The European Bioinformatics Institute's data resources: towards systems biology

Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data. Moreover, as new high-throughput technologies are developed, the types of data that are gathered en masse are diversifying. The need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation is greater than ever. The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic Acids Research, we have launched new databases covering protein–protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI). Our existing core databases have continued to evolve to meet the changing needs of biomedical researchers, and we have developed new data-access tools that help biologists to move intuitively through the different data types, thereby helping them to put the parts together to understand biology at the systems level. The EBI's data resources are all available on our website at http://www.ebi.ac.uk.

[1]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2004, Nucleic acids research.

[2]  Rolf Apweiler,et al.  IntEnz, the integrated relational enzyme database , 2004, Nucleic Acids Res..

[3]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[4]  Sameer Velankar,et al.  E-MSD: an integrated data resource for bioinformatics , 2004, Nucleic Acids Res..

[5]  C. Ball,et al.  Submission of Microarray Data to Public Repositories , 2004, PLoS biology.

[6]  Robert S. Ledley,et al.  The Protein Information Resource , 2003, Nucleic Acids Res..

[7]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.

[8]  Dmitrij Frishman,et al.  MIPS: analysis and annotation of proteins from whole genomes in 2005 , 2005, Nucleic Acids Res..

[9]  Qing Zhang,et al.  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema , 2004, Nucleic Acids Res..

[10]  Alex Bateman,et al.  The InterPro Database, 2003 brings increased coverage and new features , 2003, Nucleic Acids Res..

[11]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[12]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[13]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[14]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[15]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments , 1993, Nucleic Acids Res..

[16]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[17]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[18]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[19]  Ingmar Reuter,et al.  Integr8 and Genome Reviews: integrated views of complete genomes and proteomes , 2004, Nucleic Acids Res..

[20]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[21]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[22]  Hideaki Sugawara,et al.  DDBJ in collaboration with mass-sequencing teams on annotation , 2004, Nucleic Acids Res..

[23]  Rolf Apweiler,et al.  Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters , 2003, Nucleic Acids Res..

[24]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[25]  Damian Smedley,et al.  Ensembl 2004 , 2004, Nucleic Acids Res..

[26]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[27]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[28]  Ariane Toussaint,et al.  A new evaluation of our life‐support system , 2003, EMBO reports.

[29]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[30]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[31]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[32]  Emily Dimmer,et al.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology , 2004, Nucleic Acids Res..

[33]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[34]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[35]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[36]  Aedín C. Culhane,et al.  Expression Profiler: next generation - an online platform for analysis of microarray data , 2004, Nucleic Acids Res..

[37]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.