Technological advances of computer science and data analysis are helping to provide continuously huge volumes of biological data, which are available on the web. Such advances involve and require powerful techniques for data integration to extract pertinent knowledge and information for a specific question. Biomedical exploration of these big data often requires the use of complex queries across multiple autonomous, heterogeneous and distributed data sources. Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontology. We provide a survey of some approaches and techniques for integrating biological data, we focus on those developed in the ontology community., {"references":["N. Shadbolt, T. Berners-Lee, and W. Hall, \"The semantic web revisited,\"\nIEEE intelligent systems, vol. 21, no. 3, pp. 96–101, 2006.","A. H. Asiaee, T. Minning, P. Doshi, and R. L. Tarleton, \"A framework\nfor ontology-based question answering with application to parasite\nimmunology,\" Journal of biomedical semantics, vol. 6, no. 1, p. 1, 2015.","G. Santipantakis, K. I. Kotis, and G. A. Vouros, \"Ontology-based data\nintegration for event recognition in the maritime domain,\" in Proceedings\nof the 5th International Conference on Web Intelligence, Mining and\nSemantics. ACM, 2015, p. 6.","C. Jonquet, E. Dzal´e-Yeumo, E. Arnaud, and P. Larmande, \"Agroportal:\na proposition for ontology-based services in the agronomic domain,\" in\nIN-OVIVE'15: 3`eme atelier INt´egration de sources/masses de donn´ees\nh´et´erog`enes et Ontologies, dans le domaine des sciences du VIVant et\nde l'Environnement, 2015.","M. Iannacone, S. Bohn, G. Nakamura, J. Gerth, K. Huffer, R. Bridges,\nE. Ferragut, and J. Goodall, \"Developing an ontology for cyber security\nknowledge graphs,\" in Proceedings of the 10th Annual Cyber and\nInformation Security Research Conference. ACM, 2015, p. 12.","H. Wache, T. Voegele, U. Visser, H. Stuckenschmidt, G. Schuster,\nH. Neumann, and S. H¨ubner, \"Ontology-based integration of\ninformation-a survey of existing approaches,\" in IJCAI-01 workshop:\nontologies and information sharing, vol. 2001. Citeseer, 2001, pp.\n108–117.","D. Dou, H. Wang, and H. Liu, \"Semantic data mining: A survey of\nontology-based approaches,\" in Semantic Computing (ICSC), 2015 IEEE\nInternational Conference on. IEEE, 2015, pp. 244–251.","T. R. Gruber, \"A translation approach to portable ontology\nspecifications,\" Knowledge Acquisition, 5(2), pp. 199–220, 1993.","B. L. Jonathan and S. Y. Rhee, \"Ontologies in biology: Design\napplication and future challenges.\" 2004.\n[10] F. Manola and E. Miller, \"Rdf primer,\" World Wide Web Consortium,\n2004.\n[11] B. Grau, I. Horrocks, and B. M. et al, \"Owl 2: the next step for owl,\"\nWeb Semant, vol. 6, pp. 309–322, 2008.\n[12] A. Seaborne and E. Prud'hommeaux, \"Sparql query language for rdf,\"\nW3C Recommendation (W3C, 2008), 2008.\n[13] C. Bizer, \"Evolving the web into a global data space.\" in BNCOD, vol.\n7051, 2011, p. 1.\n[14] I. Horrocks, \"Obo flat file format syntax and semantics and mapping to\nowl web ontology language,\" University of Manchester, 2007.\n[15] J. Blake and C. Bult, \"Beyond the data deluge: Data integration and\nbio-ontologies.\" Journal of Biomedical Informatics, pp. 314–320, 2006. [16] R. Hoehndorf, P. Schofield, and G. Gkoutos, \"The role of ontologies\nin biological and biomedical research: a functional perspective,\" Brief.\nBioinform, 16 (6), pp. 1069–1080, 2015.\n[17] M. Ashburner, C. Ball, J. Blake, D. Botstein, H. Butler, J. Cherry,\nA. Davis, K.Dolinski, S. Dwight, J. Eppig, M. Harris, D. Hill,\nL. Issel-Tarver, A. Kasarskis, S. Lewis, J. Matese, J. Richardson,\nM. Ringwald, G. Rubin, and G. Sherlock, \"Gene ontology: tool for\nthe unification of biology,\" The Gene Ontology Consortium, vol. Nat.\nGenet. 25, pp. 25–29, 2000.\n[18] S. Orchard, \"Molecular interaction databases,\" Proteomics, vol. 12, pp.\n1656–1662, 2012.\n[19] K. Degtyarenko, P. de Matos, M. Ennis, J. Hastings, M. Zbinden,\nA. McNaught, R. Alcantara, M. Darsow, M. Guedj, and M. Ashburner,\n\"Chebi: a database and ontology forchemical entities of biological\ninterest,\" Nucleic Acids Res, pp. D344–D350, 2008.\n[20] L. Montecchi-Palazzi, R. Beavis, P. Binz, R. Chalkley, J. Cottrell,\nD. Creasy, J. Shofstahl, S. Seymour, and J. Garavelli, \"The psi-mod\ncommunity standard for representation of protein modification data,\"\nNat. Biotechnol., vol. 26, pp. 864–866, 2008.\n[21] R. Brinkman, M. Courtot, D. Derom, J. Fostel, Y. He, P. Lord,\nJ. Malone, H. Parkinson, B. Peters, P. Rocca-Serra, A. Ruttenberg,\nS.-A. Sansone, L. Soldatova, C. S. Jr., J. Turner, and J. Zheng,\n\"O.b.i. consortium,modeling biomedical experimental processes with\nobi,\" Biomed. Semant., vol. (Suppl. 1), 2010.\n[22] M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling,\nand D. Schomburg, \"The brenda tissue ontology (bto): the first\nall-integrating ontology of all organisms for enzyme sources,\" Nucleic\nAcids Res, pp. D507–D513, 2011.\n[23] D. Natale, C. Arighi,W. Barker, J. Blake, C. Bult, M. Caudy, H. Drabkin,\nP. D'Eustachio, A. Evsikov, H. Huang, J. Nchoutmboube, N. Roberts,\nB. Smith, J. Zhang, and C. Wu, \"The protein ontology: a structured\nrepresentation of protein forms and complexes,\" Nucleic Acids Res,\nvol. 39, pp. D539–D545, 2011.\n[24] G. Gkoutos, P. Schofield, and R. Hoehndorf, \"The units ontology: a tool\nfor integrating units of measurement in science,\" Database (Oxford),\nvol. 6, pp. D539–D545, 2012.\n[25] E. Younesi, S. Ansaril, M. Guendel, S. Ahmadi, C. Coggins, J. Hoeng,\nM. Hofmann-Apitius, and M. C. Peitsch, \"Cseo - the cigarette smoke\nexposure ontology,\" Journal of Biomedical Semantics, 2014.\n[26] E. Friederike, L. Rieswijk, C. Evelo, H. Sarimveis, P. Doganis,\nG. Drakakis, B. Fadeel, B. Hardy, J. Hastings, C. Helma, N. Jeliazkova,\nV. Jeliazkov, P. Kohonen, R. Grafstrom, P. Sopasakisa, G. Tsiliki, and\nE. Willighagen, \"Ontology, database and tools for nanomaterial safety\nevaluation,\" Journal of Biomedical Semantics, 2015.\n[27] E. Gu´erin, G. Marquet, A. Burgun, O. Lor´eal, L. Berti-Equille, U. Leser,\nand F. Moussouni, \"Integrating and warehousing liver gene expression\ndata and related biomedical resources in gedaw,\" in International\nWorkshop on Data Integration in the Life Sciences. Springer, 2005,\npp. 158–174.\n[28] K. M. Livingston, M. Bada, W. A. Baumgartner, and L. E. Hunter,\n\"Kabob: ontology-based semantic integration of biomedical databases,\"\nBMC bioinformatics, vol. 16, no. 1, p. 1, 2015.\n[29] M. Masseroli, A. Canakoglu, and S. Ceri, \"Integration and querying of\ngenomic and proteomic semantic annotations for biomedical knowledge\nextraction,\" IEEE/ACM Transactions on Computational Biology and\nBioinformatics, vol. 13, no. 2, pp. 209–219, 2016.\n[30] M. Dumontier, C. J. Baker, J. Baran, A. Callahan, and L. C. et al., \"The\nsemanticscience integrated ontology (sio) for biomedical research and\nknowledge discovery,\" Biomed Semantics, vol. vol. 5, p. p. 14, 2014.\n[31] J. Zheng, Z. Xiang, C. J. Stoeckert, and Y. Hel, \"Ontodog: a web-based\nontology community view generation tool,\" Bioinformatics, vol. vol. 30,\npp. pp. 1340–1342, 2014.\n[32] D. Ostrowski, N. Rychtyckyj, P. MacNeille, and M. Kim, \"Integration\nof big data using semantic web technologies,\" in 2016 IEEE Tenth\nInternational Conference on Semantic Computing (ICSC). IEEE, 2016,\npp. 382–385.\n[33] B.-H. Tran, C. Plumejeaud-Perreau, A. Bouju, and V. Bretagnolle,\n\"A semantic mediator for handling heterogeneity of spatio-temporal\nenvironment data,\" in Research Conference on Metadata and Semantics\nResearch. Springer, 2015, pp. 381–392.\n[34] O. Cur´e, F. Kerdjoudj, D. Faye, C. Le Duc, and M. Lamolle, \"On the\npotential integration of an ontology-based data access approach in nosql\nstores,\" International Journal of Distributed Systems and Technologies\n(IJDST), vol. 4, no. 3, pp. 17–30, 2013.\n[35] O. Cur´e, R. Hecht, C. Le Duc, and M. Lamolle, \"Data integration\nover nosql stores using access path based mappings,\" in International\nConference on Database and Expert Systems Applications. Springer,\n2011, pp. 481–495.\n[36] L. H. Childs, S. Mamlouk, J. Brandt, C. Sers, and U. Leser, \"Sofia:\na data integration framework for annotating high-throughput datasets,\"\nBioinformatics, p. btw302, 2016.\n[37] J. Huang, K. Eilbeck, J. A. Blake, D. Dou, D. A. Natale, A. Ruttenberg,\nB. Smith, M. T. Zimmermann, G. Jiang, Y. Lin et al., \"A domain\nontology for the non-coding rna field,\" in Bioinformatics and\nBiomedicine (BIBM), 2015 IEEE International Conference on. IEEE,\n2015, pp. 621–624.\n[38] C. Jonquet, M. A.Musen, and N. H. Shah, \"Building a biomedical\nontology recommender web service,\" Biomed Semantics, pp. 1–18, 2010.\n[39] J. Malone, R. Stevens, S. Jupp, T. Hancocks, H. Parkinson, and\nC. Brooksbank, \"Ten simple rules for selecting a bio-ontology,\" PLOS\nComput Biol, vol. vol. 30, pp. 12(2), e1 004 743, 2016.\n[40] E. Gu´erin, F. Moussouni, B. Courselaud, and O. Lor´eal, \"Mod´elisation\nd'un entrepˆot de donnes d´edi´e `a l'analyse du transcriptome h´epatique,\"\nActes des Journ´ees Ouvertes Biologie Informatique Math´ematiques\n(JOBIM), vol. vol. 30, pp. pp 319–324, 2008.\n[41] W. Bensz, D. Borys, K. Fujarewicz, K. Herok, R. Jaksik, M. Krasucki,\nA. Kurczyk, K. Matusik, D. Mrozek, M. Ochab et al., \"Integrated\nsystem supporting research on environment related cancers,\" in\nRecent Developments in Intelligent Information and Database Systems.\nSpringer, 2016, pp. 399–409.\n[42] C. Goble and R. Stevens, \"State of the nation in data integration for\nbioinformatics,\" Journal of biomedical informatics, vol. 41, no. 5, pp.\n687–693, 2008.\n[43] A. Kasprzyk, \"Biomart: driving a paradigm change in biological data\nmanagement,\" Database, vol. 2011, p. bar049, 2011.\n[44] S. Trißl, K. Rother, H. M¨uller, T. Steinke, I. Koch, R. Preissner,\nC. Fr¨ommel, and U. Leser, \"Columba: an integrated database of proteins,\nstructures, and annotations,\" BMC bioinformatics, vol. 6, no. 1, p. 1,\n2005.\n[45] C. M. Machado, D. Rebholz-Schuhmann, A. T. Freitas, and F. M. Couto,\n\"The semantic web in translational medicine: current applications and\nfuture directions,\" Briefings in bioinformatics, vol. 16, no. 1, pp. 89–103,\n2015.\n[46] S. Bechhofer, I. Buchan, D. De Roure, P. Missier, J. Ainsworth,\nJ. Bhagat, P. Couch, D. Cruickshank, M. Delderfield, I. Dunlop et al.,\n\"Why linked data is not enough for scientists,\" Future Generation\nComputer Systems, vol. 29, no. 2, pp. 599–611, 2013.\n[47] T. J¨org and S. Deßloch, \"Towards generating etl processes for\nincremental loading,\" in Proceedings of the 2008 international\nsymposium on Database engineering & applications. ACM, 2008,\npp. 101–110.\n[48] T. J. Lee, Y. Pouliot, V. Wagner, P. Gupta, D. W. Stringer-Calvert, J. D.\nTenenbaum, and P. D. Karp, \"Biowarehouse: a bioinformatics database\nwarehouse toolkit,\" BMC bioinformatics, vol. 7, no. 1, p. 1, 2006.\n[49] W. McLaren, B. Pritchard, D. Rios, Y. Chen, P. Flicek, and\nF. Cunningham, \"Deriving the consequences of genomic variants with\nthe ensembl api and snp effect predictor,\" Bioinformatics, vol. 26, no. 16,\npp. 2069–2070, 2010.\n[50] B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah,\nY. Zhang, D. Blankenberg, I. Albert, J. Taylor et al., \"Galaxy: a platform\nfor interactive large-scale genome analysis,\" Genome research, vol. 15,\nno. 10, pp. 1451–1455, 2005.\n[51] K. Wolstencroft, R. Haines, D. Fellows, A. Williams, D. Withers,\nS. Owen, S. Soiland-Reyes, I. Dunlop, A. Nenadic, P. Fisher et al.,\n\"The taverna workflow suite: designing and executing workflows of web\nservices on the desktop, web or in the cloud,\" Nucleic acids research,\np. gkt328, 2013."]}