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1.  The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI 
Nucleic Acids Research  2015;43(Web Server issue):W585-W588.
The European Bioinformatics Institute (EMBL-EBI—https://www.ebi.ac.uk) provides free and unrestricted access to data across all major areas of biology and biomedicine. Searching and extracting knowledge across these domains requires a fast and scalable solution that addresses the requirements of domain experts as well as casual users. We present the EBI Search engine, referred to here as ‘EBI Search’, an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities. API integration provides access to analytical tools, allowing users to further investigate the results of their search. The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences, genes, gene products, proteins, protein domains, protein families, enzymes and macromolecular structures, together with relevant life science literature.
doi:10.1093/nar/gkv316
PMCID: PMC4489232  PMID: 25855807
2.  The EMBL-EBI bioinformatics web and programmatic tools framework 
Nucleic Acids Research  2015;43(Web Server issue):W580-W584.
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
doi:10.1093/nar/gkv279
PMCID: PMC4489272  PMID: 25845596
3.  Assembly information services in the European Nucleotide Archive 
Nucleic Acids Research  2013;42(Database issue):D38-D43.
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many enhancements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.
doi:10.1093/nar/gkt1082
PMCID: PMC3965037  PMID: 24214989
4.  Analysis Tool Web Services from the EMBL-EBI 
Nucleic Acids Research  2013;41(Web Server issue):W597-W600.
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
doi:10.1093/nar/gkt376
PMCID: PMC3692137  PMID: 23671338
5.  Fast and efficient searching of biological data resources—using EB-eye 
Briefings in Bioinformatics  2010;11(4):375-384.
The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.
doi:10.1093/bib/bbp065
PMCID: PMC2905521  PMID: 20150321
text search; biological databases; integration; interoperability; web services; Apache Lucene
6.  A new bioinformatics analysis tools framework at EMBL–EBI 
Nucleic Acids Research  2010;38(Web Server issue):W695-W699.
The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.
doi:10.1093/nar/gkq313
PMCID: PMC2896090  PMID: 20439314

Results 1-6 (6)