 2):W541\u20135.","DOI":"10.1093\/nar\/gkr469"},{"key":"128_CR5","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1089\/omi.2006.10.185","volume":"10","author":"DL Rubin","year":"2006","unstructured":"Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey M-A, Smith B, Day-Richter J, Noy NF, Musen MA. National center for biomedical ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS. 2006;10:185\u201398.","journal-title":"OMICS"},{"key":"128_CR6","doi-asserted-by":"crossref","unstructured":"Jonquet C, Musen MA, Shah NH. Building a biomedical ontology recommender web service. J Biomed Semantics. 2010;1(Suppl 1):S1.","DOI":"10.1186\/2041-1480-1-S1-S1"},{"key":"128_CR7","volume-title":"Proceedings of the conference on data mining and data warehouses (SiKDD 2005)","author":"J Brank","year":"2005","unstructured":"Brank J, Grobelnik M, Mladeni\u0107 D. A survey of ontology evaluation techniques. In: Proceedings of the conference on data mining and data warehouses (SiKDD 2005). 2005."},{"key":"128_CR8","first-page":"96","volume-title":"Proceedings of international conference on knowledge engineering and knowledge management","author":"M Sabou","year":"2006","unstructured":"Sabou M, Lopez V, Motta E. Ontology selection for the real semantic Web: How to cover the Queen\u2019s birthday dinner? In: Proceedings of international conference on knowledge engineering and knowledge management. Berlin, Heidelberg: Springer; 2006. p. 96\u2013111."},{"key":"128_CR9","volume-title":"Work Soc collab constr struct knowl 16th Int world wide Web conf (WWW 2007)","author":"I Cantador","year":"2007","unstructured":"Cantador I, Fern\u00e1ndez M, Castells P. Improving ontology recommendation and reuse in WebCORE by collaborative assessments. In: Work Soc collab constr struct knowl 16th Int world wide Web conf (WWW 2007). 2007."},{"key":"128_CR10","volume-title":"Proceedings the 11th conference on artificial intelligence for applications (CAIA\u201994). San Antonio, Texas, USA","author":"A Gomez-Perez","year":"1994","unstructured":"Gomez-Perez A. Some ideas and examples to evaluate ontologies. In: Proceedings the 11th conference on artificial intelligence for applications (CAIA\u201994). San Antonio, Texas, USA. 1994."},{"key":"128_CR11","volume-title":"Technical report KSL 94\u201373","author":"A G\u00f3mez-P\u00e9rez","year":"1994","unstructured":"G\u00f3mez-P\u00e9rez A. From knowledge based systems to knowledge sharing technology: evaluation and assessment. In: Technical report KSL 94\u201373. Stanford, CA, USA: Knowledge Systems Laboratory, Stanford University; 1994."},{"key":"128_CR12","volume-title":"International workshop on formal ontology","author":"T Gruber","year":"1993","unstructured":"Gruber T. Toward principles for the design of ontologies used for knowledge sharing. In: International workshop on formal ontology. 1993."},{"key":"128_CR13","doi-asserted-by":"crossref","unstructured":"Berners-Lee T, Hendler J, Lassila O: The Semantic Web. Scientific American 2001:34\u201343.","DOI":"10.1038\/scientificamerican0501-34"},{"key":"128_CR14","unstructured":"Finin T, Reddivari P, Cost RS, Sachs J. S. A search and metadata engine for the semantic Web. In: Proceedings of the 13th ACM conference on Information and Knowledge Management (CIKM '04). 2004. p. 652\u20139."},{"key":"128_CR15","first-page":"58","volume-title":"Proc 5th ACM CIKM Int work Web Inf data manag (WIDM 2003)","author":"C Patel","year":"2003","unstructured":"Patel C, Supekar K, Lee Y, Park E: OK. A semantic Web portal for ontology searching, ranking, and classification. In: Proc 5th ACM CIKM Int work Web Inf data manag (WIDM 2003). 2003. p. 58\u201361."},{"key":"128_CR16","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1007\/1-84628-102-4_5","volume-title":"Research and development in intelligent systems XXI","author":"Y Zhang","year":"2005","unstructured":"Zhang Y, Vasconcelos W, Sleeman D. OntoSearch : an ontology search engine. In: Research and development in intelligent systems XXI. London, UK: Springer; 2005. p. 58\u201369."},{"key":"128_CR17","doi-asserted-by":"crossref","unstructured":"Alani H, Noy N, Shah N, Shadbolt N, Musen M. Searching ontologies based on content: Experiments in the biomedical domain. In Proceedings of the 4th international conference on Knowledge capture. New York: ACM; 2007:55\u201362.","DOI":"10.1145\/1298406.1298418"},{"key":"128_CR18","volume-title":"Proceedings of the demo session at the international semantic Web conference (ISWC)","author":"P Buitelaar","year":"2004","unstructured":"Buitelaar P, Eigner T, Declerck T. OntoSelect: a dynamic ontology library with support for ontology selection. In: Proceedings of the demo session at the international semantic Web conference (ISWC). 2004."},{"key":"128_CR19","first-page":"1","volume-title":"Proceedings of the international semantic Web conference (ISWC)","author":"H Alani","year":"2006","unstructured":"Alani H, Brewster C, Shadbolt N. Ranking ontologies with AKTiveRank. In: Proceedings of the international semantic Web conference (ISWC). Berlin, Heidelberg: Springer; 2006. p. 1\u201315."},{"key":"128_CR20","first-page":"45","volume-title":"IEEE work knowl acquis from distrib auton semant heterog data knowl sources","author":"S Tartir","year":"2005","unstructured":"Tartir S, Arpinar I, Moore M, Sheth A, Aleman-Meza B. OntoQA: metric-based ontology quality analysis. In: IEEE work knowl acquis from distrib auton semant heterog data knowl sources. 2005. p. 45\u201353."},{"key":"128_CR21","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.cmpb.2014.01.020","volume":"114","author":"M Mart\u00ednez-Romero","year":"2014","unstructured":"Mart\u00ednez-Romero M, V\u00e1zquez-Naya JM, Pereira J, Pazos A. BiOSS: a system for biomedical ontology selection. Comput Methods Programs Biomed. 2014;114:125\u201340.","journal-title":"Comput Methods Programs Biomed"},{"key":"128_CR22","first-page":"913","volume":"5554 LNCS","author":"M D\u2019Aquin","year":"2009","unstructured":"D\u2019Aquin M, Lewen H. Cupboard - a place to expose your ontologies to applications and the community. Lect Notes Comput Sci (including Subser Lect Notes Artif Intell Lect Notes Bioinformatics). 2009;5554 LNCS:913\u20138.","journal-title":"Lect Notes Comput Sci (including Subser Lect Notes Artif Intell Lect Notes Bioinformatics)"},{"key":"128_CR23","doi-asserted-by":"crossref","unstructured":"Tan H, Lambrix P. Selecting an ontology for biomedical text mining. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP '09). 2009;55\u201362.","DOI":"10.3115\/1572364.1572372"},{"key":"128_CR24","first-page":"171","volume":"5","author":"G Maiga","year":"2009","unstructured":"Maiga G. A flexible biomedical ontology selection tool. Strength Role ICT Dev. 2009;5:171\u201389.","journal-title":"Strength Role ICT Dev"},{"key":"128_CR25","doi-asserted-by":"crossref","unstructured":"Mart\u00ednez-Romero M, V\u00e1zquez-Naya JM, Pereira J, Pazos A. A multi-criteria approach for automatic ontology recommendation using collective knowledge. In Recommender Systems for the Social Web. Volume 32. Berlin: Springer-Verlag; 2012;89\u2013104.","DOI":"10.1007\/978-3-642-25694-3_4"},{"key":"128_CR26","volume-title":"International semantic Web conference (ISWC), poster and demo session","author":"C Jonquet","year":"2009","unstructured":"Jonquet C, Shah NH, Cherie H, Musen MA, Callendar C. Storey M-a: NCBO annotator\u202f: semantic annotation of biomedical data. In: International semantic Web conference (ISWC), poster and demo session. 2009."},{"key":"128_CR27","first-page":"1","volume-title":"7th international SWAT4LS conference","author":"P L\u00f3pez-Garc\u00eda","year":"2014","unstructured":"L\u00f3pez-Garc\u00eda P, Schulz S, Kern R. Automatic summarization for terminology recommendation\u202f: the case of the NCBO ontology recommender. In: 7th international SWAT4LS conference. 2014. p. 1\u20138."},{"key":"128_CR28","first-page":"23","volume-title":"15th international world wide Web conference (WWW 2006)","author":"M Sabou","year":"2006","unstructured":"Sabou M, Lopez V, Motta E, Uren V. Ontology selection: ontology evaluation on the real semantic Web. In: 15th international world wide Web conference (WWW 2006). 2006. p. 23\u20136."},{"key":"128_CR29","first-page":"640","volume-title":"Conf proc Am Med informatics assoc annu fall symp","author":"KA Spackman","year":"1997","unstructured":"Spackman KA, Campbell KE, C\u00f4t\u00e9 RA. SNOMED RT: a reference terminology for health care. In: Conf proc Am Med informatics assoc annu fall symp. 1997. p. 640\u20134."},{"key":"128_CR30","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25\u20139.","journal-title":"Nat Genet"},{"issue":"Database issue","key":"128_CR31","doi-asserted-by":"publisher","first-page":"D267","DOI":"10.1093\/nar\/gkh061","volume":"32","author":"O Bodenreider","year":"2004","unstructured":"Bodenreider O. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32(Database issue):D267\u201370.","journal-title":"Nucleic Acids Res"},{"key":"128_CR32","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25:1251\u20135.","journal-title":"Nat Biotechnol"},{"key":"128_CR33","unstructured":"Xiang Z, Mungall C, Ruttenberg A, He Y: Ontobee: A linked data server and browser for ontology terms. In CEUR Workshop Proceedings. Volume 833; 2011:279\u2013281"},{"key":"128_CR34","doi-asserted-by":"crossref","unstructured":"C\u00f4t\u00e9 RG, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics. 2006;7(1):97.","DOI":"10.1186\/1471-2105-7-97"},{"key":"128_CR35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-015-0456-9","volume":"16","author":"R Hoehndorf","year":"2015","unstructured":"Hoehndorf R, Slater L, Schofield PN, Gkoutos GV. Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinf. 2015;16:1\u20139.","journal-title":"BMC Bioinf"},{"key":"128_CR36","doi-asserted-by":"crossref","unstructured":"Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L. The ontology for biomedical investigations. PloS one. 2016;11(4):e0154556.","DOI":"10.1371\/journal.pone.0154556"},{"key":"128_CR37","doi-asserted-by":"crossref","unstructured":"Schriml LM, Arze C, Nadendla S, Chang YWW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease ontology: A backbone for disease semantic integration. Nucleic Acids Res. 2012;40(D1):D940\u20136.","DOI":"10.1093\/nar\/gkr972"},{"key":"128_CR38","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.jbi.2010.10.003","volume":"44","author":"JD Tenenbaum","year":"2011","unstructured":"Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P. The biomedical resource ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform. 2011;44:137\u201345.","journal-title":"J Biomed Inform"},{"key":"128_CR39","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1016\/j.websem.2011.06.005","volume":"9","author":"C Jonquet","year":"2011","unstructured":"Jonquet C, Lependu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH. NCBO resource index: ontology-based search and mining of biomedical resources. J Web Semant. 2011;9:316\u201324.","journal-title":"J Web Semant"},{"issue":"PART 1","key":"128_CR40","first-page":"444","volume":"8218 LNCS","author":"NF Noy","year":"2013","unstructured":"Noy NF, Alexander PR, Harpaz R, Whetzel PL, Fergerson RW, Musen MA. Getting lucky in ontology search: a data-driven evaluation framework for ontology ranking. Lect Notes Comput Sci (including Subser Lect Notes Artif Intell Lect Notes Bioinformatics). 2013;8218 LNCS(PART 1):444\u201359.","journal-title":"Lect Notes Comput Sci (including Subser Lect Notes Artif Intell Lect Notes Bioinformatics)"},{"key":"128_CR41","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1093\/jamia\/ocv048","volume":"22","author":"MA Musen","year":"2015","unstructured":"Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O\u2019Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA. The center for expanded data annotation and retrieval. J Am Med Inform Assoc. 2015;22:1148\u201352.","journal-title":"J Am Med Inform Assoc"},{"key":"128_CR42","volume-title":"In IN-OVIVE\u201915: 3\u00e8me atelier INt\u00e9gration de sources\/masses de donn\u00e9es h\u00e9t\u00e9rog\u00e8nes et ontologies, dans le domaine des sciences du VIVant et de l\u2019Environnement","author":"C Jonquet","year":"2015","unstructured":"Jonquet C, Dzal E, Arnaud E, Larmande P, Jonquet C, Dzal E, Arnaud E, Larmande P, Jonquet C, Dzal\u00e9-yeumo E, Arnaud E, Larmande P. AgroPortal\u202f: a proposition for ontology-based services in the agronomic domain. In: In IN-OVIVE\u201915: 3\u00e8me atelier INt\u00e9gration de sources\/masses de donn\u00e9es h\u00e9t\u00e9rog\u00e8nes et ontologies, dans le domaine des sciences du VIVant et de l\u2019Environnement. 2015."},{"key":"128_CR43","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1007\/s007999900023","volume":"3","author":"K Frantzi","year":"2000","unstructured":"Frantzi K, Ananiadou S, Mima H. Automatic recognition of multi-word terms: the C-value\/NC-value method. Int J Digit Libr. 2000;3:115\u201330.","journal-title":"Int J Digit Libr"},{"key":"128_CR44","unstructured":"Melzi S, Jonquet C. Scoring semantic annotations returned by the NCBO Annotator. In Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS\u201914). CEURWS; 2014;1320:15."},{"key":"128_CR45","doi-asserted-by":"crossref","unstructured":"Hartmann J, Palma R, G\u00f3mez-P\u00e9rez A. Ontology Repositories. In Handbook on Ontologies; 2009:551\u201371.","DOI":"10.1007\/978-3-540-92673-3_25"},{"key":"128_CR46","unstructured":"Kamdar MR, Tudorache T, Musen MA: A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0128-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13326-017-0128-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0128-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T06:46:04Z","timestamp":1659077164000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-017-0128-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,7]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["128"],"URL":"https:\/\/doi.org\/10.1186\/s13326-017-0128-y","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,7]]},"assertion":[{"value":"28 October 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 April 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 June 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"21"}}