418
13 Databases and Tools on the Internet
Lingner, C., Roberg-Perez, K.J.,Tillberg,
M., Brooks, J.E. and Garrels, J.I. The yeast
proteome database (YPD) and Caenorhabditis
elegans proteome database (WormPD): com-
prehensive resources for the organization and
comparison of model organism protein infor-
mation (2000) Nucleic Acids Res. 28,73–6
DuBois, P. MySQL cookbook (2002) O’Reilly
and Associates, Sebastopol, California
Goto, S., Okuno,Y., Hattori, M., Nishioka, T.
and Kanehisa, M. LIGAND: database of
chemical compounds and reactions in bio-
logical pathways (2002) Nucleic Acids Res. 30,
402–4
Hammond, M.P. and Birney, E. Genome infor-
mation resources – developments at Ensembl
(2004) Trends Genet. 20, 268–72
Hubbard,T., Barker, D., Birney, E., Cameron,
G., Chen,Y., Clark, L., Cox,T., Cuff, J.,
Curwen,V., Down, T., Durbin, R., Eyras, E.,
Gilbert, J., Hammond, M., Huminiecki, L.,
Kasprzyk, A., Lehvaslaiho, H., Lijnzaad, P.,
Melsopp, C., Mongin, E., Pettett, R.,
Pocock, M., Potter, S., Rust, A., Schmidt,
E., Searle, S., Slater, G., Smith, J., Spooner,
W., Stabenau, A., Stalker, J., Stupka, E.,
Ureta-Vidal, A.,Vastrik, I. and Clamp, M.
The Ensembl genome database project (2002)
Nucleic Acids Res. 30,38–41
Joshi-Tope, G.,Vastrik, I., Gopinath, G.R.,
Matthews, L., Schmidt, E., Gillespie, M.,
D’Eustachio, P., Jassal, B.,Wu, G., Birney, E.,
Stein, L. The genome knowledgebase:
a resourcefor biologists and bioinformaticists
(2003) Cold Spring Harb. Symp. Quant. Biol.
68: 237–43
Kanehisa, M., Goto, S., Kawashima, S.,
Okuno,Y. and Hattori, M. The KEGG
resource for deciphering the genome (2004)
Nucleic Acids Res. 32 Database issue, D277–80
Kulikova,T., Aldebert, P., Althorpe, N.,
Baker,W., Bates, K., Browne, P., van den
Broek, A., Cochrane, G., Duggan, K., Eber-
hardt, R., Faruque, N., Garcia-Pastor, M.,
Harte, N., Kanz, C., Leinonen, R., Lin, Q.,
Lombard,V., Lopez, R., Mancuso, R.,
McHale, M., Nardone, F., Silventoinen,V.,
Stoehr, P., Stoesser, G.,Tuli, M.A.,Tzou-
vara, K.,Vaughan, R.,Wu, D., Zhu,W. and
Apweiler, R. The EMBL Nucleotide Sequence
Database (2004) Nucleic Acids Res. 32 Data-
base issue, D27–30
Maglott, D.R., Katz, K.S., Sicotte, H. and
Pruitt, K.D. NCBI’s LocusLink and RefSeq
(2000) Nucleic Acids Res. 28, 126–8
Mulder, N.J., Apweiler, R., Attwood, T.K.,
Bairoch, A., Barrell, D., Bateman, A.,
Binns, D., Biswas, M., Bradley, P., Bork, P.,
Bucher, P., Copley, R.R., Courcelle, E., Das,
U., Durbin, R., Falquet, L., Fleischmann,
W., Griffiths-Jones, S., Haft, D., Harte, N.,
Hulo, N., Kahn, D., Kanapin, A., Krestyani-
nova, M., Lopez, R., Letunic, I., Lonsdale,
D., Silventoinen,V., Orchard, S.E., Pagni,
M., Peyruc, D., Ponting, C.P., Selengut,
J.D., Servant, F., Sigrist, C.J.,Vaughan, R.
and Zdobnov, E.M. The InterPro Database
2003 brings increased coverage and new
features (2003) Nucleic Acids Res. 31, 315–8
Pruitt, K.D. and Maglott, D.R. RefSeq and
LocusLink: NCBI gene-centered resources
(2001) Nucleic Acids Res. 29, 137–40
Pruitt, K.D., Katz, K.S., Sicotte, H. and
Maglott, D.R. Introducing RefSeq and Locus-
Link: curated human genome resources at the
NCBI (2000) Trends Genet. 16,44–7
Safran, M., Solomon, I., Shmueli, O., Lapi-
dot, M., Shen-Orr, S., Adato, A., Ben-Dor,
U., Esterman, N., Rosen, N., Peter, I.,
Olender,T., Chalifa-Caspi,V. and Lancet, D.
GeneCards 2002: towards a complete, object-
oriented, human gene compendium (2002)
Bioinformatics 18, 1542–3
Westbrook, J., Feng, Z., Jain, S., Bhat,T.N.,
Thanki, N., Ravichandran,V., Gilliland,
G.L., Bluhm,W.,Weissig, H., Greer, D.S.,
Bourne, P.E. and Berman, H.M. The Protein
Data Bank: unifying the archive (2002)
Nucleic Acids Res. 30, 245–8