@article {3,
	title = {CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jul},
	pages = {W609-14},
	abstract = {During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.},
	keywords = {Animals, Databases, Gene Regulatory Networks, Genetic, Genetic Variation, Humans, Internet, Mice, MicroRNAs, Molecular Sequence Annotation, Protein Interaction Mapping, Rats, Software, Systems Biology, Systems Integration, Transcription Factors},
	issn = {1362-4962},
	doi = {10.1093/nar/gks575},
	author = {Bleda, Marta and Tarraga, Joaquin and de Maria, Alejandro and Salavert, Francisco and Garcia-Alonso, Luz and Celma, Matilde and Martin, Ainoha and Dopazo, Joaqu{\'\i}n and Medina, Ignacio}
}
@article {5,
	title = {VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jul},
	pages = {W54-8},
	abstract = {The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es.},
	keywords = {Databases, Genetic Variation, High-Throughput Nucleotide Sequencing, Internet, Molecular Sequence Annotation, Mutation, Nucleic Acid, Polymorphism, Single Nucleotide, Software, User-Computer Interface},
	issn = {1362-4962},
	doi = {10.1093/nar/gks572},
	url = {http://nar.oxfordjournals.org/content/40/W1/W54},
	author = {Medina, Ignacio and de Maria, Alejandro and Bleda, Marta and Salavert, Francisco and Alonso, Roberto and Gonzalez, Cristina Y and Dopazo, Joaqu{\'\i}n}
}
