TY - JOUR AU - Lord, P. W. AU - Stevens, R. D. AU - Brass, A. AU - Goble, C. A. PY - 2003 DA - 2003// TI - Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg153 DO - 10.1093/bioinformatics/btg153 ID - Lord2003 ER - TY - JOUR AU - Croft, D. AU - O’Kelly, G. AU - Wu, G. AU - Haw, R. AU - Gillespie, M. AU - Matthews, L. AU - Caudy, M. AU - Garapati, P. AU - Gopinath, G. AU - Jassal, B. AU - Jupe, S. AU - Kalatskaya, I. AU - MayMahajan, S. AU - May, B. AU - Ndegwa, N. AU - Schmidt, E. AU - Shamovsky, V. AU - Yung, C. AU - Birney, E. AU - Hermjakob, H. AU - D’Eustachio, P. AU - Stein, L. PY - 2011 DA - 2011// TI - Reactome: A database of reactions, pathways and biological processes JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1018 DO - 10.1093/nar/gkq1018 ID - Croft2011 ER - TY - STD TI - 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. https://doi.org/10.1093/bib/bbx085. UR - https://doi.org/10.1093/bib/bbx085 ID - ref3 ER - TY - JOUR AU - Juty, N. AU - Ali, R. AU - Glont, M. AU - Keating, S. AU - Rodriguez, N. AU - Swat, M. J. AU - Wimalaratne, S. M. AU - Hermjakob, H. AU - le Novère, N. AU - Laibe, C. AU - Chelliah, V. PY - 2015 DA - 2015// TI - BioModels: Content, Features, Functionality, and Use JO - CPT: Pharmacometrics & Syst Pharmacol VL - 4 ID - Juty2015 ER - TY - CHAP AU - Nickerson, D. a. v. i. d. P. AU - Atalag, K. o. r. a. y. AU - de Bono, B. e. r. n. a. r. d. AU - Hunter, P. e. t. e. r. J. PY - 2016 DA - 2016// TI - The Physiome Project,openEHR Archetypes, and the Digital Patient BT - The Digital Patient PB - Sons, Inc CY - Hoboken, NJ UR - https://doi.org/10.1002/9781118952788.ch9 DO - 10.1002/9781118952788.ch9 ID - Nickerson2016 ER - TY - CHAP AU - Lopes, L. u. i. s. F. AU - Silva, F. a. b. r. í. c. i. o. A. B. AU - Couto, F. r. a. n. c. i. s. c. o. AU - Zamite, J. o. ã. o. AU - Ferreira, H. u. g. o. AU - Sousa, C. a. r. l. a. AU - Silva, M. á. r. i. o. J. PY - 2010 DA - 2010// TI - Epidemic Marketplace: An Information Management System for Epidemiological Data BT - Information Technology in Bio- and Medical Informatics, ITBAM 2010 PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg UR - https://doi.org/10.1007/978-3-642-15020-3_3 DO - 10.1007/978-3-642-15020-3_3 ID - Lopes2010 ER - TY - JOUR AU - Tchechmedjiev, A. AU - Abdaoui, A. AU - Emonet, V. AU - Zevio, S. AU - Jonquet, C. PY - 2018 DA - 2018// TI - Sifr annotator: ontology-based semantic annotation of french biomedical text and clinical notes JO - BMC bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2429-2 DO - 10.1186/s12859-018-2429-2 ID - Tchechmedjiev2018 ER - TY - JOUR AU - Wang, R. -. L. AU - Edwards, S. AU - Ives, C. PY - 2018 DA - 2018// TI - Ontology-based semantic mapping of chemical toxicities JO - Toxicology VL - 412 UR - https://doi.org/10.1016/j.tox.2018.11.005 DO - 10.1016/j.tox.2018.11.005 ID - Wang2018 ER - TY - JOUR AU - Spasic, I. AU - Ananiadou, S. AU - McNaught, J. AU - Kumar, A. PY - 2005 DA - 2005// TI - Text mining and ontologies in biomedicine: making sense of raw text JO - Briefings in Bioinformatics VL - 6 UR - https://doi.org/10.1093/bib/6.3.239 DO - 10.1093/bib/6.3.239 ID - Spasic2005 ER - TY - STD TI - 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. 10–6. https://doi.org/10.1145/1097047.1097051. UR - https://doi.org/10.1145/1097047.1097051 ID - ref10 ER - TY - JOUR AU - Lamurias, A. AU - Ferreira, J. D. AU - Couto, F. M. PY - 2015 DA - 2015// TI - Improving chemical entity recognition through h-index based semantic similarity JO - Journal of Cheminformatics VL - 7 UR - https://doi.org/10.1186/1758-2946-7-S1-S13 DO - 10.1186/1758-2946-7-S1-S13 ID - Lamurias2015 ER - TY - JOUR AU - Ji, X. AU - Ritter, A. AU - Yen, P. -. Y. PY - 2017 DA - 2017// TI - Using ontology-based semantic similarity to facilitate the article screening process for systematic reviews JO - J Biomed Informa VL - 69 UR - https://doi.org/10.1016/j.jbi.2017.03.007 DO - 10.1016/j.jbi.2017.03.007 ID - Ji2017 ER - TY - JOUR AU - Ferreira, J. D. AU - Couto, F. M. PY - 2010 DA - 2010// TI - Semantic Similarity for Automatic Classification of Chemical Compounds JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000937 DO - 10.1371/journal.pcbi.1000937 ID - Ferreira2010 ER - TY - STD TI - 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. 317–24. https://doi.org/10.1109/BIBE.2004.1317360. UR - https://doi.org/10.1109/BIBE.2004.1317360 ID - ref14 ER - TY - JOUR AU - Guo, X. AU - Liu, R. AU - Shriver, C. D. AU - Hu, H. AU - Liebman, M. N. PY - 2006 DA - 2006// TI - Assessing semantic similarity measures for the characterization of human regulatory pathways JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl042 DO - 10.1093/bioinformatics/btl042 ID - Guo2006 ER - TY - JOUR AU - Zhang, S. -. B. AU - Tang, Q. -. R. PY - 2016 DA - 2016// TI - Protein–protein interaction inference based on semantic similarity of gene ontology terms JO - J Theor Biol VL - 401 UR - https://doi.org/10.1016/j.jtbi.2016.04.020 DO - 10.1016/j.jtbi.2016.04.020 ID - Zhang2016 ER - TY - JOUR AU - Köhler, S. AU - Schulz, M. H. AU - Krawitz, P. AU - Bauer, S. AU - Dölken, S. AU - Ott, C. E. AU - Mundlos, C. AU - Horn, D. AU - Mundlos, S. AU - Robinson, P. N. PY - 2009 DA - 2009// TI - Clinical diagnostics in human genetics with semantic similarity searches in ontologies JO - Am J Hum Genet VL - 85 UR - https://doi.org/10.1016/j.ajhg.2009.09.003 DO - 10.1016/j.ajhg.2009.09.003 ID - Köhler2009 ER - TY - STD TI - Supek F, Škunca N. Visualizing gene ontology annotations. 2016. arXiv preprint arXiv:1602.07103. ID - ref18 ER - TY - JOUR AU - Peng, J. AU - Li, H. AU - Liu, Y. AU - Juan, L. AU - Jiang, Q. AU - Wang, Y. AU - Chen, J. PY - 2016 DA - 2016// TI - Intego2: a web tool for measuring and visualizing gene semantic similarities using gene ontology JO - BMC genomics VL - 17 ID - Peng2016 ER - TY - JOUR AU - Clemente, J. AU - Satou, K. AU - Valiente, G. PY - 2005 DA - 2005// TI - Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology JO - Genome Inform VL - 16 ID - Clemente2005 ER - TY - STD TI - Grego T, Ferreira JD, Pesquita C, Bastos H, Vila Viçosa D, Freire JM, Couto FM. Chemical and Metabolic Pathway Semantic Similarity. Technical report, Department of Informatics, Faculty of Sciences, University of Lisbon. 2010. https://doi.org/DOI:10455/3335. UR - https://doi.org/DOI:10455/3335 ID - ref21 ER - TY - JOUR AU - Ning, W. AU - Yu, M. AU - Kong, D. PY - 2016 DA - 2016// TI - Evaluating semantic similarity between chinese biomedical terms through multiple ontologies with score normalization: An initial study JO - J Biomed Informa VL - 64 UR - https://doi.org/10.1016/j.jbi.2016.10.017 DO - 10.1016/j.jbi.2016.10.017 ID - Ning2016 ER - TY - JOUR AU - Cheng, L. AU - Jiang, Y. AU - Ju, H. AU - Sun, J. AU - Peng, J. AU - Zhou, M. AU - Hu, Y. PY - 2018 DA - 2018// TI - Infacront: calculating cross-ontology term similarities using information flow by a random walk JO - BMC genomics VL - 19 UR - https://doi.org/10.1186/s12864-017-4338-6 DO - 10.1186/s12864-017-4338-6 ID - Cheng2018 ER - TY - JOUR AU - Pesquita, C. AU - Faria, D. AU - Falcão, A. O. AU - Lord, P. W. AU - Couto, F. M. PY - 2009 DA - 2009// TI - Semantic similarity in biomedical ontologies JO - PLoS computational biology VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000443 DO - 10.1371/journal.pcbi.1000443 ID - Pesquita2009 ER - TY - JOUR AU - Rodríguez, M. A. AU - Egenhofer, M. J. PY - 2003 DA - 2003// TI - Determining Semantic Similarity among Entity Classes from Different Ontologies JO - Knowl Creation Diff Utilization VL - 15 ID - Rodríguez2003 ER - TY - JOUR AU - Al-Mubaid, H. AU - Nguyen, H. A. PY - 2009 DA - 2009// TI - Measuring Semantic Similarity Between Biomedical Concepts Within Multiple Ontologies JO - IEEE Transactions on Systems, Man, and Cybernetics VL - 39 UR - https://doi.org/10.1109/TSMCC.2009.2020689 DO - 10.1109/TSMCC.2009.2020689 ID - Al-Mubaid2009 ER - TY - JOUR AU - Sánchez, D. AU - Batet, M. PY - 2013 DA - 2013// TI - A semantic similarity method based on information content exploiting multiple ontologies JO - Expert Syst Appl VL - 40 UR - https://doi.org/10.1016/j.eswa.2012.08.049 DO - 10.1016/j.eswa.2012.08.049 ID - Sánchez2013 ER - TY - JOUR AU - Pedersen, T. AU - Pakhomov, S. V. S. AU - Patwardhan, S. AU - Chute, C. G. PY - 2007 DA - 2007// TI - Measures of semantic similarity and relatedness in the biomedical domain JO - J Biomed Informa VL - 40 UR - https://doi.org/10.1016/j.jbi.2006.06.004 DO - 10.1016/j.jbi.2006.06.004 ID - Pedersen2007 ER - TY - JOUR AU - Schlicker, A. AU - Albrecht, M. PY - 2007 DA - 2007// TI - FunSimMat: a comprehensive functional similarity database JO - Nucleic Acids Research VL - 36 UR - https://doi.org/10.1093/nar/gkm806 DO - 10.1093/nar/gkm806 ID - Schlicker2007 ER - TY - JOUR AU - Smith, B. AU - Ashburner, M. AU - Rosse, C. AU - Bard, J. AU - Bug, W. AU - Ceusters, W. AU - Goldberg, L. J. AU - Eilbeck, K. AU - Ireland, A. AU - Mungall, C. J. AU - Leontis, N. AU - Rocca-Serra, P. AU - Ruttenberg, A. AU - Sansone, S. -. A. AU - Scheuermann, R. H. AU - Shah, N. H. AU - Whetzel, P. L. AU - Lewis, S. PY - 2007 DA - 2007// TI - The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration JO - Nat Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1346 DO - 10.1038/nbt1346 ID - Smith2007 ER - TY - STD TI - 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. 27–30. http://ceur-ws.org/Vol-1515/#regular9. UR - http://ceur-ws.org/Vol-1515/#regular9 ID - ref31 ER - TY - BOOK PY - 2008 DA - 2008// TI - A Dictionary of Epidemiology PB - Oxford University Press CY - Oxford ID - ref32 ER - TY - STD TI - Ferreira JD, Pesquita C, Couto FM, Silva MJ. Bringing epidemiology into the Semantic Web. In: International Conference on Biomedical Ontologies: 2012. http://ceur-ws.org/Vol-897/#. UR - http://ceur-ws.org/Vol-897/# ID - ref33 ER - TY - JOUR AU - Zhang, M. L. AU - Zhou, Z. H. PY - 2007 DA - 2007// TI - ML-KNN: A lazy learning approach to multi-label learning JO - Pattern Recogn Lett VL - 40 UR - https://doi.org/10.1016/j.patcog.2006.12.019 DO - 10.1016/j.patcog.2006.12.019 ID - Zhang2007 ER - TY - STD TI - 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. ID - ref35 ER - TY - JOUR AU - Pesquita, C. AU - Faria, D. AU - Bastos, H. AU - Ferreira, A. E. N. AU - Falcão, A. O. AU - Couto, F. M. PY - 2008 DA - 2008// TI - Metrics for GO based protein semantic similarity: a systematic evaluation JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-S5-S4 DO - 10.1186/1471-2105-9-S5-S4 ID - Pesquita2008 ER - TY - CHAP AU - Lin, D. PY - 1998 DA - 1998// TI - An information-theoretic definition of similarity BT - International Conference on Machine Learning PB - Morgan Kaufmann Publishers CY - San Francisco ID - Lin1998 ER - TY - STD TI - Gentleman R. Visualizing and distances using GO. Technical report. 2007. https://doi.org/10.1186/1471-2105-7-491. UR - https://doi.org/10.1186/1471-2105-7-491 ID - ref38 ER - TY - CHAP AU - Ferreira, J. D. AU - Couto, F. M. PY - 2011 DA - 2011// TI - Generic semantic relatedness measure for biomedical ontologies BT - International Conference on Biomedical Ontologies PB - University at Buffalo CY - Buffalo ID - Ferreira2011 ER -