Public web-based services from the European Bioinformatics Institute

@article{Harte2004PublicWS,
  title={Public web-based services from the European Bioinformatics Institute},
  author={Nicola Harte and Ville Silventoinen and Emmanuel Quevillon and Stephen Robinson and Kimmo Kallio and Xavier Fustero and Pravin Patel and Petteri Jokinen and Rodrigo Lopez},
  journal={Nucleic acids research},
  year={2004},
  volume={32 Web Server issue},
  pages={
          W3-9
        }
}
The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all parts of the scientific community in ways that promote scientific progress. To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services. These can be… 

Figures and Tables from this paper

Web Services at the European Bioinformatics Institute
We present a new version of the European Bioinformatics Institute Web Services, a complete suite of SOAP-based web tools for structural and functional analysis, with new and improved applications.
EMBL Nucleotide Sequence Database in 2006
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The
EMBL Nucleotide Sequence Database: developments in 2005
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to
The IMGT/HLA database
TLDR
It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences, and regular updates to the website ensure that new and confirmatory sequences are dispersed to the Hla community, and the wider research and clinical communities.
UniProtKB/Swiss-Prot.
TLDR
The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, paying particular attention to the specificities of plant protein annotation, and some of the tools and databases that are linked to each entry.
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.
TLDR
The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, and some of the tools and databases that are linked to each entry.
Bioinformatics Web Services
TLDR
This paper will introduce bioinformatics web services, and survey the different existing tools and mechanisms available to develop.
Sequence Similarity Search portal
This project brings the bioinformatics community a new development concept in which users can access all data and applications hosted in the main research centers as if they were installed on their
Web tools for predictive toxicology model building
  • N. Jeliazkova
  • Computer Science
    Expert opinion on drug metabolism & toxicology
  • 2012
TLDR
The topic of this review is a set of recently published web tools that facilitate predictive toxicology model building, offering web access to chemical structure-based methods, although some of the frameworks could also provide bioinformatics or hybrid data analysis functionalities.
Bioinformatics Web Services
TLDR
The Cyberinfrastructure Group at the Virginia Bioinformatics Institute (VBI) has adopted the Web service architecture and wrapped a wide variety of bio informatics applications and data resources using the technology.
...
...

References

SHOWING 1-10 OF 36 REFERENCES
The EMBL Nucleotide Sequence Database
TLDR
The EMBL Nucleotide Sequence Database incorporates, organizes and distributes nucleotide sequences from public sources, and the EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases as well as many other specialist molecular biology databases.
The Ensembl genome database project
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic
WU-Blast2 server at the European Bioinformatics Institute
TLDR
The European Bioinformatics Institute's WU-Blast2 server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software.
The InterPro Database, 2003 brings increased coverage and new features
TLDR
The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications, an increase of nearly 15% since the inception of Inter pro.
E-MSD: an integrated data resource for bioinformatics.
TLDR
A novel search interface is implemented that begins to integrate separate MSD search services in a single graphical tool and a new visualization tool that can present both structure and sequence data in a unified interface is built.
UniProt: the Universal Protein knowledgebase
TLDR
The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
The Gene Ontology ( GO ) database and informatics resource Gene Ontology Consortium
TLDR
The Gene Ontology (GO) project provides structured, controlled vocabularies and classi®cations that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences.
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
TLDR
The CluSTr database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins, based on analysis of all pairwise comparisons between protein sequences, yielding a hierarchical organisation of clusters.
Recent improvements to the PROSITE database
TLDR
The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements.
InterProScan - an integration platform for the signature-recognition methods in InterPro
TLDR
The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request.
...
...