European molecular biology laboratory (EMBL)
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The European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL), offers extensive bioinformatics research and services, operating from the Wellcome Trust Genome Campus in Hinxton, UK. Established in 1992, EBI curates a vast library of life-science data, providing globally accessible databases and tools to support molecular biology research. The institute emphasizes collaboration, continually updating its databases with new nucleotide and protein sequence information from various sources to support the scientific community.
European molecular biology laboratory (EMBL)
- 1. European Molecular Biology Laboratory (EMBL) Hafiz.M.Zeeshan.Raza Research Associate_HEC_NRPU [email protected] COMSATS UNIVERSITY SAHIWAL
- 2. Overview • EBI (EMBL) • Intro and Services • Relational databases
- 3. INTRODUCTION • The European Bioinformatics Institute (EBI) is a center for research and services in bioinformatics, and is part of European Molecular Biology Laboratory(EMBL) • EMBL-EBI grew out of EMBL’s pioneering work to provide public biological database to research community.
- 4. It is located on the Welcome Trust Genome Campus in Hinxton, UK along with welcome trust sanger institute.
- 5. BACKGROUND TO THE STUDY • Founded in 1974, the European Molecular Biology Laboratory (EMBL) now operates across five locations: “Heidelbery, Hamburg, Grenoble, Monterotondo, and EMBL-EBI in Hinxton”. • Established in 1992, the European Bioinformatics Institute (EBI) gathers, curates, and maintains a vast library of data resulting from life-science experiments, covering the full spectrum of molecular biology. • This Industry Program promotes pre-competitive collaboration and ensures that the institute’s public offerings align with companies’ needs. • As of October 2015 EMBL-EBI employed a staff of 570 drawn from 57 nations.
- 7. Aims and Scopes • EMBL-EBI maintains a comprehensive range of freely available and up-to- date databases, which collectively cover the full range of molecular biology, from nucleotide sequences to full systems. • It has a mandate to make its tools and infrastructure freely available to the global scientific community. • EMBL-EBI is a central partner in global efforts to exchange information, set standards, develop new methods, and curate complex information. • This study includes exploration of the costs and cost savings involved in using EMBL-EBI data and services, its value to users, and its impacts on the wider commercial, healthcare, and research communities.
- 8. Continue… • EMBL-EBI gathers biological information from both published literature and directly from experimental research. • This data is then processed, incorporated into all relevant databases, classified, annotated, and aligned with existing data to become a value-added resource. • These resources are provided as defined services. The most strategically important databases are accompanied by comprehensive tools and training. • This allows scientists to share data, perform complex queries, and analyze results in different ways. Scientists can work locally by downloading EMBL-EBI data and software or use web services to access EMBL-EBI resources programmatically.
- 13. The EMBL Nucleotide Sequence database • The main activity of the group is the development, maintenance and distribution of a comprehensive database of nucleotide sequences. • The EMBL nucleotide sequence database, produced in collaboration with GenBank and the DNA database of Japan, is Europe’s primary nucleotide sequence data resource. • Each of these three groups collect a portion of the total sequence data reported world- wide. All new and updated database entries are exchanged between the groups on a daily basis. • The rate of growth of the database continues to accelerate. As an example, release 44 (September 1995), with more than 360 million bases from 506 192 entries, represents an annual increase of ∼2.5 times the number of entries and 1.7 times the number of bases.
- 14. Continue… • Important sources of data have been secured through collaborations with genomic sequencing projects and other groups, such as phylogenetic research groups, who produce large quantities of new nucleotide sequence data. • The ongoing collaboration with the European Patent Office has resulted in the capture of nucleotide and protein sequences which were published in patent documents between 1960 and 1993 and previously not publicly available in electronic form. • A typical entry contains a sequence, a brief description for cataloging purposes, the taxonomic description of the source organism, bibliographic information, and the feature table, containing locations of coding regions and other biologically significant sites.
- 15. The SWISS-PROT Protein Sequence database • The SWISS-PROT protein sequence database is maintained collaboratively by the EMBL Data Library and Amos Bairoch of the University of Geneva. • It is distributed in the same file format as the Nucleotide Sequence database, with which it is fully cross-referenced. SWISS-PROT entries are derived from various sources including translations of DNA sequences in the EMBL database, adapted from the Protein Identification Resource collection extracted from the literature, and directly submitted by researchers. • Its strengths are the quality and consistency of its annotation, non- redundancy, and the cross-references to other databases, especially to the EMBL nucleotide sequence database, PROSITE and PDB.
- 16. DATA ACQUISITION • Today, approximately 95% of all nucleotide sequence data are directly submitted to one of the collaborating databases (EMBL, GenBank and DDBJ). • This has reduced the delay between determination of a sequence and appearance of that sequence in the database compared to earlier years. • The entries created by each group are exchanged on a daily basis. The remaining 5% are still extracted from the literature (especially patent documents), which is a time-consuming and error-prone task.
- 17. EBI World Wide Web server • The EBI WWW server provides the most advanced network access to a broad range of molecular biology information resources. • In addition to the EBI molecular biology archives, sequence similarity search and database query/retrieval services are offered. • Users can also directly submit their data using the direct submission entry page. Connect to the EBI WWW server using the URL: http://www.ebi.ac.uk which give access to the EBI home page and links to all EBI services.
- 19. EBI NETWORK SERVICES • In addition to archiving sequence and genome data, the EBI provides an ever-expanding number of free network services to external users. • The EBI databases and software archives are currently accessible via electronic mail fileserver, FTP, gopher and World Wide Web (WWW). • New and updated entries from all three collaborating nucleotide sequence databases are added daily to the network servers, making it possible to retrieve entries and perform sequence similarity searches on the very latest nucleotide data. • The complete collection of additional specialist molecular biology databases is also available.
- 20. EBI Gopher server • The EBI Gopher server simplifies the use of network services by hiding complexity behind a simple graphical user interface. • The files are arranged in a hierarchy of directories like in the FTP server, but have more detailed titles. • In addition to accessing the EBI molecular biology archives, links are provided to other information resources in Europe and world-wide. • Gopher clients can access the server at gopher.ebi.ac.uk.
- 21. Services