Advertisement

Omics Data Management and Annotation

  • Arye Harel
  • Irina Dalah
  • Shmuel Pietrokovski
  • Marilyn Safran
  • Doron Lancet
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 719)

Abstract

Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter.

Key words

Data management Omics data integration GeneCards Project life cycle Relational database Heuristics Versioning Quality assurance Annotation Data modeling 

Notes

Acknowledgments

We thank the members of the GeneCards team: Iris Bahir, Tirza Doniger, Tsippi Iny Stein, Hagit Krugh, Noam Nativ, Naomi Rosen, and Gil Stelzer. The GeneCards project is funded by Xennex Inc., the Weizmann Institute of Science Crown Human Genome Center, and the EU SYNLET (FP6 project number 043312) and SysKID (FP7 project number 241544) grants.

References

  1. 1.
    Liolios, K., Mavromatis, K., Tavernarakis, N., and Kyrpides, N. C. (2008) The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36, 475–9.CrossRefGoogle Scholar
  2. 2.
    Data Management International, http://www.dama.org/i4a/pages/index.cfm?pageid=1.
  3. 3.
    Tech FAQ. What is Data Management?, http://www.tech-faq.com/data-management.shtml.
  4. 4.
    Chaussabel, D., Ueno, H., Banchereau, J., and Quinn, C. (2009) Data management: it starts at the bench. Nat Immunol 10, 1225–7.PubMedCrossRefGoogle Scholar
  5. 5.
    Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198–207.PubMedCrossRefGoogle Scholar
  6. 6.
    Batley, J., and Edwards, D. (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46, 333–6.PubMedCrossRefGoogle Scholar
  7. 7.
    Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., Golaz, O., Sanchez, J. C., Yan, J. X., Gooley, A. A., Hughes, G., Humphery-Smith, I., Williams, K. L., and Hochstrasser, D. F. (1996) From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (NY) 14, 61–5.CrossRefGoogle Scholar
  8. 8.
    Field, D., Sansone, S. A., Collis, A., Booth, T., Dukes, P., Gregurick, S. K., Kennedy, K., Kolar, P., Kolker, E., Maxon, M., Millard, S., Mugabushaka, A. M., Perrin, N., Remacle, J. E., Remington, K., Rocca-Serra, P., Taylor, C. F., Thorley, M., Tiwari, B., and Wilbanks, J. (2009) Megascience. ‘Omics data sharing’. Science 326, 234–6.PubMedCrossRefGoogle Scholar
  9. 9.
    Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M. J., Angiuoli, S. V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., De Vos, P., DePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glockner, F. O., Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S. E., Li, K., Lister, A. L., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Mizrachi, I., Moxon, R., Nelson, K., Parkhill, J., Proctor, L., White, O., Sansone, S. A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T., San Gil, I., Wilson, G., and Wipat, A. (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26, 541–7.PubMedCrossRefGoogle Scholar
  10. 10.
    Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R., Li, D., Gu, W., Yang, Z., Xuan, Z., Ryder, O. A., Leung, F. C., Zhou, Y., Cao, J., Sun, X., Fu, Y., Fang, X., Guo, X., Wang, B., Hou, R., Shen, F., Mu, B., Ni, P., Lin, R., Qian, W., Wang, G., Yu, C., Nie, W., Wang, J., Wu, Z., Liang, H., Min, J., Wu, Q., Cheng, S., Ruan, J., Wang, M., Shi, Z., Wen, M., Liu, B., Ren, X., Zheng, H., Dong, D., Cook, K., Shan, G., Zhang, H., Kosiol, C., Xie, X., Lu, Z., Zheng, H., Li, Y., Steiner, C. C., Lam, T. T., Lin, S., Zhang, Q., Li, G., Tian, J., Gong, T., Liu, H., Zhang, D., Fang, L., Ye, C., Zhang, J., Hu, W., Xu, A., Ren, Y., Zhang, G., Bruford, M. W., Li, Q., Ma, L., Guo, Y., An, N., Hu, Y., Zheng, Y., Shi, Y., Li, Z., Liu, Q., Chen, Y., Zhao, J., Qu, N., Zhao, S., Tian, F., Wang, X., Wang, H., Xu, L., Liu, X., Vinar, T., Wang, Y., Lam, T. -W., Yiu, S. -M., Liu, S., Zhang, H., Li, D., Huang, Y., Wang, X., Yang, G., Jiang, Z., Wang, J., Qin, N., Li, L., Li, J., Bolund, L., Kristiansen, K., Wong, G. K., Olson, M., Zhang, X., Li, S., Yang, H., Wang, J., and Wang, J. (2009) The sequence and de novo assembly of the giant panda genome. Nature 463, 311–7.PubMedCrossRefGoogle Scholar
  11. 11.
    (2008) Big Data special issue. Nature 455.Google Scholar
  12. 12.
    Howe, D., Costanzo, M., Fey, P., Gojobori, T., Hannick, L., Hide, W., Hill, D. P., Kania, R., Schaeffer, M., St Pierre, S., Twigger, S., White, O., and Rhee, S. Y. (2008) Big data: the future of biocuration. Nature 455, 47–50.PubMedCrossRefGoogle Scholar
  13. 13.
    Haquin, S., Oeuillet, E., Pajon, A., Harris, M., Jones, A. T., van Tilbeurgh, H., Markley, J. L., Zolnai, Z., and Poupon, A. (2008) Data management in structural genomics: an overview. Methods Mol Biol 426, 49–79.PubMedCrossRefGoogle Scholar
  14. 14.
    Gribskov, M. (2003) Challenges in data management for functional genomics. OMICS 7, 3–5.PubMedCrossRefGoogle Scholar
  15. 15.
    Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2006) GenBank. Nucleic Acids Res 34, D16–20.PubMedCrossRefGoogle Scholar
  16. 16.
    Birney, E., Andrews, T. D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X. M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H. R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K. C., Cameron, G., Durbin, R., Cox, A., Hubbard, T., and Clamp, M. (2004) An overview of Ensembl. Genome Res 14, 925–8.PubMedCrossRefGoogle Scholar
  17. 17.
    Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., and Bairoch, A. (2007) UniProtKB/Swiss-Prot. Methods Mol Biol 406, 89–112.PubMedCrossRefGoogle Scholar
  18. 18.
    Schofield, P. N., Bubela, T., Weaver, T., Portilla, L., Brown, S. D., Hancock, J. M., Einhorn, D., Tocchini-Valentini, G., Hrabe de Angelis, M., and Rosenthal, N. (2009) Post-publication sharing of data and tools. Nature 461, 171–3.PubMedCrossRefGoogle Scholar
  19. 19.
    Pennisi, E. (2009) Data sharing. Group calls for rapid release of more genomics data. Science 324, 1000–1.PubMedCrossRefGoogle Scholar
  20. 20.
    Merali, Z., and Giles, J. (2005) Databases in peril. Nature 435, 1010–1.PubMedCrossRefGoogle Scholar
  21. 21.
    Human Genomes Project, http://www.1000genomes.org.
  22. 22.
    Smigielski, E. M., Sirotkin, K., Ward, M., and Sherry, S. T. (2000) dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28, 352–5.PubMedCrossRefGoogle Scholar
  23. 23.
    Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M., Pasternak, S., Wheeler, D. A., Willis, T. D., Yu, F., Yang, H., Zeng, C., Gao, Y., Hu, H., Hu, W., Li, C., Lin, W., Liu, S., Pan, H., Tang, X., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q., Zhao, H., Zhou, J., Gabriel, S. B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R. C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z., Huang, W., Chu, X., He, Y., Jin, L., Liu, Y., Sun, W., Wang, H., Wang, Y., Xiong, X., Xu, L., Waye, M. M., Tsui, S. K., Xue, H., Wong, J. T., Galver, L. M., Fan, J. B., Gunderson, K., Murray, S. S., Oliphant, A. R., Chee, M. S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J. F., Phillips, M. S., Roumy, S., Sallee, C., Verner, A., Hudson, T. J., Kwok, P. Y., Cai, D., Koboldt, D. C., Miller, R. D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L. C., Mak, W., Song, Y. Q., Tam, P. K., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A., Tanaka, T., Tsunoda, T., Deloukas, P., Bird, C. P., Delgado, M., Dermitzakis, E. T., Gwilliam, R., Hunt, S., Morrison, J., Powell, D., Stranger, B. E., Whittaker, P., Bentley, D. R., Daly, M. J., de Bakker, P. I., Barrett, J., Chretien, Y. R., Maller, J., McCarroll, S., Patterson, N., Pe’er, I., Price, A., Purcell, S., Richter, D. J., Sabeti, P., Saxena, R., Schaffner, S. F., Sham, P. C., Varilly, P., Stein, L. D., Krishnan, L., Smith, A. V., Tello-Ruiz, M. K., Thorisson, G. A., Chakravarti, A., Chen, P. E., Cutler, D. J., Kashuk, C. S., Lin, S., Abecasis, G. R., Guan, W., Li, Y., Munro, H. M., Qin, Z. S., Thomas, D. J., McVean, G., Auton, A., Bottolo, L., Cardin, N., Eyheramendy, S., Freeman, C., Marchini, J., Myers, S., Spencer, C., Stephens, M., Donnelly, P., Cardon, L. R., Clarke, G., Evans, D. M., Morris, A. P., Weir, B. S., Mullikin, J. C., Sherry, S. T., Feolo, M., Skol, A., Zhang, H., Matsuda, I., Fukushima, Y., Macer, D. R., Suda, E., Rotimi, C. N., Adebamowo, C. A., Ajayi, I., Aniagwu, T., Marshall, P. A., Nkwodimmah, C., Royal, C. D., Leppert, M. F., Dixon, M., Peiffer, A., Qiu, R., Kent, A., Kato, K., Niikawa, N., Adewole, I. F., Knoppers, B. M., Foster, M. W., Clayton, E. W., Watkin, J., Muzny, D., Nazareth, L., Sodergren, E., Weinstock, G. M., Yakub, I., Birren, B. W., Wilson, R. K., Fulton, L. L., Rogers, J., Burton, J., Carter, N. P., Clee, C. M., Griffiths, M., Jones, M. C., McLay, K., Plumb, R. W., Ross, M. T., Sims, S. K., Willey, D. L., Chen, Z., Han, H., Kang, L., Godbout, M., Wallenburg, J. C., L’Archeveque, P., Bellemare, G., Saeki, K., An, D., Fu, H., Li, Q., Wang, Z., Wang, R., Holden, A. L., Brooks, L. D., McEwen, J. E., Guyer, M. S., Wang, V. O., Peterson, J. L., Shi, M., Spiegel, J., Sung, L. M., Zacharia, L. F., Collins, F. S., Kennedy, K., Jamieson, R., and Stewart, J. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–61.PubMedCrossRefGoogle Scholar
  24. 24.
    Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25–9.PubMedCrossRefGoogle Scholar
  25. 25.
    Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Scheuermann, R. H., Shah, N., Whetzel, P. L., and Lewis, S. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25, 1251–5.PubMedCrossRefGoogle Scholar
  26. 26.
    ClearForest, Text Analytics Solutions, http://www.clearforest.com/index.asp.
  27. 27.
  28. 28.
    DDBJ: DNA Data Bank of Japan, http://www.ddbj.nig.ac.jp.
  29. 29.
    Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M., Baker, W., Baldwin, A., Bates, K., Bhattacharyya, S., Browne, P., van den Broek, A., Castro, M., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Kanz, C., Kulikova, T., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., McHale, M., McWilliam, H., Mukherjee, G., Nardone, F., Pastor, M. P., Sobhany, S., Stoehr, P., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., and Apweiler, R. (2006) EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res 34, D10–5.PubMedCrossRefGoogle Scholar
  30. 30.
    Sussman, J. L., Lin, D., Jiang, J., Manning, N. O., Prilusky, J., Ritter, O., and Abola, E. E. (1998) Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr D Biol Crystallogr 54, 1078–84.PubMedCrossRefGoogle Scholar
  31. 31.
    Rebhan, M., Chalifa-Caspi, V., Prilusky, J., and Lancet, D. (1998) GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics 14, 656–64.PubMedCrossRefGoogle Scholar
  32. 32.
    Safran, M., Chalifa-Caspi, V., Shmueli, O., Olender, T., Lapidot, M., Rosen, N., Shmoish, M., Peter, Y., Glusman, G., Feldmesser, E., Adato, A., Peter, I., Khen, M., Atarot, T., Groner, Y., and Lancet, D. (2003) Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res 31, 142–6.PubMedCrossRefGoogle Scholar
  33. 33.
    Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., Ben-Dor, U., Esterman, N., Rosen, N., Peter, I., Olender, T., Chalifa-Caspi, V., and Lancet, D. (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18, 1542–3.PubMedCrossRefGoogle Scholar
  34. 34.
    Stelzer, G., Inger, A., Olender, T., Iny-Stein, T., Dalah, I., Harel, A., Safran, M., and Lancet, D. (2009) GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. OMICS 13, 477–87.PubMedCrossRefGoogle Scholar
  35. 35.
    Harel, A., Inger, A., Stelzer, G., Strichman-Almashanu, L., Dalah, I., Safran, M., and Lancet, D. (2009) GIFtS: annotation ­landscape analysis with GeneCards. BMC Bioinformatics 10, 348.PubMedCrossRefGoogle Scholar
  36. 36.
    Liebel, U., Kindler, B., and Pepperkok, R. (2004) ‘Harvester’: a fast meta search engine of human protein resources. Bioinformatics 20, 1962–3.PubMedCrossRefGoogle Scholar
  37. 37.
    Pang, K. C., Stephen, S., Engstrom, P. G., Tajul-Arifin, K., Chen, W., Wahlestedt, C., Lenhard, B., Hayashizaki, Y., and Mattick, J. S. (2005) RNAdb – a comprehensive mammalian noncoding RNA database. Nucleic Acids Res 33, D125–30.PubMedCrossRefGoogle Scholar
  38. 38.
    Hamosh, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., and McKusick, V. A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33, D514–7.PubMedCrossRefGoogle Scholar
  39. 39.
  40. 40.
    Morris, J. A., Gayther, S. A., Jacobs, I. J., and Jones, C. (2008) A Perl toolkit for LIMS development. Source Code Biol Med 3, 4.PubMedCrossRefGoogle Scholar
  41. 41.
  42. 42.
    Parkinson, J., Anthony, A., Wasmuth, J., Schmid, R., Hedley, A., and Blaxter, M. (2004) PartiGene – constructing partial genomes. Bioinformatics 20, 1398–404.PubMedCrossRefGoogle Scholar
  43. 43.
    Schmid, R., and Blaxter, M. (2009) EST processing: from trace to sequence. Methods Mol Biol 533, 189–220.PubMedGoogle Scholar
  44. 44.
    The maxd software: supporting genomic expression analysis, http://www.bioinf.manchester.ac.uk/microarray/maxd.
  45. 45.
    Gribskov, M., Fana, F., Harper, J., Hope, D. A., Harmon, A. C., Smith, D. W., Tax, F. E., and Zhang, G. (2001) PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res 29, 111–3.PubMedCrossRefGoogle Scholar
  46. 46.
  47. 47.
    Harris, M., and Jones, T. A. (2002) Xtrack – a web-based crystallographic notebook. Acta Crystallogr D Biol Crystallogr 58, 1889–91.PubMedCrossRefGoogle Scholar
  48. 48.
    Zolnai, Z., Lee, P. T., Li, J., Chapman, M. R., Newman, C. S., Phillips, G. N., Jr., Rayment, I., Ulrich, E. L., Volkman, B. F., and Markley, J. L. (2003) Project management system for structural and functional proteomics: Sesame. J Struct Funct Genomics 4, 11–23.PubMedCrossRefGoogle Scholar
  49. 49.
    Prilusky, J., Oueillet, E., Ulryck, N., Pajon, A., Bernauer, J., Krimm, I., Quevillon-Cheruel, S., Leulliot, N., Graille, M., Liger, D., Tresaugues, L., Sussman, J. L., Janin, J., van Tilbeurgh, H., and Poupon, A. (2005) HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr D Biol Crystallogr 61, 671–8.PubMedCrossRefGoogle Scholar
  50. 50.
    Goh, C. S., Lan, N., Echols, N., Douglas, S. M., Milburn, D., Bertone, P., Xiao, R., Ma, L. C., Zheng, D., Wunderlich, Z., Acton, T., Montelione, G. T., and Gerstein, M. (2003) SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Res 31, 2833–8.PubMedCrossRefGoogle Scholar
  51. 51.
  52. 52.
    Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., and Lewis, S. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12, 1599–610.PubMedCrossRefGoogle Scholar
  53. 53.
    Karolchik, D., Baertsch, R., Diekhans, M., Furey, T. S., Hinrichs, A., Lu, Y. T., Roskin, K. M., Schwartz, M., Sugnet, C. W., Thomas, D. J., Weber, R. J., Haussler, D., and Kent, W. J. (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31, 51–4.PubMedCrossRefGoogle Scholar
  54. 54.
    Brazma, A. (2001) On the importance of standardisation in life sciences. Bioinformatics 17, 113–4.PubMedCrossRefGoogle Scholar
  55. 55.
    Taylor, C. F., Field, D., Sansone, S. A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P. A., Bogue, M., Booth, T., Brazma, A., Brinkman, R. R., Michael Clark, A., Deutsch, E. W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J. M., Hardy, N. W., Hermjakob, H., Julian, R. K., Jr., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Le Novere, N., Leebens-Mack, J., Lewis, S. E., Lord, P., Mallon, A. M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J. M., Robertson, D. G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo-Lopez, J., Scheuermann, R. H., Schober, D., Smith, B., Snape, J., Stoeckert, C. J., Jr., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26, 889–96.PubMedCrossRefGoogle Scholar
  56. 56.
    Jones, A. R., Miller, M., Aebersold, R., Apweiler, R., Ball, C. A., Brazma, A., Degreef, J., Hardy, N., Hermjakob, H., Hubbard, S. J., Hussey, P., Igra, M., Jenkins, H., Julian, R. K., Jr., Laursen, K., Oliver, S. G., Paton, N. W., Sansone, S. A., Sarkans, U., Stoeckert, C. J., Jr., Taylor, C. F., Whetzel, P. L., White, J. A., Spellman, P., and Pizarro, A. (2007) The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol 25, 1127–33.PubMedCrossRefGoogle Scholar
  57. 57.
    Sansone, S. A., Rocca-Serra, P., Brandizi, M., Brazma, A., Field, D., Fostel, J., Garrow, A. G., Gilbert, J., Goodsaid, F., Hardy, N., Jones, P., Lister, A., Miller, M., Morrison, N., Rayner, T., Sklyar, N., Taylor, C., Tong, W., Warner, G., and Wiemann, S. (2008) The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies?”. OMICS 12, 143–9.PubMedCrossRefGoogle Scholar
  58. 58.
    Field, D., Garrity, G., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., and Thomson, N. (2005) eGenomics: cataloguing our complete genome collection. Comp Funct Genomics 6, 363–8.PubMedCrossRefGoogle Scholar
  59. 59.
    Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29, 365–71.PubMedCrossRefGoogle Scholar
  60. 60.
    Webb, S. C., Attwood, A., Brooks, T., Freeman, T., Gardner, P., Pritchard, C., Williams, D., Underhill, P., Strivens, M. A., Greenfield, A., and Pilicheva, E. (2004) LIMaS: the JAVA-based application and database for microarray experiment tracking. Mamm Genome 15, 740–7.PubMedCrossRefGoogle Scholar
  61. 61.
    Ball, C. A., Awad, I. A., Demeter, J., Gollub, J., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Matese, J. C., Nitzberg, M., Wymore, F., Zachariah, Z. K., Brown, P. O., and Sherlock, G. (2005) The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 33, D580–2.PubMedCrossRefGoogle Scholar
  62. 62.
    Pajon, A., Ionides, J., Diprose, J., Fillon, J., Fogh, R., Ashton, A. W., Berman, H., Boucher, W., Cygler, M., Deleury, E., Esnouf, R., Janin, J., Kim, R., Krimm, I., Lawson, C. L., Oeuillet, E., Poupon, A., Raymond, S., Stevens, T., van Tilbeurgh, H., Westbrook, J., Wood, P., Ulrich, E., Vranken, W., Xueli, L., Laue, E., Stuart, D. I., and Henrick, K. (2005) Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins 58, 278–84.PubMedCrossRefGoogle Scholar
  63. 63.
    Orchard, S., Hermjakob, H., Binz, P. A., Hoogland, C., Taylor, C. F., Zhu, W., Julian, R. K., Jr., and Apweiler, R. (2005) Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics 5, 337–9.PubMedCrossRefGoogle Scholar
  64. 64.
    Lindon, J. C., Nicholson, J. K., Holmes, E., Keun, H. C., Craig, A., Pearce, J. T., Bruce, S. J., Hardy, N., Sansone, S. A., Antti, H., Jonsson, P., Daykin, C., Navarange, M., Beger, R. D., Verheij, E. R., Amberg, A., Baunsgaard, D., Cantor, G. H., Lehman-McKeeman, L., Earll, M., Wold, S., Johansson, E., Haselden, J. N., Kramer, K., Thomas, C., Lindberg, J., Schuppe-Koistinen, I., Wilson, I. D., Reily, M. D., Robertson, D. G., Senn, H., Krotzky, A., Kochhar, S., Powell, J., van der Ouderaa, F., Plumb, R., Schaefer, H., and Spraul, M. (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23, 833–8.PubMedCrossRefGoogle Scholar
  65. 65.
    Digital Curation Centre, http://www.dcc.ac.uk.
  66. 66.
  67. 67.
    Joyce, A. R., and Palsson, B. Ø. (2006) The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 7, 198–210.PubMedCrossRefGoogle Scholar
  68. 68.
  69. 69.
    Mounicou, S., Szpunar, J., and Lobinski, R. (2009) Metallomics: the concept and methodology. Chem Soc Rev 38, 1119–38.PubMedCrossRefGoogle Scholar
  70. 70.
    Ippolito, J. E., Xu, J., Jain, S., Moulder, K., Mennerick, S., Crowley, J. R., Townsend, R. R., and Gordon, J. I. (2005) An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers. Proc Natl Acad Sci USA 102, 9901–6.PubMedCrossRefGoogle Scholar
  71. 71.
    Pefkaros, K. 2008 Using object-oriented analysis and design over traditional structured analysis and design. International Journal of Business Research. International Academy of Business and Economics. HighBeam Research. http://www.highbeam.com. 2 Jan. 2011.
  72. 72.
    Whitten, J. L., Bentley, L. D., and Dittman, K. C. (2004) Systems Analysis and Design Methods, 6th ed. McGraw-Hill Irwin, New York.Google Scholar
  73. 73.
    Todman, C. (2001) Designing a Data Warehouse: Supporting Customer Relationship Management, 1st ed., pp 25–58. Prentice-Hall PTR, New Jersey.Google Scholar
  74. 74.
    CIS 3400 Database Management Systems Course – Baruch College CUNY, http://cisnet.baruch.cuny.edu/holowczak/classes/3400.
  75. 75.
  76. 76.
  77. 77.
  78. 78.
  79. 79.
  80. 80.
  81. 81.
  82. 82.
  83. 83.
    Universal Protein Resource (UniProtKB), http://www.uniprot.org.
  84. 84.
  85. 85.
    Eyre, T. A., Ducluzeau, F., Sneddon, T. P., Povey, S., Bruford, E. A., and Lush, M. J. (2006) The HUGO Gene Nomenclature Database, 2006 updates. Nucleic Acids Res 34, D319–21.PubMedCrossRefGoogle Scholar
  86. 86.
    Rosen, N., Chalifa-Caspi, V., Shmueli, O., Adato, A., Lapidot, M., Stampnitzky, J., Safran, M., and Lancet, D. (2003) GeneLoc: exon-based integration of human genome maps. Bioinformatics 19, i222–4.PubMedCrossRefGoogle Scholar
  87. 87.
  88. 88.
  89. 89.
  90. 90.
    Bugzilla – server software for managing software development, http://www.bugzilla.org.
  91. 91.
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J Mol Biol 215, 403–10.PubMedGoogle Scholar
  92. 92.
  93. 93.
    Perl for bioinformatics and internet, http://bip.weizmann.ac.il/course/prog.
  94. 94.
  95. 95.
    Extensible Markup Language (XML), http://www.w3.org/XML.
  96. 96.
    Concurrent Versions System (CVS) Overview, http://www.thathost.com/wincvs-howto/cvsdoc/cvs_1.html#SEC1.
  97. 97.
  98. 98.

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Arye Harel
    • 1
  • Irina Dalah
    • 1
  • Shmuel Pietrokovski
    • 1
  • Marilyn Safran
    • 1
  • Doron Lancet
    • 1
  1. 1.Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael

Personalised recommendations