Omics Data Management and Annotation

Methods in Molecular Biology

Volumn 719, Issue , 2011, Pages 71-96

  Harel, Arye ^a   Dalah, Irina ^a   Pietrokovski, Shmuel ^a   Safran, Marilyn ^a   Lancet, Doron ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

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

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; INFORMATION SYSTEM; METHODOLOGY; MOLECULAR GENETICS; PERSONNEL; QUALITY CONTROL; STANDARD;

ANIMALS; COMPUTATIONAL BIOLOGY; DATA DISPLAY; DATABASES, GENETIC; HUMANS; INFORMATION MANAGEMENT; MOLECULAR SEQUENCE ANNOTATION; QUALITY CONTROL; RESEARCH PERSONNEL; SOFTWARE;

EID: 79958283060     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-027-0_3     Document Type: Chapter

References (98)

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.
2. Data Management International, http://www. dama.org/i4a/pages/index.cfm?pageid=1.
3. Tech FAQ. What is Data Management?, http://www.tech-faq.com/data-management. shtml.
4. Chaussabel, D., Ueno, H., Banchereau, J., and Quinn, C. (2009) Data management: it starts at the bench. Nat Immunol 10, 1225–7.
5. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198–207.
6. Batley, J., and Edwards, D. (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46, 333–6.
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.
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.
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.
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.
11. Big Data special issue. Nature 455.
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.
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.
14. Gribskov, M. (2003) Challenges in data management for functional genomics. OMICS 7, 3–5.
15. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2006) GenBank. Nucleic Acids Res 34, D16–20.
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.
17. Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., and Bairoch, A. (2007) UniProtKB/Swiss-Prot. Methods Mol Biol 406, 89–112.
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.
19. Pennisi, E. (2009) Data sharing. Group calls for rapid release of more genomics data. Science 324, 1000–1.
20. Merali, Z., and Giles, J. (2005) Databases in peril. Nature 435, 1010–1.
21. Human Genomes Project, http://www. 1000genomes.org.
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.
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.
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.
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.
26. ClearForest, Text Analytics Solutions, http://www.clearforest.com/index.asp.
27. novo|seek, http://www.novoseek.com/Welcome.action.
28. DDBJ: DNA Data Bank of Japan, http://www.ddbj.nig.ac.jp.
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.
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.
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.
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.
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.
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.
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.
36. Liebel, U., Kindler, B., and Pepperkok, R. (2004) ‘Harvester’: a fast meta search engine of human protein resources. Bioinformatics 20, 1962–3.
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.
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.
39. Laboratory information management system, h t t p: / / e n . w i k i p e d i a . o r g / w i k i / Laborat or y_i nf or mat i on_management _ system.
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.
41. Genome Canada LIMS, http://wishart. biology.ualberta.ca/labm/index.htm
42. Parkinson, J., Anthony, A., Wasmuth, J., Schmid, R., Hedley, A., and Blaxter, M. (2004) PartiGene – constructing partial genomes. Bioinformatics 20, 1398–404.
43. Schmid, R., and Blaxter, M. (2009) EST processing: from trace to sequence. Methods Mol Biol 533, 189–220.
44. The maxd software: supporting genomic expression analysis, http://www.bioinf. manchester.ac.uk/microarray/maxd.
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.
46. Predict-IV, www.predict-iv.toxi.uni-wuerzburg. de/participants/participant_7.
47. Harris, M., and Jones, T. A. (2002) Xtrack – a web-based crystallographic notebook. Acta Crystallogr D Biol Crystallogr 58, 1889–91.
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.
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.
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.
51. ProteinScapeTM, http://www.protagen.de/index.php?option=com_content&task=view &id=95&Itemid=288.
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.
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.
54. Brazma, A. (2001) On the importance of standardisation in life sciences. Bioinformatics 17, 113–4.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
65. Digital Curation Centre, http://www.dcc. ac.uk.
66. Biosharing, http://biosharing.org.
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.
68. Omes and Omics, http://omics.org/index. php/Omes_and_Omics.
69. Mounicou, S., Szpunar, J., and Lobinski, R. (2009) Metallomics: the concept and methodology. Chem Soc Rev 38, 1119–38.
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.
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. Whitten, J. L., Bentley, L. D., and Dittman, K. C. (2004) Systems Analysis and Design Methods, 6th ed. McGraw-Hill Irwin, New York.
73. Todman, C. (2001) Designing a Data Warehouse: Supporting Customer Relationship Management, 1st ed., pp 25–58. Prentice-Hall PTR, New Jersey.
74. CIS 3400 Database Management Systems Course – Baruch College CUNY, http://cisnet.baruch.cuny.edu/holowczak/classes/3400.
75. MySQL, http://dev.mysql.com.
76. Perl, http://www.perl.org.
77. BioPerl, http://www.bioperl.org.
78. Glimpse, http://www.webglimpse.org.
79. Lucene, http://lucene.apache.org.
80. HGNC, http://www.genenames.org.
81. Entrez gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene.
82. Ensembl, http://www.ensembl.org/index. html.
83. Universal Protein Resource (UniProtKB), http://www.uniprot.org.
84. GeneCards sources, http://www.genecards. org/sources.shtml.
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.
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.
87. phpMyAdmin, http://www.phpmyadmin. net/home_page/index.php.
88. Solr, http://lucene.apache.org/solr.
89. Propel, http://propel.phpdb.org/trac.
90. Bugzilla – server software for managing software development, http://www.bugzilla.org.
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.
92. Trace at NCBI, http://www.ncbi.nlm.nih. gov/Traces.
93. Perl for bioinformatics and internet, http://bip.weizmann.ac.il/course/prog.
94. Artemis, http://www.sanger.ac.uk/Software/Artemis.
95. Extensible Markup Language (XML), http://www.w3.org/XML.
96. Concurrent Versions System (CVS) Overview, http://www.thathost.com/wincvs-howto/cvsdoc/cvs_1.html#SEC1.
97. Eclipse project, http://www.eclipse.org/eclipse.
98. Sequel Pro, http://www.sequelpro.com.