TY - JOUR AU - Michael, A. AU - Catherine, A. B. AU - Judith, A. B. AU - David, B. AU - Heather, B. AU - J. Michael, C. AU - Allan, P. D. AU - Kara, D. AU - Selina, S. D. AU - Janan, T. E. AU - Midori, A. H. AU - David, P. H. AU - Laurie, I. T. AU - Andrew, K. AU - Suzanna, L. AU - John, C. M. AU - Joel, E. R. AU - Martin, R. AU - Gerald, M. R. AU - Gavin, S. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Michael2000 ER - TY - JOUR AU - Wu, X. AU - Zhu, L. AU - Guo, J. AU - Zhang, D. K. AU - Lin, K. PY - 2006 DA - 2006// TI - Prediction of yeast protein-protein interaction network: insights from the gene ontology and annotations JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl219 DO - 10.1093/nar/gkl219 ID - Wu2006 ER - TY - JOUR AU - Stelzl, U. AU - Worm, U. AU - Lalowski, M. AU - Haenig, C. AU - Brembeck, F. H. AU - Goehler, H. AU - Stroedicke, M. AU - Zenkner, M. AU - Schoenherr, A. AU - Koeppen, S. AU - Timm, J. AU - Mintzlaff, S. AU - Abraham, C. AU - Bock, N. AU - Kietzmann, S. AU - Goedde, A. AU - Toksöz, E. AU - Droege, A. AU - Krobitsch, S. AU - Korn, B. AU - Birchmeier, W. AU - Lehrach, H. AU - Wanker, E. E. PY - 2005 DA - 2005// TI - A human protein-protein interaction network: a resource for annotating the proteome JO - Cell VL - 122 UR - https://doi.org/10.1016/j.cell.2005.08.029 DO - 10.1016/j.cell.2005.08.029 ID - Stelzl2005 ER - TY - JOUR AU - Yu, J. AU - Yang, H. PY - 2002 DA - 2002// TI - A draft sequence of the rice genome (oryza sativa l. ssp. indica) JO - Science VL - 296 ID - Yu2002 ER - TY - JOUR AU - Sequencing, C. AU - Consortium, A. PY - 2005 DA - 2005// TI - Initial sequence of the chimpanzee genome and comparison with the human genome JO - Nature VL - 437 UR - https://doi.org/10.1038/nature04072 DO - 10.1038/nature04072 ID - Sequencing2005 ER - TY - JOUR AU - Khatri, P. AU - Drăghici, S. PY - 2005 DA - 2005// TI - Ontological analysis of gene expression data: current tools, limitations, and open problems JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti565 DO - 10.1093/bioinformatics/bti565 ID - Khatri2005 ER - TY - JOUR AU - Shen, R. AU - Chinnaiyan, A. M. AU - Ghosh, D. PY - 2008 DA - 2008// TI - Pathway analysis reveals functional convergence of gene expression profiles in breast cancer JO - BMC Med Genomics VL - 1 UR - https://doi.org/10.1186/1755-8794-1-28 DO - 10.1186/1755-8794-1-28 ID - Shen2008 ER - TY - JOUR AU - Jansen, R. AU - Yu, H. AU - Greenbaum, D. AU - Kluger, Y. AU - Krogan, N. J. AU - Chung, S. AU - Emili, A. AU - Snyder, M. AU - Greenblatt, J. F. AU - Gerstein, M. PY - 2003 DA - 2003// TI - A bayesian networks approach for predicting protein-protein interactions from genomic data JO - Science VL - 302 UR - https://doi.org/10.1126/science.1087361 DO - 10.1126/science.1087361 ID - Jansen2003 ER - TY - JOUR AU - David, M. AU - Christine, B. AU - Elisabeth, R. AU - Pierre, M. AU - Denis, T. AU - Bernard, J. PY - 2004 DA - 2004// TI - Gotoolbox: functional analysis of gene datasets based on gene ontology JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-12-r101 DO - 10.1186/gb-2004-5-12-r101 ID - David2004 ER - TY - JOUR AU - Rhodes, D. R. AU - Tomlins, S. A. AU - Varambally, S. AU - Mahavisno, V. AU - Barrette, T. AU - Kalyana-Sundaram, S. AU - Ghosh, D. AU - Pandey, A. AU - Chinnaiyan, A. M. PY - 2005 DA - 2005// TI - Probabilistic model of the human protein-protein interaction network JO - Nat Biotechnol VL - 23 UR - https://doi.org/10.1038/nbt1103 DO - 10.1038/nbt1103 ID - Rhodes2005 ER - TY - JOUR AU - Mazandu, G. K. AU - Chimusa, E. R. AU - Mulder, N. J. PY - 2016 DA - 2016// TI - Gene ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery. JO - Brief Bioinform VL - 18 ID - Mazandu2016 ER - TY - JOUR AU - Catia, P. AU - Daniel, F. AU - Andre, F. O. AU - Phillip, L. AU - Francisco, M. C. PY - 2009 DA - 2009// TI - Semantic similarity in biomedical ontologies JO - Plos Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000443 DO - 10.1371/journal.pcbi.1000443 ID - Catia2009 ER - TY - JOUR AU - Sidahmed, B. AU - Malika, S. T. AU - Olivier, P. AU - Amedeo, N. AU - Marie-Dominique, D. PY - 2010 DA - 2010// TI - Intelligo: a new vector-based semantic similarity measure including annotation origin JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-588 DO - 10.1186/1471-2105-11-588 ID - Sidahmed2010 ER - TY - JOUR AU - Jain, S. AU - Bader, G. D. PY - 2010 DA - 2010// TI - An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-562 DO - 10.1186/1471-2105-11-562 ID - Jain2010 ER - TY - CHAP AU - Resnik, P. PY - 1995 DA - 1995// TI - Using information content to evaluate semantic similarity in a taxonomy BT - Proceedings of the 14th International Joint Conference on Artificial Intelligence San Francisco PB - Morgan Kaufmann Publishers Inc CY - CA, USA ID - Resnik1995 ER - TY - STD TI - Lin D. An information-theoretic definition of similarity. In: Proceedings of the 15th International Conference on Machine Learning Morgan Kaufmann. Morgan Kaufmann: 1998. p. 296–304. ID - ref16 ER - TY - STD TI - Jiang JJ, Conrath DW. Semantic similarity based on corpus statistics and lexical taxonomy. Int Conf Res Comput Linguist (ROCLING X). 1999;9008. ID - ref17 ER - TY - JOUR AU - Schlicker, A. AU - Domingues, F. S. AU - Rahnenführer, J. AU - Lengauer, T. PY - 2006 DA - 2006// TI - A new measure for functional similarity of gene products based on gene ontology JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-302 DO - 10.1186/1471-2105-7-302 ID - Schlicker2006 ER - TY - JOUR AU - Pesquita, C. AU - Faria, D. AU - Bastos, H. AU - Falco, A. AU - Couto, F. M. PY - 2007 DA - 2007// TI - Evaluating go-based semantic similarity measures JO - Ismb/eccb Sig Meet Program Mater Iscb VL - 37 ID - Pesquita2007 ER - TY - JOUR AU - Chabalier, J. AU - Mosser, J. AU - Burgun, A. PY - 2007 DA - 2007// TI - A transversal approach to predict gene product networks from ontology-based similarity JO - BMC Bioinformatics VL - 1 UR - https://doi.org/10.1186/1471-2105-8-235 DO - 10.1186/1471-2105-8-235 ID - Chabalier2007 ER - TY - JOUR AU - Pozo, A. D. AU - Pazos, F. AU - Valencia, A. PY - 2008 DA - 2008// TI - Defining functional distances over gene ontology JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-50 DO - 10.1186/1471-2105-9-50 ID - Pozo2008 ER - TY - JOUR AU - Wu, H. AU - Su, Z. AU - Mao, F. AU - Olman, V. AU - Xu, Y. PY - 2005 DA - 2005// TI - Prediction of functional modules based on comparative genome analysis and gene ontology application JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki573 DO - 10.1093/nar/gki573 ID - Wu2005 ER - TY - JOUR AU - Cheng, J. AU - Cline, M. AU - Martin, J. AU - Finkelstein, D. AU - Awad, T. AU - Kulp, D. AU - Siani-Rose, M. A. PY - 2004 DA - 2004// TI - A knowledge based clustering algorithm driven by gene ontology JO - J Biopharm Stat VL - 14 UR - https://doi.org/10.1081/BIP-200025659 DO - 10.1081/BIP-200025659 ID - Cheng2004 ER - TY - JOUR AU - Yu, H. AU - Gao, L. AU - Tu, K. AU - Guo, Z. PY - 2005 DA - 2005// TI - Broadly predicting specific gene functions with expression similarity and taxonomy similarity JO - Gene VL - 352 UR - https://doi.org/10.1016/j.gene.2005.03.033 DO - 10.1016/j.gene.2005.03.033 ID - Yu2005 ER - TY - CHAP AU - Pekar, V. AU - Staab, S. PY - 2002 DA - 2002// TI - Taxonomy Learning: Factoring the Structure of a Taxonomy Into a Semantic Classification Decision BT - Proceedings of the 19th international conference on Computational linguistics PB - Association for Computational Linguistics CY - Morristown ID - Pekar2002 ER - TY - JOUR AU - Wang, J. Z. AU - Du, Z. AU - Payattakool, R. AU - Yu, P. S. AU - Chen, C. F. PY - 2007 DA - 2007// TI - A new method to measure the semantic similarity of go terms JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm087 DO - 10.1093/bioinformatics/btm087 ID - Wang2007 ER - TY - JOUR AU - Batet, M. AU - Sánchez, D. AU - Valls, A. PY - 2011 DA - 2011// TI - An ontology-based measure to compute semantic similarity in biomedicine JO - J Biomed Inform VL - 44 UR - https://doi.org/10.1016/j.jbi.2010.09.002 DO - 10.1016/j.jbi.2010.09.002 ID - Batet2011 ER - TY - STD TI - Budanitsky A. Lexical semantic relatedness and its application in natural language processing. 1999. http://www.cs.toronto.edu/pub/gh/Budanitsky-99.pdf. UR - http://www.cs.toronto.edu/pub/gh/Budanitsky-99.pdf ID - ref28 ER - TY - CHAP AU - Seco, N. AU - Veale, T. AU - Hayes, J. PY - 2004 DA - 2004// TI - An intrinsic information content metric for semantic similarity in wordnet BT - Eureopean Conference on Artificial Intelligence, Ecai’2004, Including Prestigious Applicants of Intelligent Systems, Pais 2004, Valencia, Spain, August PB - IOS Press CY - Amsterdam ID - Seco2004 ER - TY - CHAP AU - Couto, F. M. AU - Coutinho, P. M. PY - 2005 DA - 2005// TI - Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors BT - ACM CIKM International Conference on Information and Knowledge Management PB - ACM CY - New York ID - Couto2005 ER - TY - STD TI - Budanitsky A, Hirst G. Semantic distance in wordnet: An experimental, application-oriented evaluation of five measures. In: The Workshop on Wordnet & Other Lexical Resources: 2001. ID - ref31 ER - TY - JOUR AU - Ehsani, R. AU - Drabløs, F. PY - 2016 DA - 2016// TI - Topoicsim: a new semantic similarity measure based on gene ontology JO - BMC Bioinformatics VL - 17 UR - https://doi.org/10.1186/s12859-016-1160-0 DO - 10.1186/s12859-016-1160-0 ID - Ehsani2016 ER - TY - JOUR AU - Pesquita, C. AU - Faria, D. AU - Bastos, H. AU - Ferreira, A. 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 - STD TI - Cross V. Tversky’s parameterized similarity ratio model: A basis for semantic relatedness. In: Fuzzy Information Processing Society, 2006. Nafips 2006 Meeting of the North American. IEEE: 2006. p. 541–546. ID - ref34 ER - TY - JOUR AU - Lee, H. K. AU - Hsu, A. K. AU - Sajdak, J. AU - Qin, J. AU - Pavlidis, P. PY - 2004 DA - 2004// TI - Coexpression analysis of human genes across many microarray data sets JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1910904 DO - 10.1101/gr.1910904 ID - Lee2004 ER - TY - JOUR AU - Mistry, M. AU - Pavlidis, P. PY - 2008 DA - 2008// TI - Gene ontology term overlap as a measure of gene functional similarity JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-327 DO - 10.1186/1471-2105-9-327 ID - Mistry2008 ER - TY - JOUR AU - David, M. AU - Christine, B. AU - Elisabeth, R. AU - Pierre, M. AU - Denis, T. AU - Bernard, J. PY - 2004 DA - 2004// TI - Gotoolbox: functional analysis of gene datasets based on gene ontology JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-12-r101 DO - 10.1186/gb-2004-5-12-r101 ID - David2004 ER - TY - STD TI - Gentleman R. Visualizing and distances using go. 2010. https://www.bioconductor.org/packages/devel/bioc/vignettes/GOstats/inst/doc/GOvis.pdf. UR - https://www.bioconductor.org/packages/devel/bioc/vignettes/GOstats/inst/doc/GOvis.pdf ID - ref38 ER - TY - STD TI - Sheehan B, Quigley A, Gaudin B, Dobson S. A relation based measure of semantic similarity for gene ontology annotations. 2008; 9:468. ID - ref39 ER - TY - STD TI - Torsello A, Hidovic D, Pelillo M. Four metrics for efficiently comparing attributed trees. 2004; 2:467–70. ID - ref40 ER - TY - JOUR AU - Bible, P. W. AU - Sun, H. W. AU - Morasso, M. I. AU - Loganantharaj, R. AU - Wei, L. PY - 2017 DA - 2017// TI - The effects of shared information on semantic calculations in the gene ontology JO - Comput Struct Biotechnol J VL - 15 UR - https://doi.org/10.1016/j.csbj.2017.01.009 DO - 10.1016/j.csbj.2017.01.009 ID - Bible2017 ER - TY - STD TI - Dutta P, Basu S, Kundu M. Assessment of semantic similarity between proteins using information content and topological properties of the gene ontology graph. IEEE/ACM Trans Comput Biol Bioinforma. 2017. ID - ref42 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 - Huang, Q. AU - You, Z. AU - Zhang, X. AU - Yong, Z. PY - 2015 DA - 2015// TI - Prediction of protein protein interactions with clustered amino acids and weighted sparse representation JO - Int J Mol Sci VL - 16 UR - https://doi.org/10.3390/ijms160510855 DO - 10.3390/ijms160510855 ID - Huang2015 ER - TY - JOUR AU - Mei, S. AU - Zhu, H. PY - 2014 DA - 2014// TI - Adaboost based multi-instance transfer learning for predicting proteome-wide interactions between salmonella and human proteins JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0110488 DO - 10.1371/journal.pone.0110488 ID - Mei2014 ER - TY - STD TI - Duong D, Eskin E, Li J. A novel word2vec based tool to estimate semantic similarity of genes by using gene ontology terms. bioRxiv. 2017. ID - ref46 ER - TY - JOUR AU - Diaz-Montana, J. J. AU - Diaz-Diaz, N. AU - Gomez-Vela, F. PY - 2017 DA - 2017// TI - Gfd-net a novel semantic similarity methodology for the analysis of gene networks JO - J Biomed Inform VL - 68 UR - https://doi.org/10.1016/j.jbi.2017.02.013 DO - 10.1016/j.jbi.2017.02.013 ID - Diaz-Montana2017 ER - TY - JOUR AU - Guzzi, P. H. AU - Mina, M. AU - Guerra, C. AU - Cannataro, M. PY - 2012 DA - 2012// TI - Semantic similarity analysis of protein data: assessment with biological features and issues JO - Brief Bioinformatics VL - 13 UR - https://doi.org/10.1093/bib/bbr066 DO - 10.1093/bib/bbr066 ID - Guzzi2012 ER - TY - JOUR AU - Consortium, U. PY - 2010 DA - 2010// TI - The universal protein resource (uniprot) in 2010 JO - Nucleic Acids Res VL - 38 Database UR - https://doi.org/10.1093/nar/gkp846 DO - 10.1093/nar/gkp846 ID - Consortium2010 ER - TY - STD TI - Saccharomyces Genome Database. http://downloads.yeastgenome.org. UR - http://downloads.yeastgenome.org ID - ref50 ER - TY - JOUR AU - Xenarios, I. AU - Rice, D. AU - Salwinski, L. AU - Baron, M. AU - Marcotte, E. AU - Eisenberg, D. PY - 2000 DA - 2000// TI - Dip: the database of interacting proteins JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.289 DO - 10.1093/nar/28.1.289 ID - Xenarios2000 ER - TY - JOUR AU - Razick, S. AU - Magklaras, G. AU - Donaldson, I. PY - 2008 DA - 2008// TI - irefindex: a consolidated protein interaction database with provenance JO - BMC bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-405 DO - 10.1186/1471-2105-9-405 ID - Razick2008 ER - TY - JOUR AU - Wu, X. AU - Pang, E. AU - Lin, K. AU - Pei, Z. M. PY - 2013 DA - 2013// TI - Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and ic-based hybrid method JO - Plos One VL - 8 UR - https://doi.org/10.1371/journal.pone.0066745 DO - 10.1371/journal.pone.0066745 ID - Wu2013 ER - TY - STD TI - The Collaborative Evaluation of Semantic Similarity Measures tool. http://xldb.di.fc.ul.pt/tools/cessm/. Accessed 30 Jan 2018. UR - http://xldb.di.fc.ul.pt/tools/cessm/ ID - ref54 ER -