{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T06:35:05Z","timestamp":1756190105466},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"S10","license":[{"start":{"date-parts":[[2019,5,1]],"date-time":"2019-05-01T00:00:00Z","timestamp":1556668800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T00:00:00Z","timestamp":1559088000000},"content-version":"vor","delay-in-days":28,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,5]]},"DOI":"10.1186\/s12859-019-2810-9","type":"journal-article","created":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T00:02:50Z","timestamp":1559088170000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Multi-domain semantic similarity in biomedical research"],"prefix":"10.1186","volume":"20","author":[{"given":"Jo\u00e3o D.","family":"Ferreira","sequence":"first","affiliation":[]},{"given":"Francisco M.","family":"Couto","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,5,29]]},"reference":[{"issue":"10","key":"2810_CR1","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"PW Lord","year":"2003","unstructured":"Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003; 19(10):1275\u201383. \n                    https:\/\/doi.org\/10.1093\/bioinformatics\/btg153\n                    \n                  .","journal-title":"Bioinformatics"},{"issue":"SUPPL. 1","key":"2810_CR2","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1093\/nar\/gkq1018","volume":"39","author":"D Croft","year":"2011","unstructured":"Croft D, O\u2019Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, MayMahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D\u2019Eustachio P, Stein L. Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Res. 2011; 39(SUPPL. 1):691\u20137. \n                    https:\/\/doi.org\/10.1093\/nar\/gkq1018\n                    \n                  .","journal-title":"Nucleic Acids Res"},{"key":"2810_CR3","doi-asserted-by":"crossref","unstructured":"Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, et al.The biocyc collection of microbial genomes and metabolic pathways. Brief Bioinformatics. 2017. \n                    https:\/\/doi.org\/10.1093\/bib\/bbx085\n                    \n                  .","DOI":"10.1093\/bib\/bbx085"},{"issue":"2","key":"2810_CR4","first-page":"3","volume":"4","author":"N Juty","year":"2015","unstructured":"Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, le Nov\u00e8re N, Laibe C, Chelliah V. BioModels: Content, Features, Functionality, and Use. CPT: Pharmacometrics & Syst Pharmacol. 2015; 4(2):3. \n                    https:\/\/doi.org\/10.1002\/psp4.3\n                    \n                  .","journal-title":"CPT: Pharmacometrics & Syst Pharmacol"},{"key":"2810_CR5","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1002\/9781118952788.ch9","volume-title":"The Digital Patient","author":"David P. Nickerson","year":"2016","unstructured":"Nickerson DP, Atalag K, de Bono B, Hunter PJ. The physiome project, openehr archetypes and the digital patient. The Digital Patient: Advancing Healthcare, Research and Education.Wiley; 2016."},{"key":"2810_CR6","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/978-3-642-15020-3_3","volume-title":"Information Technology in Bio- and Medical Informatics, ITBAM 2010","author":"Luis F. Lopes","year":"2010","unstructured":"Lopes LF, Silva FAB, Couto FM, Zamite J, Ferreira H, Sousa C, Silva MJ. Epidemic Marketplace: an information management system for epidemiological data In: Khuri S, Lhotsk\u00e0 L, Pisanti N, editors. Information Technology in Bio- and Medical-Informatics. ITBAM 2010. Lecture Notes in Computer Science. Berlin: Springer: 2010. p. 31\u201344."},{"issue":"1","key":"2810_CR7","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1186\/s12859-018-2429-2","volume":"19","author":"A Tchechmedjiev","year":"2018","unstructured":"Tchechmedjiev A, Abdaoui A, Emonet V, Zevio S, Jonquet C. Sifr annotator: ontology-based semantic annotation of french biomedical text and clinical notes. BMC bioinformatics. 2018; 19(1):405.","journal-title":"BMC bioinformatics"},{"key":"2810_CR8","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.tox.2018.11.005","volume":"412","author":"R-L Wang","year":"2018","unstructured":"Wang R-L, Edwards S, Ives C. Ontology-based semantic mapping of chemical toxicities. Toxicology. 2018; 412:89\u2013100.","journal-title":"Toxicology"},{"issue":"3","key":"2810_CR9","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1093\/bib\/6.3.239","volume":"6","author":"I Spasic","year":"2005","unstructured":"Spasic I, Ananiadou S, McNaught J, Kumar A. Text mining and ontologies in biomedicine: making sense of raw text. Briefings in Bioinformatics. 2005; 6(3):239\u201351.","journal-title":"Briefings in Bioinformatics"},{"key":"2810_CR10","doi-asserted-by":"crossref","unstructured":"Varelas G, Voutsakis E, Raftopoulou P, Petrakis EGM, Milios EE. Semantic similarity methods in wordNet and their application to information retrieval on the web. In: International Workshop on Web Information and Data Management: 2005. p. 10\u20136. \n                    https:\/\/doi.org\/10.1145\/1097047.1097051\n                    \n                  .","DOI":"10.1145\/1097047.1097051"},{"issue":"Suppl 1 Text mi","key":"2810_CR11","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1758-2946-7-S1-S13","volume":"7","author":"A Lamurias","year":"2015","unstructured":"Lamurias A, Ferreira JD, Couto FM. Improving chemical entity recognition through h-index based semantic similarity. Journal of Cheminformatics. 2015; 7(Suppl 1 Text mining for chemistry and the CHEMDNER track):13. \n                    https:\/\/doi.org\/10.1186\/1758-2946-7-S1-S13\n                    \n                  .","journal-title":"Journal of Cheminformatics"},{"key":"2810_CR12","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.jbi.2017.03.007","volume":"69","author":"X Ji","year":"2017","unstructured":"Ji X, Ritter A, Yen P-Y. Using ontology-based semantic similarity to facilitate the article screening process for systematic reviews. J Biomed Informa. 2017; 69:33\u201342.","journal-title":"J Biomed Informa"},{"issue":"9","key":"2810_CR13","doi-asserted-by":"publisher","first-page":"1000937","DOI":"10.1371\/journal.pcbi.1000937","volume":"6","author":"JD Ferreira","year":"2010","unstructured":"Ferreira JD, Couto FM. Semantic Similarity for Automatic Classification of Chemical Compounds. PLoS Comput Biol. 2010; 6(9):1000937. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1000937\n                    \n                  .","journal-title":"PLoS Comput Biol"},{"key":"2810_CR14","doi-asserted-by":"crossref","unstructured":"Azuaje F, Bodenreider O. Incorporating ontology-driven similarity knowledge into functional genomics: an exploratory study. In: IEEE Symposium on Bioinformatics and Bioengineering. IEEE: 2004. p. 317\u201324. \n                    https:\/\/doi.org\/10.1109\/BIBE.2004.1317360\n                    \n                  .","DOI":"10.1109\/BIBE.2004.1317360"},{"issue":"8","key":"2810_CR15","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1093\/bioinformatics\/btl042","volume":"22","author":"X Guo","year":"2006","unstructured":"Guo X, Liu R, Shriver CD, Hu H, Liebman MN. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics. 2006; 22(8):967\u201373. doi:10.1093\/bioinformatics\/btl042.","journal-title":"Bioinformatics"},{"key":"2810_CR16","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.jtbi.2016.04.020","volume":"401","author":"S-B Zhang","year":"2016","unstructured":"Zhang S-B, Tang Q-R. Protein\u2013protein interaction inference based on semantic similarity of gene ontology terms. J Theor Biol. 2016; 401:30\u201337.","journal-title":"J Theor Biol"},{"issue":"4","key":"2810_CR17","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1016\/j.ajhg.2009.09.003","volume":"85","author":"S K\u00f6hler","year":"2009","unstructured":"K\u00f6hler S, Schulz MH, Krawitz P, Bauer S, D\u00f6lken S, Ott CE, Mundlos C, Horn D, Mundlos S, Robinson PN. Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am J Hum Genet. 2009; 85(4):457\u201364. \n                    https:\/\/doi.org\/10.1016\/j.ajhg.2009.09.003\n                    \n                  .","journal-title":"Am J Hum Genet"},{"key":"2810_CR18","unstructured":"Supek F, \u0160kunca N. Visualizing gene ontology annotations. 2016. arXiv preprint arXiv:1602.07103."},{"issue":"5","key":"2810_CR19","first-page":"553","volume":"17","author":"J Peng","year":"2016","unstructured":"Peng J, Li H, Liu Y, Juan L, Jiang Q, Wang Y, Chen J. Intego2: a web tool for measuring and visualizing gene semantic similarities using gene ontology. BMC genomics. 2016; 17(5):553.","journal-title":"BMC genomics"},{"issue":"2","key":"2810_CR20","first-page":"45","volume":"16","author":"J Clemente","year":"2005","unstructured":"Clemente J, Satou K, Valiente G. Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology. Genome Inform. 2005; 16(2):45\u201355.","journal-title":"Genome Inform"},{"key":"2810_CR21","unstructured":"Grego T, Ferreira JD, Pesquita C, Bastos H, Vila Vi\u00e7osa D, Freire JM, Couto FM. Chemical and Metabolic Pathway Semantic Similarity. Technical report, Department of Informatics, Faculty of Sciences, University of Lisbon. 2010. \n                    https:\/\/doi.org\/DOI:10455\/3335\n                    \n                  ."},{"key":"2810_CR22","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/j.jbi.2016.10.017","volume":"64","author":"W Ning","year":"2016","unstructured":"Ning W, Yu M, Kong D. Evaluating semantic similarity between chinese biomedical terms through multiple ontologies with score normalization: An initial study. J Biomed Informa. 2016; 64:273\u201387.","journal-title":"J Biomed Informa"},{"issue":"1","key":"2810_CR23","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1186\/s12864-017-4338-6","volume":"19","author":"L Cheng","year":"2018","unstructured":"Cheng L, Jiang Y, Ju H, Sun J, Peng J, Zhou M, Hu Y. Infacront: calculating cross-ontology term similarities using information flow by a random walk. BMC genomics. 2018; 19(1):919.","journal-title":"BMC genomics"},{"issue":"7","key":"2810_CR24","doi-asserted-by":"publisher","first-page":"1000443","DOI":"10.1371\/journal.pcbi.1000443","volume":"5","author":"C Pesquita","year":"2009","unstructured":"Pesquita C, Faria D, Falc\u00e3o AO, Lord PW, Couto FM. Semantic similarity in biomedical ontologies. PLoS computational biology. 2009; 5(7):1000443. \n                    https:\/\/doi.org\/10.1371\/journal.pcbi.1000443\n                    \n                  .","journal-title":"PLoS computational biology"},{"issue":"2","key":"2810_CR25","first-page":"442","volume":"15","author":"MA Rodr\u00edguez","year":"2003","unstructured":"Rodr\u00edguez MA, Egenhofer MJ. Determining Semantic Similarity among Entity Classes from Different Ontologies. Knowl Creation Diff Utilization. 2003; 15(2):442\u201356. \n                    https:\/\/doi.org\/10.1109\/TKDE.2003.1185844\n                    \n                  .","journal-title":"Knowl Creation Diff Utilization"},{"issue":"4","key":"2810_CR26","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1109\/TSMCC.2009.2020689","volume":"39","author":"H Al-Mubaid","year":"2009","unstructured":"Al-Mubaid H, Nguyen HA. Measuring Semantic Similarity Between Biomedical Concepts Within Multiple Ontologies. IEEE Transactions on Systems, Man, and Cybernetics. 2009; 39(4):389\u201398. \n                    https:\/\/doi.org\/10.1109\/TSMCC.2009.2020689\n                    \n                  .","journal-title":"IEEE Transactions on Systems, Man, and Cybernetics"},{"issue":"4","key":"2810_CR27","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1016\/j.eswa.2012.08.049","volume":"40","author":"D S\u00e1nchez","year":"2013","unstructured":"S\u00e1nchez D, Batet M. A semantic similarity method based on information content exploiting multiple ontologies. Expert Syst Appl. 2013; 40(4):1393\u20139. \n                    https:\/\/doi.org\/10.1016\/j.eswa.2012.08.049\n                    \n                  .","journal-title":"Expert Syst Appl"},{"issue":"3","key":"2810_CR28","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.jbi.2006.06.004","volume":"40","author":"T Pedersen","year":"2007","unstructured":"Pedersen T, Pakhomov SVS, Patwardhan S, Chute CG. Measures of semantic similarity and relatedness in the biomedical domain. J Biomed Informa. 2007; 40(3):288\u201399. \n                    https:\/\/doi.org\/10.1016\/j.jbi.2006.06.004\n                    \n                  .","journal-title":"J Biomed Informa"},{"issue":"Database","key":"2810_CR29","doi-asserted-by":"publisher","first-page":"D434","DOI":"10.1093\/nar\/gkm806","volume":"36","author":"A. Schlicker","year":"2007","unstructured":"Schlicker A, Albrecht M. FunSimMat: A comprehensive functional similarity database. Nucleic Acids Research. 2008; 36(SUPPL. 1). \n                    https:\/\/doi.org\/10.1093\/nar\/gkm806\n                    \n                  .","journal-title":"Nucleic Acids Research"},{"issue":"11","key":"2810_CR30","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 NH, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007; 25(11):1251\u20135. \n                    https:\/\/doi.org\/10.1038\/nbt1346\n                    \n                  .","journal-title":"Nat Biotechnol"},{"key":"2810_CR31","unstructured":"Kamdar MR, Tudorache T, Musen MA. Investigating Term Reuse and Overlap in Biomedical Ontologies. In: Proceedings of the 6th International Conference on Biomedical Ontology, ICBO: 2015. p. 27\u201330. \n                    http:\/\/ceur-ws.org\/Vol-1515\/#regular9\n                    \n                  ."},{"key":"2810_CR32","volume-title":"A Dictionary of Epidemiology","year":"2008","unstructured":"In: Porta M, (ed).A Dictionary of Epidemiology, 5th (edn). Oxford: Oxford University Press; 2008."},{"key":"2810_CR33","unstructured":"Ferreira JD, Pesquita C, Couto FM, Silva MJ. Bringing epidemiology into the Semantic Web. In: International Conference on Biomedical Ontologies: 2012. \n                    http:\/\/ceur-ws.org\/Vol-897\/#\n                    \n                  ."},{"issue":"7","key":"2810_CR34","doi-asserted-by":"publisher","first-page":"2038","DOI":"10.1016\/j.patcog.2006.12.019","volume":"40","author":"ML Zhang","year":"2007","unstructured":"Zhang ML, Zhou ZH. ML-KNN: A lazy learning approach to multi-label learning. Pattern Recogn Lett. 2007; 40(7):2038\u201348. \n                    https:\/\/doi.org\/10.1016\/j.patcog.2006.12.019\n                    \n                  .","journal-title":"Pattern Recogn Lett"},{"key":"2810_CR35","unstructured":"Resnik P. Using information content to evaluate semantic similarity in a taxonomy. In: International Joint Conference on Artificial Intelligence: 1995. http:\/\/arxiv.org\/abs\/9511007v1.9511007v1."},{"issue":"Suppl 5","key":"2810_CR36","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-9-S5-S4","volume":"9","author":"C Pesquita","year":"2008","unstructured":"Pesquita C, Faria D, Bastos H, Ferreira AEN, Falc\u00e3o AO, Couto FM. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics. 2008; 9(Suppl 5):4. \n                    https:\/\/doi.org\/10.1186\/1471-2105-9-S5-S4\n                    \n                  .","journal-title":"BMC Bioinformatics"},{"key":"2810_CR37","volume-title":"International Conference on Machine Learning","author":"D Lin","year":"1998","unstructured":"Lin D. An information-theoretic definition of similarity. In: International Conference on Machine Learning. San Francisco: Morgan Kaufmann Publishers: 1998. p. 296\u2013304."},{"key":"2810_CR38","doi-asserted-by":"crossref","unstructured":"Gentleman R. Visualizing and distances using GO. Technical report. 2007. \n                    https:\/\/doi.org\/10.1186\/1471-2105-7-491\n                    \n                  .","DOI":"10.1186\/1471-2105-7-491"},{"key":"2810_CR39","volume-title":"International Conference on Biomedical Ontologies","author":"JD Ferreira","year":"2011","unstructured":"Ferreira JD, Couto FM. Generic semantic relatedness measure for biomedical ontologies. In: International Conference on Biomedical Ontologies. Buffalo: University at Buffalo: 2011."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2810-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2810-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2810-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,27]],"date-time":"2020-05-27T23:06:29Z","timestamp":1590620789000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2810-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5]]},"references-count":39,"journal-issue":{"issue":"S10","published-print":{"date-parts":[[2019,5]]}},"alternative-id":["2810"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2810-9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5]]},"assertion":[{"value":"29 May 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"246"}}