The European Bioinformatics Institute's data resources: towards systems biology
@article{Brooksbank2005TheEB, title={The European Bioinformatics Institute's data resources: towards systems biology}, author={Cath Brooksbank and Graham Cameron and Janet M. Thornton}, journal={Nucleic Acids Research}, year={2005}, volume={33}, pages={D46 - D53} }
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…
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References
SHOWING 1-10 OF 41 REFERENCES
The KEGG resource for deciphering the genome
- BiologyNucleic Acids Res.
- 2004
A knowledge-based approach for network prediction is developed, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes.
MIPS: analysis and annotation of proteins from whole genomes
- Computer Science, BiologyNucleic Acids Res.
- 2004
The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information and develops databases covering computable information such as the basic evolutionary relations among all genes.
NCBI GEO: mining millions of expression profiles—database and tools
- BiologyNucleic Acids Res.
- 2005
Recent database developments that facilitate effective mining and visualization of gene expression data are described, providing features to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise.
Reactome - A Knowledgebase of Biological Pathways
- BiologyOTM Workshops
- 2005
The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle.
The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data
- BiologyNature Biotechnology
- 2004
This work proposes a community standard data model for the representation and exchange of protein interaction data, jointly developed by members of the Proteomics Standards Initiative (PSI) and the Human Proteome Organization (HUPO).
E-MSD: an integrated data resource for bioinformatics
- BiologyNucleic Acids Res.
- 2004
The Macromolecular Structure Database (MSD) group has worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases, and exchange of annotation information has enriched the structural information inThe MSD database with annotation from wider sequence-oriented resources.
EnsMart: a generic system for fast and flexible access to biological data.
- Computer Science, BiologyGenome research
- 2004
The EnsMart system, a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools, has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
- BiologyNucleic Acids Res.
- 2003
The SWISS-PROT protein knowledgebase connects amino acid sequences with the current knowledge in the Life Sciences by providing an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions.
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
- BiologyNucleic Acids Res.
- 2005
This analysis focuses on bacterial and archaeal DNA sequences in which annotation has been upgraded through the integration of data from many sources, including the EMBL Nucleotide Sequence Database, the UniProt Knowledgebase, InterPro, CluSTr, GOA and HOGENOM.
BIND--The Biomolecular Interaction Network Database.
- Chemistry, BiologyNucleic acids research
- 2001
The BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry.