Information Technology Reference
In-Depth Information
information resource relies on the active participation of the life sciences community. This
will require an increased educational effort on our part. It is also dependent on the
commitment of scientific societies, publishers and funding agencies to provide a framework
to facilitate community efforts and give due credit to the participating scientists.
As a closing remark, we would like to thank all the persons involved in the
development of Swiss-Prot at the SIB and EBI as well as all the funding agencies and
companies that have financially contributed to the continuous evolution of the Swiss-Prot
knowledgebase.
Acknowledgements
The work described in this article covers activities funded by various sources including
NIH:1 U01 HG02712-01, EU:BioMinT; QLRT-2001-02770, EU:Temblor; QLRT-2001-
00015, EU:BioBabel; QLRI-CT-2001-00981, SNF:3100-063879. The above review
originally appeared in
Briefings in Bioinformatics
, 5:39-55(2004) and is reproduced here by
permission of the Journal.
References
[1]
Boeckmann, B., Bairoch, A., Apweiler, R.
et al
. (2003), 'The SWISS-PROT protein knowledgebase
and its supplement TrEMBL in 2003',
Nucleic Acids Res.,
Vol. 31, pp. 354-370.
[2]
Bairoch, A. (2000), 'Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through
exciting times!',
Bioinformatics
, Vol. 16, pp. 48-64.
[3]
Apweiler, R., Bairoch, A., Wu, C.H.
et al
. (2004), 'UniProt: the universal protein knowledgebase',
Nucleic Acids Res.,
Vol. 32, pp. D115-119.
[4]
Dayhoff, M.O., Eck, R.V., Chang, M.A., and Sochard, M.R. (1965), 'Atlas of Protein Sequence and
Structure', Vol. 1. National Biomedical Research Foundation, Silver Spring, MD.
[5]
Moore, J., Engelberg, A. and Bairoch, A. (1988), 'Using PC/GENE for protein and nucleic acid
analysis',
Biotechniques
, Vol. 6, pp. 566-572.
[6]
Monigatti, F., Gasteiger, E., Bairoch, A.
et al
. (2002), 'The Sulfinator: predicting tyrosine sulfation
sites in protein sequences',
Bioinformatics
, Vol. 18, pp. 769-70.
[7]
Bologna, G., Veuthey, A.-L., Yvon, C.
et al
. (2004), 'N-terminal myristoylation predictions by
ensembles of neural networks',
Proteomics
, Vol. 4, pp. 1626-1632..
[8]
Hulo, N., Sigrist, C., LeSaux, V.
et al
. (2004), 'Recent improvements to the PROSITE database',
Nucleic Acids Res.,
Vol. 32, pp. D134-137.
[9]
Gattiker, A., Michoud, K., Rivoire, C.
et al.
(2003), 'Automated annotation of microbial proteomes in
Swiss-Prot',
Comput. Biol. Chem
., Vol. 27, pp. 49-58.
[10]
Bairoch, A. (2000), 'The ENZYME database in 2000',
Nucleic Acids Res
., Vol. 28, pp. 304-305.
[11]
Farriol-Mathis, N., Garavelli, J.S., Boeckmann B.,
et al.
(2004), 'Annotation of post-translational
modifications in the Swiss-Prot knowledgebase',
Proteomics
, Vol. 4, pp. 1537-1550.
[12]
Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000), 'Gene ontology: tool for the unification of
biology. The Gene Ontology Consortium',
Nat. Genet
., Vol. 25, pp. 25-29.
[13]
Etzold, T., Argos, P. (1993), 'SRS - an indexing and retrieval tool for flat file data libraries',
Comput.
Appl. Biosci
., Vol. 9, pp. 49-57.
[14]
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A.,
et al.
(2003), 'The InterPro Database, 2003
brings increased coverage and new features',
Nucleic Acids Res
., Vol. 31, pp. 315-318.
[15]
Gasteiger, E., Jung, E., Bairoch, A. (2001), 'SWISS-PROT: Connecting biological knowledge via a
protein database',
Curr. Issues Mol. Biol.
, Vol. 3, pp. 47-55.
[16]
Gasteiger, E., Gattiker, A., Hoogland, C. et al. (2003), 'ExPASy - the proteomics server for in-depth
protein knowledge and analysis'.
Nucleic Acids Res.,
Vol. 31, pp. 3784-3788.
[17]
Phan, I.Q., Pilbout, S.F., Fleischmann, W., Bairoch, A. (2003) 'NEWT, a new taxonomy portal'.
Nucleic Acids Res.,
Vol. 31, pp. 3822-3823.