The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments

Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005

Volumn , Issue , 2005, Pages 186-196

  Orchard, Sandra ^a   Montecchi Palazzi, Luisa ^b   Hermjakob, Henning ^a   Apweiler, Rolf ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATA; COMMON PROCESS; EXPERIMENTAL PROCEDURE; HUMAN PROTEOME; PROTEOMIC; PUBLIC REPOSITORIES; ROADMAP; SAMPLE PREPARATION; USER COMMUNITIES;

DATA TRANSFER; ELECTRONIC DATA INTERCHANGE; MASS SPECTROMETRY; STANDARDS;

VOCABULARY CONTROL;

PROTEIN; PROTEOME;

ARTICLE; BIOLOGY; CHEMISTRY; GENETICS; LINGUISTICS; MASS SPECTROMETRY; PROTEIN DATABASE;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MASS SPECTROMETRY; PROTEINS; PROTEOME; VOCABULARY, CONTROLLED;

EID: 15944393188     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, k. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G.M. Rubin, J.A. Blake, C. Bult, M. Dolan, H. Drabkin, J.T. Eppig, D.P. Hill, L. Ni, M. Ringwald, R. Balakrishnan, J.M. Cherry, K.R. Christie, M.C. Costanzo, S.S. Dwight, S. Engel, D.G. Fisk, J.E. Hirschman, E.L. Hong, R.S. Nash, A. Sethuraman, C.L. Theesfeld, D. Botstein, K. Dolinski, B. Feierbach, T. Berardini, S. Mundodi, S.Y. Rhee, R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee, R. Chisholm, P. Gaudet, W. Kibbe, R. Kishore, E.M. Schwarz, P. Sternberg, M. Gwinn, L. Hannick, J. Wortman, M. Berriman, V. Wood, N. de la Cruz, P. Tonellato, P. Jaiswal, T. Seigfried, R. White; Nucleic Acids Res, 32 D258 (2004).
2. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A. Natale, C. O'Donovan, N. Redaschi, L.S. Yeh. Nucleic Acids Res. 32:D115 (2004).
3. S. Orchard, C. Taylor, W. Zhu, R. K. Julian Jr, H. Hermjakob, R. Apweiler Expert Review in Proteomics (in press).
4. J. Whitfield Nature. 428, 592. (2004).
5. P. Legrain, L. Selig. FEBS Lett. 480, 32 (2000).
6. S. Orchard, H. Hermjakob, R. Apweiler. Proteomics, 3, 1374 (2003).
7. S. Orchard, C. F.. Taylor, H. Hermjakob, Weimin-Zhu, R. K. Julian Jr, R. Apweiler Proteomics, (in press).
8. H. Hermjakob, L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, B. Roechert, P. Roepstorff, A. Valencia, H. Margalit, J. Armstrong, A. Bairoch, G. Cesareni, D. Sherman, R. Apweiler. Nucleic Acids Res., 32, D452 (2004).
9. G.D. Bader, D. Betel, C.W.V. Hogue. Nucleic Acids. Res. 31:248 (2003).
10. I. Xenarios, L. Salwinski, X.J. Duan, P. Higney, S.M. Kim, D. Eisenberg. Nucleic Acids. Res. 30:303 (2002).
11. A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, G. Cesareni.. FEBS Letts 513: 135 (2002).
12. S. Peri, J.D. Navarro, T.Z. Kristiansen, R. Amanchy, V. Surendranath, Muthusamy, T.K. Gandhi, K.N. Chandrika, N. Deshpande, S. Suresh, B.P. Rashmi, K. Shanker, N. Padma, V. Niranjan, H.C. Harsha, N. Talreja, B.M. Vrushabendra, M.A. Ramya, A.J. Yatish, M. Joy, H.N. Shivashankar, M.P.Kavitha, M. Menezes, D.R. Choudhury, N. Ghosh, R. Saravana, S. Chandran, S. Mohan, C.K. Jonnalagadda, K.Prasad, C. Kumar-Sinha, K.S. Deshpande, A. Pandey. Nucleic Acids Res. 32 D497 (2004).
13. http://www.hybrigenics.fr.
14. H.W. Mewes, C. Amid, R. Arnold. Nucleic Acids Res. 32 D41 (2004).
15. M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J.C. Doyle, H. Kitano, A. P. Arkin, B.J. Bornstein, D. Bray, A. Cornish-Bowden, A.A. Cuellar, S. Dronov, E.D. Gilles, M. Ginkel, V. Gor, I.I. Goryanin, W.J. Hedley, T.C. Hodgman, J.H. Hofmeyr, P.J. Hunter, N.S. Juty, J.L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L.M. Loew, D. Lucio, P. Mendes, E. Minch, E.D. Mjolsness, Y. Nakayama, M.R. Nelson, P.F. Nielsen, T. Sakurada, J.C. Schaff, B.E. Shapiro, T.S. Shimizu, H.D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang;. Bioinformatics 19:524-531 (2003).
16. H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik., L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S.G. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, R. Apweiler. Nat Biotechnol. 22 177 (2004).
17. J.S. Garavelli Proteomics. 4, 1527 (2004).
18. C.F. Taylor, N.W. Paton, K.L.Garwood, P.D. Kirby, D.A. Stead, Z. Yin, E.W. Deutsch, L. Selway, J. Walker, I. Riba-Garcia, S. Mohammed, M.J. Deery, J.A. Howard, T. Dunkley, R. Aebersold, B. Kell, K.S. Lilley, P. Roepstorff, J.R. Yates 3rd, A. Brass, A.J. Brown, P. Cash, S.J. Gaskell, S.J. Hubbard, S.G. Oliver. Nat Biotechnol. 2003, 21, 24 (2003).
19. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P.Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze- Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron. Nat Genet., 29, 365 (2001).