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Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates (+2 others)
2017 Database: The Journal of Biological Databases and Curation  
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.  ...  Abstract The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations.  ...  Acknowledgements We acknowledge the work and contributions to the core database infrastructure of Arne Stabenau, Ewan Birney and other early Ensembl developers.  ... 
doi:10.1093/database/bax020 pmid:28365736 pmcid:PMC5467575 fatcat:cyjhn5h6eve3jopkwrbt23gwne

Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation [article]

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates (+2 others)
2016 bioRxiv   pre-print
The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations.  ...  The Ensembl "Core" database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources.  ...  Acknowledgments and funding  ... 
doi:10.1101/087239 fatcat:td5frmusmfal5pa56hjnonv44u

The Ensembl Core Software Libraries

A. Stabenau
2004 Genome Research  
The core software libraries provide a practical and effective means for programmers to access these data.  ...  Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases.  ...  Such a project must provide persistent data storage and programmatic ways to access its information.  ... 
doi:10.1101/gr.1857204 pmid:15123588 pmcid:PMC479122 fatcat:akhaie2ourbr5gx2bllmga3q3a

PomBase: a comprehensive online resource for fission yeast

V. Wood, M. A. Harris, M. D. McDowall, K. Rutherford, B. W. Vaughan, D. M. Staines, M. Aslett, A. Lock, J. Bahler, P. J. Kersey, S. G. Oliver
2011 Nucleic Acids Research  
The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access.  ...  PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries.  ...  ACKNOWLEDGEMENTS The authors thank members of the Ensembl and Ensembl Genomes teams for contributions to the PomBase data pipelines.  ... 
doi:10.1093/nar/gkr853 pmid:22039153 pmcid:PMC3245111 fatcat:g346pl5zdrdq7bv7wwyhu2lgia

Ensembl variation resources

Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney (+1 others)
2010 BMC Genomics  
The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system.  ...  Description: The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes.  ...  We thank the other members of the greater Ensembl group at the EBI and the WTSI and Guy Coates, Pete Clapham and Tim Cutts for maintaining the Ensembl computer systems.  ... 
doi:10.1186/1471-2164-11-293 pmid:20459805 pmcid:PMC2894800 fatcat:3f65senktbg7tnax5llz4focg4

The European Bioinformatics Institute's data resources

Catherine Brooksbank, Graham Cameron, Janet Thornton
2009 Nucleic Acids Research  
All of the resources described here can be accessed from the EMBL-EBI website:  ...  It has also put the need for unrestricted access to biological data at the centre of biology.  ...  FUNDING Funding for open access charge: Wellcome Trust. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp986 pmid:19934258 pmcid:PMC2808956 fatcat:lha7vmv3fnhipb7kunhmvunveu

transPLANT Resources for Triticeae Genomic Data

Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M. Bolser, Kai C. Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer (+17 others)
2016 The Plant Genome  
. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences.  ...  The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat  ...  The IPK resources Barley Blast Server, BARLEX, and Kmasker e!  ... 
doi:10.3835/plantgenome2015.06.0038 pmid:27898761 fatcat:qbt3ggpfgvbz3okorau7zvsnca

Online resources of cancer data: barriers, benefits and lessons

E. Gadaleta, N. R. Lemoine, C. Chelala
2010 Briefings in Bioinformatics  
However, a key factor in the utility, sustainability and future use of a novel resource lies in its ability to allow for data sharing and to be interoperable with major international cancer research efforts  ...  This article will introduce some of these efforts, the interoperable cancer data-mining resources and repositories, from a user-perspective.  ...  Table 1 : 1 Publicly available Marts Resource Description URL Ensembl Database of genomic data for vertebrates and other eukaryotes http://www.ensembl.org Ensembl Bacteria Annotated bacterial  ... 
doi:10.1093/bib/bbq010 pmid:20348133 fatcat:tinslegov5hyxnx44bm2qvz6ua

pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman, Stein Aerts
2011 PLoS ONE  
Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate  ...  The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles.  ...  Acknowledgments We thank Rhoda Kinsella for BioMart XML configuration files and helpful advice on building an Ensembl BioMart, Nathan Harmston for providing a look-up table between BioCreAtIvE I document  ... 
doi:10.1371/journal.pone.0024716 pmid:21980353 pmcid:PMC3183000 fatcat:lw5ih535hraqvbwukaxom4ynum

MyHits: improvements to an interactive resource for analyzing protein sequences

M. Pagni, V. Ioannidis, L. Cerutti, M. Zahn-Zabal, C. V. Jongeneel, J. Hau, O. Martin, D. Kuznetsov, L. Falquet
2007 Nucleic Acids Research  
databases of predicted protein sequences inferred from various genomic and High Throughput Genomic nucleotidic sequences (8).  ...  BIOLOGICAL DATABASES The protein sequences that are currently included are obtained from UniProt (5), RefSeq (6), the peptide subsection of ENSEMBL (7) and trGen, trEST, trome which are locally produced  ...  ACKNOWLEDGEMENTS We thank many people that have contributed, be it with suggestions, testing and technical support to the maintenance and development of MyHits: Volker Flegel, Roberto Fabbretti, Christian  ... 
doi:10.1093/nar/gkm352 pmid:17545200 pmcid:PMC1933190 fatcat:djtbc7x5wbewbjpcvoxsdbdr5e

A database and API for variation, dense genotyping and resequencing data

Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham
2010 BMC Bioinformatics  
These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation.  ...  Results: Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes.  ...  ; Guy Coates, Pete Clapham and Tim Cutts for maintaining the Ensembl computer systems; the other members of the  ... 
doi:10.1186/1471-2105-11-238 pmid:20459810 pmcid:PMC2882931 fatcat:2yosg4clebgefb3oql3iqbfr2i

Ensembl 2011

P. Flicek, M. R. Amode, D. Barrell, K. Beal, S. Brent, Y. Chen, P. Clapham, G. Coates, S. Fairley, S. Fitzgerald, L. Gordon, M. Hendrix (+40 others)
2010 Nucleic Acids Research  
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible  ...  The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research.  ...  Ensembl core software and data access To improve website performance for users, we have created a second mirror of the Ensembl website in the USA.  ... 
doi:10.1093/nar/gkq1064 pmid:21045057 pmcid:PMC3013672 fatcat:4gdkokx2xbekhooywtflpvuvri

Ensembl 2008

P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer (+47 others)
2007 Nucleic Acids Research  
of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome  ...  The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model  ...  Funding to pay the Open Access publication charges for this article was provided by the Wellcome Trust. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm988 pmid:18000006 pmcid:PMC2238821 fatcat:pzl3e3ahrrb77as4eqynxux3dm

The discovery net system for high throughput bioinformatics

A. Rowe, D. Kalaitzopoulos, M. Osmond, M. Ghanem, Y. Guo
2003 Bioinformatics  
Using the Discovery Net system and a range of different bioinformatics tools, we built a Grid based application for Genome Annotation.  ...  This includes workflows for automatic nucleotide annotation, annotation of predicted proteins and text analysis based on metabolic profiles and text analysis. Contact: asr99@doc.ic.ac.uk  ...  We would also like to thank Dr Catherine Rice and Dr Nigel Carter at The Wellcome Trust Sanger Institute for their help and expertise.  ... 
doi:10.1093/bioinformatics/btg1031 pmid:12855463 fatcat:jkbh5rr2u5hx5me5dnec4nxeui

An Overview of Ensembl

E. Birney
2004 Genome Research  
Highly illustrated and based heavily on early 20th century original sources, the book traces the roots of genetics in breeding analysis and studies of cytology, evolution, and reproductive biology that  ...  emerged from the key ideas and model systems of classical genetics.  ...  These researchers generally need good Web access, the ability to run similarity searches, and the ability to download small, localized data sets, in particular, DNA sequence.  ... 
doi:10.1101/gr.1860604 pmid:15078858 pmcid:PMC479121 fatcat:qdzew6me25fd5ikizpyzal2kb4
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