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Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
2017
Database: The Journal of Biological Databases and Curation
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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]
2016
bioRxiv
pre-print
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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
2004
Genome Research
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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
2011
Nucleic Acids Research
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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
2010
BMC Genomics
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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
2009
Nucleic Acids Research
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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
2016
The Plant Genome
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. 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
2010
Briefings in Bioinformatics
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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
2011
PLoS ONE
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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
2007
Nucleic Acids Research
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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
2010
BMC Bioinformatics
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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
2010
Nucleic Acids Research
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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
2007
Nucleic Acids Research
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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
2003
Bioinformatics
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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
2004
Genome Research
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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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