-
1
-
-
0036500993
-
Systems biology: A brief overview
-
Kitano, H. Systems biology: a brief overview. Science 295, 1662-1664 (2002).
-
(2002)
Science
, vol.295
, pp. 1662-1664
-
-
Kitano, H.1
-
2
-
-
21644477195
-
How will big pictures emerge from a sea of biological data?
-
Pennisi, E. How will big pictures emerge from a sea of biological data? Science 309, 94 (2005).
-
(2005)
Science
, vol.309
, pp. 94
-
-
Pennisi, E.1
-
3
-
-
0035895496
-
Computational biology. Bioinformatics - Trying to swim in a sea of data
-
Roos, D. S. Computational biology. Bioinformatics - trying to swim in a sea of data. Science 291, 1260-1261 (2001).
-
(2001)
Science
, vol.291
, pp. 1260-1261
-
-
Roos, D.S.1
-
4
-
-
18044400410
-
Information technology to the rescue!
-
Augen, J. Information technology to the rescue! Nature Biotechnol. 19, BE39-BE40 (2001).
-
(2001)
Nature Biotechnol.
, vol.19
-
-
Augen, J.1
-
5
-
-
0141561891
-
Integrating 'omic' information: A bridge between genomics and systems biology
-
Ge, H., Walhout, A. J. & Vidal, M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 19, 551-560 (2003).
-
(2003)
Trends Genet.
, vol.19
, pp. 551-560
-
-
Ge, H.1
Walhout, A.J.2
Vidal, M.3
-
6
-
-
1642380513
-
Practical data integration in biopharmaceutical research and development
-
June
-
Carel, R. Practical data integration in biopharmaceutical research and development. PharmaGenomics 22-35 (June 2003).
-
(2003)
PharmaGenomics
, pp. 22-35
-
-
Carel, R.1
-
7
-
-
33846088142
-
The Molecular Biology Database Collection: 2006 Update
-
Galperin, M. Y. The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res. 34, D3-D5 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Galperin, M.Y.1
-
8
-
-
0012526835
-
-
O'Reilly, Beijing; Sebastopol, California
-
Cerami, E. Web services essentials (O'Reilly, Beijing; Sebastopol, California, 2002).
-
(2002)
Web Services Essentials
-
-
Cerami, E.1
-
9
-
-
0041589545
-
Biological SOAP servers and web services provided by the public sequence data bank
-
Sugawara, H. & Miyazaki, S. Biological SOAP servers and web services provided by the public sequence data bank. Nucleic Acids Res. 31, 3836-3839 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3836-3839
-
-
Sugawara, H.1
Miyazaki, S.2
-
10
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
11
-
-
23144460649
-
SOAP-based services provided by the European Bioinformatics Institute
-
Pillai, S. et al. SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Res. 33, W25-W28 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Pillai, S.1
-
12
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich, J. E. et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611-1618 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
-
13
-
-
1842845736
-
The Bio* toolkits - A brief overview
-
Mangalam, H. The Bio* toolkits - a brief overview. Brief. Bioinformatics 3, 296-302 (2002).
-
(2002)
Brief. Bioinformatics
, vol.3
, pp. 296-302
-
-
Mangalam, H.1
-
14
-
-
0036679515
-
XEMBL: Distributing EMBL data in XML format
-
Wang, L., Riethoven, J. J. & Robinson, A. XEMBL: distributing EMBL data in XML format. Bioinformatics 18, 1147-1148 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 1147-1148
-
-
Wang, L.1
Riethoven, J.J.2
Robinson, A.3
-
15
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Bairoch, A. et al. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154-D159 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Bairoch, A.1
-
16
-
-
21544461263
-
PAX of mind for pathway researchers
-
Luciano, J. S. PAX of mind for pathway researchers. Drug Discov. Today 10, 937-942 (2005).
-
(2005)
Drug Discov. Today
, vol.10
, pp. 937-942
-
-
Luciano, J.S.1
-
17
-
-
2442595958
-
CellML: Its future, present and past
-
Lloyd, C. M., Halstead, M. D. & Nielsen, P. F. CellML: its future, present and past. Prog. Biophys. Mol. Biol. 85, 433-450 (2004).
-
(2004)
Prog. Biophys. Mol. Biol.
, vol.85
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.2
Nielsen, P.F.3
-
18
-
-
0037163144
-
Design and implementation of microarray gene expression markup language (MAGE-ML)
-
RESEARCH0046
-
Spellman, P. T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046 (2002).
-
(2002)
Genome Biol.
, vol.3
-
-
Spellman, P.T.1
-
19
-
-
25844474606
-
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005)
-
Orchard, S. et al. Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). Proteomics 5, 3552-3555 (2005).
-
(2005)
Proteomics
, vol.5
, pp. 3552-3555
-
-
Orchard, S.1
-
20
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
-
21
-
-
23044485115
-
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers
-
Green, M. L. & Karp, P. D. Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res. 33, 4035-4039 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 4035-4039
-
-
Green, M.L.1
Karp, P.D.2
-
22
-
-
0034117360
-
TAMBIS: Transparent access to multiple bioinformatics information sources
-
Stevens, R. et al. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics 16, 184-185 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 184-185
-
-
Stevens, R.1
-
23
-
-
18844466577
-
SEMEDA: Ontology based semantic integration of biological databases
-
Köhler, J., Philippi, S. & Lange, M. SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19, 2420-2427 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 2420-2427
-
-
Köhler, J.1
Philippi, S.2
Lange, M.3
-
24
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner, M. et al. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
-
(2000)
Nature Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
25
-
-
3042642160
-
Using XML technology for the ontology-based semantic integration of life science databases
-
Philippi, S. & Köhler, J. Using XML technology for the ontology-based semantic integration of life science databases. IEEE Trans. Inf. Technol. Biomed. 8, 154-160 (2004).
-
(2004)
IEEE Trans. Inf. Technol. Biomed.
, vol.8
, pp. 154-160
-
-
Philippi, S.1
Köhler, J.2
-
27
-
-
9144233525
-
Database resources of the National Center for Biotechnology Information: Update
-
Wheeler, D. L. et al. Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 32, D35-D40 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Wheeler, D.L.1
-
28
-
-
0037462510
-
Communication. Science and the semantic web
-
Hendler, J. Communication. Science and the semantic web. Science 299, 520-521 (2003).
-
(2003)
Science
, vol.299
, pp. 520-521
-
-
Hendler, J.1
-
29
-
-
0142039154
-
Will genomics revolutionise pharmaceutical R&D?
-
Noble, D. Will genomics revolutionise pharmaceutical R&D? Trends Biotechnol. 21, 333-337 (2003).
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 333-337
-
-
Noble, D.1
-
30
-
-
35048835647
-
On the application of formal principles to life science data: A case study in the gene ontology
-
Smith, B., Köhler, J. & Kumar, A. On the application of formal principles to life science data: a case study in the gene ontology. Proc. Data Integr. Life Sci. First Int. Workshop 79-94 (2004).
-
(2004)
Proc. Data Integr. Life Sci. First Int. Workshop
, pp. 79-94
-
-
Smith, B.1
Köhler, J.2
Kumar, A.3
-
31
-
-
33646834101
-
Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy
-
6 Sep doi:10.1016/j.compbiomed.2005.04.007
-
Zhang, S. & Bodenreider, O. Law and order: assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy. Comput. Biol. Med. 6 Sep 2005 (doi:10.1016/j.compbiomed.2005.04.007).
-
(2005)
Comput. Biol. Med.
-
-
Zhang, S.1
Bodenreider, O.2
-
32
-
-
0033786867
-
Representing and analysing molecular and cellular function using the computer
-
van Helden, J. et al. Representing and analysing molecular and cellular function using the computer. Biol. Chem. 381, 921-935 (2000).
-
(2000)
Biol. Chem.
, vol.381
, pp. 921-935
-
-
Van Helden, J.1
-
33
-
-
0036594338
-
Conceptual data modelling for bioinformatics
-
Bornberg-Bauer, E. & Paton, N. W. Conceptual data modelling for bioinformatics. Brief. Bioinformatics 3, 166-180 (2002).
-
(2002)
Brief. Bioinformatics
, vol.3
, pp. 166-180
-
-
Bornberg-Bauer, E.1
Paton, N.W.2
-
34
-
-
12344296271
-
Designing databases to store biological information
-
Nelson, M. R., Reisinger, S. J. & Henry, S. G. Designing databases to store biological information. BioSilico 1, 134-142 (2003).
-
(2003)
BioSilico
, vol.1
, pp. 134-142
-
-
Nelson, M.R.1
Reisinger, S.J.2
Henry, S.G.3
-
35
-
-
0037337307
-
A systematic approach to modeling, capturing, and disseminating proteomics experimental data
-
Taylor, C. F. et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnol. 21, 247-254 (2003).
-
(2003)
Nature Biotechnol.
, vol.21
, pp. 247-254
-
-
Taylor, C.F.1
-
37
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp, P. D. et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33, 6083-6089 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
-
38
-
-
0041706175
-
Data integration - Connecting the dots
-
Searls, D. B. Data integration - connecting the dots. Nature Biotechnol. 21, 844-845 (2003).
-
(2003)
Nature Biotechnol.
, vol.21
, pp. 844-845
-
-
Searls, D.B.1
-
39
-
-
0031797096
-
What we do not know about sequence analysis and sequence databases
-
Karp, P. D. What we do not know about sequence analysis and sequence databases. Bioinformatics 14, 753-754 (1998).
-
(1998)
Bioinformatics
, vol.14
, pp. 753-754
-
-
Karp, P.D.1
-
40
-
-
9144252016
-
The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology
-
Camon, E. et al. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262-D266 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Camon, E.1
-
41
-
-
0042423439
-
Automated annotation of microbial proteomes in SWISS-PROT
-
Gattiker, A. et al. Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27, 49-58 (2003).
-
(2003)
Comput. Biol. Chem.
, vol.27
, pp. 49-58
-
-
Gattiker, A.1
-
42
-
-
4844231570
-
Incongruence between test statistics and P values in medical papers
-
Garcia-Berthou, E. & Alcaraz, C. Incongruence between test statistics and P values in medical papers. BMC Med. Res. Methodol. 4, 13 (2004).
-
(2004)
BMC Med. Res. Methodol.
, vol.4
, pp. 13
-
-
Garcia-Berthou, E.1
Alcaraz, C.2
-
43
-
-
4844222268
-
Increased measurement accuracy for sequence-verified microarray probes
-
Mecham, B. H. et al. Increased measurement accuracy for sequence-verified microarray probes. Physiol. Genomics 18, 308-315 (2004).
-
(2004)
Physiol. Genomics
, vol.18
, pp. 308-315
-
-
Mecham, B.H.1
-
44
-
-
0242361278
-
Predictive ability of DNA microarrays for cancer outcomes and correlates: An empirical assessment
-
Ntzani, E. E. & Ioannidis, J. P. Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessment. Lancet 362, 1439-1444 (2003).
-
(2003)
Lancet
, vol.362
, pp. 1439-1444
-
-
Ntzani, E.E.1
Ioannidis, J.P.2
-
45
-
-
0036517472
-
A comprehensive review of genetic association studies
-
Hirschhorn, J. N., Lohmueller, K., Byrne, E. & Hirschhorn, K. A comprehensive review of genetic association studies. Genet. Med. 4, 45-61 (2002).
-
(2002)
Genet. Med.
, vol.4
, pp. 45-61
-
-
Hirschhorn, J.N.1
Lohmueller, K.2
Byrne, E.3
Hirschhorn, K.4
-
47
-
-
0037433717
-
Evaluation of annotation strategies using an entire genome sequence
-
Iliopoulos, I. et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 19, 717-726 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 717-726
-
-
Iliopoulos, I.1
-
48
-
-
30744459862
-
What makes a gene name? Named entity recognition in the biomedical literature
-
Leser, U. & Hakenberg, J. What makes a gene name? Named entity recognition in the biomedical literature. Brief. Bioinformatics 6, 357-369 (2005).
-
(2005)
Brief. Bioinformatics
, vol.6
, pp. 357-369
-
-
Leser, U.1
Hakenberg, J.2
-
49
-
-
0141576559
-
Strengthening the United States' database protection laws: Balancing public access and private control
-
Resnik, D. B. Strengthening the United States' database protection laws: balancing public access and private control. Sci. Eng. Ethics 9, 301-318 (2003).
-
(2003)
Sci. Eng. Ethics
, vol.9
, pp. 301-318
-
-
Resnik, D.B.1
-
50
-
-
0035955369
-
Intellectual property. Europe's database experiment
-
Maurer, S. M., Hugenholtz, P. B. & Onsrud, H. J. Intellectual property. Europe's database experiment. Science 294, 789-790 (2001).
-
(2001)
Science
, vol.294
, pp. 789-790
-
-
Maurer, S.M.1
Hugenholtz, P.B.2
Onsrud, H.J.3
-
51
-
-
21744445793
-
Databases in peril
-
Merali, Z. & Giles, J. Databases in peril. Nature 435, 1010-1011 (2005).
-
(2005)
Nature
, vol.435
, pp. 1010-1011
-
-
Merali, Z.1
Giles, J.2
-
52
-
-
0031733588
-
The demise of public data on the web?
-
Ellis, L. B. & Kalumbi, D. The demise of public data on the web? Nature Biotechnol. 16, 1323-1324 (1998).
-
(1998)
Nature Biotechnol.
, vol.16
, pp. 1323-1324
-
-
Ellis, L.B.1
Kalumbi, D.2
-
53
-
-
0042861557
-
A universal legal framework as a prerequisite for database interoperability
-
Greenbaum, D. & Gerstein, M. A universal legal framework as a prerequisite for database interoperability. Nature Biotechnol. 21, 979-982 (2003).
-
(2003)
Nature Biotechnol.
, vol.21
, pp. 979-982
-
-
Greenbaum, D.1
Gerstein, M.2
-
54
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data
-
Brazma, A. et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genet. 29, 365-371 (2001).
-
(2001)
Nature Genet.
, vol.29
, pp. 365-371
-
-
Brazma, A.1
-
55
-
-
33646873187
-
Will a biological database be different from a biological journal?
-
Bourne, P. Will a biological database be different from a biological journal? PLoS Comput. Biol. 1, 179-181 (2005).
-
(2005)
PLoS Comput. Biol.
, vol.1
, pp. 179-181
-
-
Bourne, P.1
-
56
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
57
-
-
35048880554
-
Columba: Multidimensional data integration of protein annotations
-
Rother, K. et al. Columba: multidimensional data integration of protein annotations. Proc. Data Integr. Life Sci. First Int. Workshop 156-171 (2004).
-
(2004)
Proc. Data Integr. Life Sci. First Int. Workshop
, pp. 156-171
-
-
Rother, K.1
-
58
-
-
0036184680
-
The EBI SRS server - Recent developments
-
Zdobnov, E. M., Lopez, R., Apweiler, R. & Etzold, T. The EBI SRS server - recent developments. Bioinformatics 18, 368-373 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 368-373
-
-
Zdobnov, E.M.1
Lopez, R.2
Apweiler, R.3
Etzold, T.4
-
59
-
-
0034952253
-
DiscoveryLink: A system for integrated access to life sciences data sources
-
Haas, L. M. et al. DiscoveryLink: a system for integrated access to life sciences data sources. IBM Syst. J. 40, 489-511 (2001).
-
(2001)
IBM Syst. J.
, vol.40
, pp. 489-511
-
-
Haas, L.M.1
-
60
-
-
19944389921
-
Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures
-
Köhler, J. et al. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures. In Silico Biol. 5, 33-44 (2004).
-
(2004)
In Silico Biol.
, vol.5
, pp. 33-44
-
-
Köhler, J.1
-
61
-
-
0038745614
-
Integrating biological databases
-
Stein, L. D. Integrating biological databases. Nature Rev. Genet. 4, 337-345 (2003).
-
(2003)
Nature Rev. Genet.
, vol.4
, pp. 337-345
-
-
Stein, L.D.1
-
62
-
-
12344279003
-
Integration of life science databases
-
Köhler, J. Integration of life science databases. Drug Discov. Today 2, 61-69 (2004).
-
(2004)
Drug Discov. Today
, vol.2
, pp. 61-69
-
-
Köhler, J.1
-
63
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
-
64
-
-
18444387984
-
Transcription Regulatory Regions Database (TRRD): Its status in 2002
-
Kolchanov, N. A. et al. Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res. 30, 312-317 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 312-317
-
-
Kolchanov, N.A.1
|