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References

  1. Aebersold, R., Agar, J.N., Amster, I.J., Baker, M.S., Bertozzi, C.R., Boja, E.S., Costello, C.E., Cravatt, B.F., Fenselau, C., Garcia, B.A., et al. (2018). How many human proteoforms are there ? Nat Chem Biol 14, 206–214.
  2. Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Eberhard, C., et al. (2016). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses : 2016 update. Nucleic Acids Res 44, W3–W10.
  3. Akune, Y., Hosoda, M., Kaiya, S., Shinmachi, D., and Aoki-Kinoshita, K.F. (2010). The RINGS resource for glycome informatics analysis and data mining on the Web. Omics J. Integr. Biol. 14, 475–486.
  4. Allende, C., Sohn, E., and Little, C. (2015). Treelink : data integration, clustering and visualization of phylogenetic trees. BMC Bioinformatics 16, 414.
  5. Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M. (2004). KCaM (KEGG Carbohydrate Matcher) : a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res 32, W267–72.
  6. Aoki-Kinoshita, K., Agravat, S., Aoki, N.P., Arpinar, S., Cummings, R.D., Fujita, A., Fujita, N., Hart, G.M., Haslam, S.M., Kawasaki, T., et al. (2016). GlyTouCan 1.0—The international glycan structure repository. Nucleic Acids Res. 44, D1237-1242.
  7. Banin, E., Neuberger, Y., Altshuler, Y., Halevi, A., Inbar, O., Nir, D., Dukler, A., and 献一笠井 (2002). A Novel Linear Code® Nomenclature for Complex Carbohydrates. Trends Glycosci Glycotechnol 14, 127–137.
  8. Bard, J.B.L., and Rhee, S.Y. (2004). Ontologies in biology : design, applications and future challenges. Nat Rev Genet 5, 213.
  9. Barsnes, H., Vizcaíno, J.A., Eidhammer, I., and Martens, L. (2009). PRIDE Converter : making proteomics data-sharing easy. Nat Biotechnol 27, 598.
  10. Bateman, A., Martin, M.J., O’Donovan, C., Magrane, M., Alpi, E., Antunes, R., Bely, B., Bingley, M., Bonilla, C., Britto, R., et al. (2017). UniProt : the universal protein knowledgebase. Nucleic Acids Res 45, D158–D169.
  11. Battle, R., and Benson, E. (2008). Bridging the semantic Web and Web 2.0 with Representational State Transfer (REST). Web Semant. Sci. Serv. Agents World Wide Web 6, 61–69.
  12. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Ostell, J., Pruitt, K.D., and Sayers, E.W. (2018). GenBank. Nucleic Acids Res 46, D41–D47.
  13. Bohne-Lang, A., Lang, E., Förster, T., and von der Lieth, C.W. (2001). LINUCS : linear notation for unique description of carbohydrate sequences. Carbohydr Res 336, 1–11.
  14. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., et al. (2001). Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet 29, 365.
  15. Buneman, P., Khanna, S., and Wang-Chiew, T. (2001). Why and Where : A Characterization of Data Provenance. In Lecture Notes in Computer Science, pp. 316–330.
  16. Campbell, M.P., Ranzinger, R., Lütteke, T., Mariethoz, J., Hayes, C.A., Zhang, J., Akune, Y., Aoki-Kinoshita, K.F., Damerell, D., Carta, G., et al. (2014). Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics 15 Suppl 1, S9.
  17. Cook, C.E., Bergman, M.T., Cochrane, G., Apweiler, R., and Birney, E. (2018). The European Bioinformatics Institute in 2017 : data coordination and integration. Nucleic Acids Res 46, D21–D29.
  18. Cummings, R.D. (2009). The repertoire of glycan determinants in the human glycome. Mol. Biosyst. 5, 1087–1104.
  19. Doubet, S., and Albersheim, P. (1992). CarbBank. Glycobiology 2, 505.
  20. Doubet, S., Bock, K., Smith, D., Darvill, A., and Albersheim, P. (1989). The Complex Carbohydrate Structure Database. Trends Biochem Sci 14, 475–477.
  21. Dudhe, A., and Sherekar, S.S. (2014). Performance Analysis of SOAP and RESTful Mobile Web Services in Cloud Environment. IJCA Spec. Issue Recent Trends Inf. Secur. RTINFOSEC, 1–4.
  22. Fillbrunn, A., Dietz, C., Pfeuffer, J., Rahn, R., Landrum, G.A., and Berthold, M.R. (2017). KNIME for reproducible cross-domain analysis of life science data. J Biotechnol 261, 149–156.
  23. Gaitatzes, A., Johnson, S.H., Smadbeck, J.B., and Vasmatzis, G. (2018). Genome U-Plot : a whole genome visualization. Bioinformatics 34, 1629–1634.
  24. Goble, C., and Stevens, R. (2008). State of the nation in data integration for bioinformatics. J Biomed Inf. 41, 687–693.
  25. Gomez-Cabrero, D., Abugessaisa, I., Maier, D., Teschendorff, A., Merkenschlager, M., Gisel, A., Ballestar, E., Bongcam-Rudloff, E., Conesa, A., and Tegnér, J. (2014). Data integration in the era of omics : current and future challenges. BMC Syst Biol 8 Suppl 2, I1.
  26. Greenwood, M., Goble, C., Stevens, R., Zhao, J., Addis, M., Marvin, D., Moreau, L., and Oinn, T. (2003). Provenance of e-Science Experiments-experience from Bioinformatics. p.
  27. Halevy, A.Y. (2001). Answering queries using views : A survey. VLDB J 10, 270–294.
  28. Hamid, J.S., Hu, P., Roslin, N.M., Ling, V., Greenwood, C.M.T., and Beyene, J. (2009). Data integration in genetics and genomics : methods and challenges. Hum Genomics Proteomics 2009.
  29. Harvey, D.J., Merry, A.H., Royle, L., Campbell, M.P., and Rudd, P.M. (2011). Symbol nomenclature for representing glycan structures : Extension to cover different carbohydrate types. Proteomics 11, 4291–4295.
  30. Herget, S., Ranzinger, R., Maass, K., and Lieth, C.-W.V.D. (2008). GlycoCT-a unifying sequence format for carbohydrates. Carbohydr. Res. 343, 2162–2171.
  31. Hermjakob, H. (2006). The HUPO proteomics standards initiative–overcoming the fragmentation of proteomics data. Proteomics 6 Suppl 2, 34–38.
  32. Hoehndorf, R., Schofield, P.N., and Gkoutos, G.V. (2015). The role of ontologies in biological and biomedical research : a functional perspective. Brief Bioinform 16, 1069–1080.
  33. Hsiao, S.-W., Sun, Y.S., Ao, F.-C., and Chen, M.C. (2011). A Secure Proxy-Based Cross-Domain Communication for Web Mashups. In 2011 IEEE Ninth European Conference on Web Services, p.
  34. Joshi, H.J., von der Lieth, C.-W., Packer, N.H., and Wilkins, M.R. (2010). GlycoViewer : a tool for visual summary and comparative analysis of the glycome. Nucleic Acids Res. 38, W667-670.
  35. Joshi, H.J., Jørgensen, A., Schjoldager, K.T., Halim, A., Dworkin, L.A., Steentoft, C., Wandall, H.H., Clausen, H., and Vakhrushev, S.Y. (2018). GlycoDomainViewer : a bioinformatics tool for contextual exploration of glycoproteomes. Glycobiology 28, 131–136.
  36. Karim, M.R., Michel, A., Zappa, A., Baranov, P., Sahay, R., and Rebholz-Schuhmann, D. (2017). Improving data workflow systems with cloud services and use of open data for bioinformatics research. Brief Bioinform.
  37. Kelso, J., Hoehndorf, R., and Prüfer, K. (2010). Ontologies in Biology. In Theory and Applications of Ontology : Computer Applications, (Springer, Dordrecht), pp. 347–371.
  38. Khoury, G.A., Baliban, R.C., and Floudas, C.A. (2011). Proteome-wide post-translational modification statistics : frequency analysis and curation of the swiss-prot database. Sci Rep 1, 90.
  39. Kikuchi, N., Kameyama, A., Nakaya, S., Ito, H., Sato, T., Shikanai, T., Takahashi, Y., and Narimatsu, H. (2005). The carbohydrate sequence markup language (CabosML) : an XML description of carbohydrate structures. Bioinformatics 21, 1717–1718.
  40. Kolarich, D., Rapp, E., Struwe, W.B., Haslam, S.M., Zaia, J., McBride, R., Agravat, S., Campbell, M.P., Kato, M., Ranzinger, R., et al. (2013). The minimum information required for a glycomics experiment (MIRAGE) project : improving the standards for reporting mass-spectrometry-based glycoanalytic data. Mol. Cell. Proteomics MCP 12, 991–995.
  41. Komatsoulis, G.A., Warzel, D.B., Hartel, F.W., Shanbhag, K., Chilukuri, R., Fragoso, G., Coronado, S. de, Reeves, D.M., Hadfield, J.B., Ludet, C., et al. (2008). caCORE version 3 : Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inf. 41, 106–123.
  42. Konishi, Y., and Aoki-Kinoshita, K.F. (2012). The GlycomeAtlas tool for visualizing and querying glycome data. Bioinforma. Oxf. Engl. 28, 2849–2850.
  43. Lapatas, V., Stefanidakis, M., Jimenez, R.C., Via, A., and Schneider, M.V. (2015). Data integration in biological research : an overview. J Biol Res 22, 9.
  44. Lauc, G., Pezer, M., Rudan, I., and Campbell, H. (2016). Mechanisms of disease : The human N-glycome. Biochim. Biophys. Acta BBA – Gen. Subj. 1860, 1574–1582.
  45. Launay, G., Salza, R., Multedo, D., Thierry-Mieg, N., and Ricard-Blum, S. (2015). MatrixDB, the extracellular matrix interaction database : updated content, a new navigator and expanded functionalities. Nucleic Acids Res. 43, D321-327.
  46. Le Pendu, J., Nyström, K., and Ruvoën-Clouet, N. (2014). Host–pathogen co-evolution and glycan interactions. Curr Opin Virol 7, 88–94.
  47. Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tárraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R., et al. (2011). The European Nucleotide Archive. Nucleic Acids Res 39, D28–D31.
  48. Leser, U., and Naumann, F. (2007). Informationsintegration : Architekturen und Methoden zur Integration verteilter und heterogener Datenquellen.
  49. von der Lieth, C.-W., Freire, A.A., Blank, D., Campbell, M.P., Ceroni, A., Damerell, D.R., Dell, A., Dwek, R.A., Ernst, B., Fogh, R., et al. (2011). EUROCarbDB : An open-access platform for glycoinformatics. Glycobiology 21, 493–502.
  50. Lisacek, F., Mariethoz, J., Alocci, D., Rudd, P.M., Abrahams, J.L., Campbell, M.P., Packer, N.H., St\a ahle, J., Widmalm, G., Mullen, E., et al. (2016). Databases and Associated Tools for Glycomics and Glycoproteomics. In Methods in Molecular Biology, pp. 235–264.
  51. Liu, Y., McBride, R., Stoll, M., Palma, A.S., Silva, L., Agravat, S., Aoki-Kinoshita, K.F., Campbell, M.P., Costello, C.E., Dell, A., et al. (2017). The minimum information required for a glycomics experiment (MIRAGE) project : improving the standards for reporting glycan microarray-based data. Glycobiology 27, 280–284.
  52. Luscombe, N.M., Greenbaum, D., and Gerstein, M. (2001). What is bioinformatics ? A proposed definition and overview of the field. Methods Inf Med 40, 346–358.
  53. Lütteke, T. (2008). Web resources for the glycoscientist. Chembiochem 9, 2155–2160.
  54. Lütteke, T., Bohne-Lang, A., Loss, A., Goetz, T., Frank, M., and von der Lieth, C.-W. (2006). GLYCOSCIENCES.de : an Internet portal to support glycomics and glycobiology research. Glycobiology 16, 71R-81R.
  55. Manzoni, C., Kia, D.A., Vandrovcova, J., Hardy, J., Wood, N.W., Lewis, P.A., and Ferrari, R. (2018). Genome, transcriptome and proteome : the rise of omics data and their integration in biomedical sciences. Brief Bioinform 19, 286–302.
  56. Masseroli, M., Mons, B., Bongcam-Rudloff, E., Ceri, S., Kel, A., Rechenmann, F., Lisacek, F., and Romano, P. (2014). Integrated Bio-Search : challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics 15, S2.
  57. Matsubara, M., Aoki-Kinoshita, K.F., Aoki, N.P., Yamada, I., and Narimatsu, H. (2017). WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures. J Chem Inf Model 57, 632–637.
  58. Munevar, S. (2017). Unlocking Big Data for better health. Nat Biotechnol 35, 684–686.
  59. Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A., et al. (2004). Taverna : a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20, 3045–3054.
  60. Packer, N.H., Lieth, C.-W. von der, Aoki‐Kinoshita, K.F., Lebrilla, C.B., Paulson, J.C., Raman, R., Rudd, P., Sasisekharan, R., Taniguchi, N., and York, W.S. (2008). Frontiers in glycomics : Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11–13, 2006). PROTEOMICS 8, 8–20.
  61. Patwardhan, A. (2017). Trends in the Electron Microscopy Data Bank (EMDB). Acta Crystallogr Struct Biol 73, 503–508.
  62. Pérez, S., Sarkar, A., Rivet, A., Breton, C., and Imberty, A. (2015). Glyco3D : A Portal for Structural Glycosciences. In Glycoinformatics, (Humana Press, New York, NY), pp. 241–258.
  63. Pérez, S., Sarkar, A., Rivet, A., Drouillard, S., Breton, C., and Imberty, A. (2016). Glyco3D : A Suite of Interlinked Databases of 3D Structures of Complex Carbohydrates, Lectins, Antibodies, and Glycosyltransferases. In A Practical Guide to Using Glycomics Databases, pp. 133–161.
  64. Ponniah, P. (2004). Data Warehousing Fundamentals : A Comprehensive Guide for IT Professionals (John Wiley & Sons).
  65. Prasad, T.S.K., Mohanty, A.K., Kumar, M., Sreenivasamurthy, S.K., Dey, G., Nirujogi, R.S., Pinto, S.M., Madugundu, A.K., Patil, A.H., Advani, J., et al. (2017). Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 27, 133–144.
  66. Quesada-Martínez, M., Duque-Ramos, A., Iniesta-Moreno, M., and Fernández-Breis, J.T. (2017). Preliminary Analysis of the OBO Foundry Ontologies and Their Evolution Using OQuaRE. Stud Health Technol Inf. 235, 426–430.
  67. Ranzinger, R., Herget, S., Wetter, T., and von der Lieth, C.-W. (2008). GlycomeDB – integration of open-access carbohydrate structure databases. BMC Bioinformatics 9, 384.
  68. Ranzinger, R., Aoki-Kinoshita, K.F., Campbell, M.P., Kawano, S., Lütteke, T., Okuda, S., Shinmachi, D., Shikanai, T., Sawaki, H., Toukach, P., et al. (2015). GlycoRDF : an ontology to standardize glycomics data in RDF. Bioinformatics 31, 919–925.
  69. Sahoo, S.S., Thomas, C., Sheth, A., Henson, C., and York, W.S. (2005). GLYDE-an expressive XML standard for the representation of glycan structure. Carbohydr Res 340, 2802–2807.
  70. Sahoo, S.S., Thomas, C., Sheth, A., York, W.S., and Tartir, S. (2006). Knowledge modeling and its application in life sciences. In Proceedings of the 15th International Conference on World Wide Web – WWW ’06, p.
  71. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003). Cytoscape : A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res 13, 2498–2504.
  72. Shoaib, M., Ansari, A.A., and Ahn, S.-M. (2017). cMapper : gene-centric connectivity mapper for EBI-RDF platform. Bioinformatics 33, 266–271.
  73. Silva, J.C.F., Carvalho, T.F.M., Basso, M.F., Deguchi, M., Pereira, W.A., Sobrinho, R.R., Vidigal, P.M.P., Brustolini, O.J.B., Silva, F.F., Dal-Bianco, M., et al. (2017). Geminivirus data warehouse : a database enriched with machine learning approaches. BMC Bioinformatics 18, 240.
  74. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., et al. (2007). The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255.
  75. Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., and Brass, A. (2000). TAMBIS : transparent access to multiple bioinformatics information sources. Bioinformatics 16, 184–185.
  76. Struwe, W.B., Agravat, S., Aoki-Kinoshita, K.F., Campbell, M.P., Costello, C.E., Dell, A., Feizi, T., Haslam, S.M., Karlsson, N.G., Khoo, K.-H., et al. (2016). The minimum information required for a glycomics experiment (MIRAGE) project : sample preparation guidelines for reliable reporting of glycomics datasets. Glycobiology 26, 907–910.
  77. Tanabe, M., and Kanehisa, M. (2012). Using the KEGG Database Resource. In Current Protocols in Bioinformatics, p.
  78. Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.-A., Julian, R.K., Jr, Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., et al. (2007). The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25, 887.
  79. Tiemeyer, M., Aoki, K., Paulson, J., Cummings, R.D., York, W.S., Karlsson, N.G., Lisacek, F., Packer, N.H., Campbell, M.P., Aoki, N.P., et al. (2017). GlyTouCan : an accessible glycan structure repository. Glycobiology 27, 915–919.
  80. Toukach, P.V. (2011). Bacterial carbohydrate structure database 3 : principles and realization. J Chem Inf Model 51, 159–170.
  81. Turk, Ž. (2006). Construction informatics : Definition and ontology. Adv. Eng. Inform. 20, 187–199.
  82. Varki, A., Cummings, R.D., Aebi, M., Packer, N.H., Seeberger, P.H., Esko, J.D., Stanley, P., Hart, G., Darvill, A., Kinoshita, T., et al. (2015). Symbol Nomenclature for Graphical Representations of Glycans. Glycobiology 25, 1323–1324.
  83. Vizcaíno, J.A., Csordas, A., del-Toro, N., Dianes, J.A., Griss, J., Lavidas, I., Mayer, G., Perez-Riverol, Y., Reisinger, F., Ternent, T., et al. (2016). 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 44, D447–D456.
  84. Weidman, S., and Arrison, T. (2010). Steps Toward Large-Scale Data Integration in the Sciences : Summary of a Workshop (Washington (DC) : National Academies Press (US)).
  85. York, W.S., Agravat, S., Aoki-Kinoshita, K.F., McBride, R., Campbell, M.P., Costello, C.E., Dell, A., Feizi, T., Haslam, S.M., Karlsson, N., et al. (2014). MIRAGE : the minimum information required for a glycomics experiment. Glycobiology 24, 402–406.
  86. Zerbino, D.R., Achuthan, P., Akanni, W., Amode, M.R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C.G., et al. (2018). Ensembl 2018. Nucleic Acids Res 46, D754–D761.
  87. Zhang, H. (2016). Overview of Sequence Data Formats. Methods Mol Biol 1418, 3–17.
  88. Ziegler, P., and Dittrich, K.R. (2004). Three Decades of Data Integration — all Problems Solved ? In IFIP International Federation for Information Processing, pp. 3–12.
  89. (2010). Essentials of Glycobiology (Cold Spring Harbor (NY) : Cold Spring Harbor Laboratory Press).
  90. W3C Semantic Web Activity Homepage.
  91. History of the World Wide Web – Wikipedia.
  92. HTML – Wikipedia.
  93. webcomponents.org – Discuss & share web components.