JEnsembl: a version-aware Java API to Ensembl data systems

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale...

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Vydané v:Bioinformatics Ročník 28; číslo 21; s. 2724 - 2731
Hlavní autori: Paterson, Trevor, Law, Andy
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Oxford Oxford University Press 01.11.2012
Predmet:
API
Bioinformatics
Biological and medical sciences
Computational Biology
Data retrieval
Databases, Factual
Fundamental and applied biological sciences. Psychology
General aspects
Genomic Library
Indonesia
Information Storage and Retrieval - methods
Java (programming language)
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Modular
Original Papers
Perl
Project development
Software
Java
Asia
Indonesia
Data
JAVA language
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
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Shrnutí:Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact:  jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Associate Editor: Alfonso Valencia
ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/bts525