A review of standards for data exchange within systems biology

Proteomics

Volumn 7, Issue 6, 2007, Pages 857-867

  Strömbäck, Lena ^a   Hall, David ^a   Lambrix, Patrick ^a  

^a LINKÖPING UNIVERSITY   (Sweden)

Author keywords

Cellular pathways; Data exchange; Molecular interactions; Ontologies; Standardization

Indexed keywords

COMPLEX FORMATION; COMPUTER SYSTEM; CONTENT ANALYSIS; DATA EXTRACTION; DATA SYNTHESIS; HUMAN; INFORMATION PROCESSING; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEOMICS; REVIEW; STANDARDIZATION; SYSTEMS BIOLOGY;

COMPUTER SIMULATION; INFORMATION SCIENCE; SOFTWARE; SYSTEMS BIOLOGY;

EID: 33947725809     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200600438     Document Type: Review

References (33)

1. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J. et al., Nature Biotechnology, 2004, 22, 177-183.
2. Collins, F. S., Green, E. D., Guttmacher, A. E., Guyer, M. S., Nature, 2003, 422, 835-847.
3. Achard, F., Vaysseix, G., Barillot, E., Bioinformatics, 2001, 17, 115-125.
4. McEntire, R., Karp, P., Abernethy, N., Benton, D. et al., Proc. Int. Conf. Intell. Syst. Mol. Biol. 2001, 8, 239-250.
5. Brazma, A., Krestyaninova, M., Sarkans, U., Nat. Rev. Genet., 2006, 7, 593-605.
6. Strömbäck, L., Lambrix, P., Bioinformatics, 2005, 21, 4401-4407.
7. Strömbäck, L., Jakoniene, V., Tan, H., Lambrix, P., Brief. Bioinform., 2006, 7, 331-338.
8. Hucka, M., Finney, A., Sauro, H. M. et al., Bioinformatics, 2003, 19, 524-531.
9. Luciano, J., Genome Technol. 2006, 15-16.
10. Wang, X., Gorlitsky, R., Almeida, J. S., Nat. Biotechnol., 2005, 23, 1099-1103.
11. Lambrix, P., in: Dubitzky, W., Azuaje, F., (Eds.), Artificial Intelligence Methods and Tools for Systems Biology, Springer 2004, Chapter 8, pp. 129-146.
12. Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L., in: Baker, C. J., Cheung, K.-H. (Eds.) Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, Springer Verlag 2006, pp. 85-99.
13. Staab, S., Studer, R., (Eds.) Handbook on Ontologies, Springer Verlag, 2003.
14. Bodenreider, O., Stevens, R., Brief. Bioinform., 2006, 7, 256-274.
15. Ashburner, M., Ball, C., Blake, J. A., Botstein, D. et al., Nat. Genet., 2000, 25, 25-29.
16. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G. et al., Nat. Genet, 2001, 29, 365-371.
17. Orchard, S., Hermjakob, H., Julian, R. K., Jr., Runte, K. et al., Proteomics 2004, 4, 490-491.
18. Le Novère, N., Finney, A., Hucka, M., Bhalla, U. S. et al., Nat. Biotechnol. 2005, 23, 1509-1515.
19. Hedley, W. J., Nelson, M. R., Bullivant, D. P., Nielsen, P. F., Philos. Transact. A Math. Phys. Eng. Sci. 2001, 359, 1073-1089.
20. Murray-Rust, P., Rzepa, H. S., J. Chem. Inf. Comput. Sci., 2003, 43, 757-772.
21. Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M. et al., Nucleic Acids Res. 2006, 34, D10-D15
22. Cerami, E., XML for Bioinformatics, Springer Science, Business Media, New York 2005, pp. 17-47.
23. Kamijo, K., Mizuguchi, H., Kenmochi, A., Sato, M. et al., Mass Spectrom. Soc., 2003, 51, 542-549.
24. Spellman, P. T., Miller, M., Stewart, J., Troup, C. et al., Genome Biol., 2002, 3, research0046.1-0046.9.
25. Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M. et al., Nat. Biotechnol., 2004, 22, 1459-1466.
26. Orchard, S., Taylor, C. F., Hermjakob, H., Weimin-Zhu et al., Proteomics 2004, 4, 2363-2365.
27. Stanislaus, R., Jiang, L. H., Swartz, M., Arthur, J., Almeida, J. S., BMC Bioinformatics 2004, 5, 9.
28. Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P. et al., Simulation 2003, 79, 740-747.
29. Westbrook, J., Ito, N., Nakamura, H., Henrick, K. et al., Bioinformatics 2005, 21, 988-992.
30. Kim, J.-H., Ahn, G.-T., Lee, M.-J., Lee, S.-H., Proc. KORUS 2003, 2, 173-177.
31. Orchard, S., Hermjakob, H., Taylor, C., Binz, P.-A. et al., Proteomics 2006, 6, 738-741.
32. th International Workshop on Database and Expert Systems Applications, IEEE Computer Society 2005, pp. 575-579.
33. Strömbäck, L., Hall, D. in: by Grust, T., Höpfner, H., Illarramendi, A., Jablonski, S. et al. (Eds.) Current Trends in Database Technology - EDBT 2006 Workshops, LNSC 4254, Springer Verlag, 2006, pp. 220-233.