Published online 12 June 2012 Nucleic Acids Research, 2012, Vol. 40, Web Server issue W609–W614 doi:10.1093/nar/gks575 CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources Marta Bleda1,2, Joaquin Tarraga1,3, Alejandro de Maria1, Francisco Salavert1,2, Luz Garcia-Alonso 1 , Matilde Celma 4 , Ainoha Martin4, Joaquin Dopazo1,2,3,* and Ignacio Medina1,3,* 1Department of Bioinformatics and Genomics, Centro de Investigacio´ n Prı´ncipe Felipe (CIPF), 46012 Valencia, Spain, 2CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain, 3Functional Genomics Node (INB) at CIPF, 46012 Valencia, Spain and 4Research Center on Software Production Methods (ProS). DSIC Universitat Polite` cnica de Vale` ncia (UPV), 46007 Valencia, Spain Received March 23, 2012; Revised May 18, 2012; Accepted May 21, 2012 ABSTRACT During the past years, the advances in high- throughput technologies have produced an unprece- dented 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 sup- ported 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 neces- sity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database contain- ing 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. INTRODUCTION During the past years, the increase in scientiﬁc knowledge and the massive data production have caused an exponential growth in the number and size of biological databases and repositories. However, data size, which can reach hundreds of gigabytes, involves serious problems of data access through Internet and data storage in local disks. Other challenging issues associated to biological data are that much relevant information is spread out in different databases or repositories, different identiﬁers or standards are used and data can be very frequently updated as new experiments are conducted. This is a par- ticular problem when analyzing high-throughput experi- ments such as expression proﬁling, genotyping or massive sequencing data because much heterogeneous biological information is required for its interpretation. To address these daily problems, we have developed a comprehensive infrastructure that comprises a relational database containing biological information and a web services application programming interface (API) to query all these data. This relational database integrates biological information from different sources and includes (i) core features such as genes, transcripts and exons or proteins; (ii) regulatory elements such as transcription factors (TFs) and TF binding sites, microRNA (miRNA) and curated and non-curated miRNA targets or CpG islands; (iii) many functional ontologies from Open Biomedical Ontologies (OBO) Foundry (1); (iv) variation data such as single-nucleotide polymorphisms (SNPs), phenotypic-related SNPs, known mutations or structural variation and (v) systems biology information such as pathways or protein interactome. Web services API have been implemented in represen- tational state transfer (REST) style that allows an easy, lightweight, fast and intuitive way of querying data in the database. Outputs can be obtained in plain tabulated text *To whom correspondence should be addressed. Tel: +34 96 328 96 80; Fax: +34 96 328 97 01; Email: imedina@cipf.es Correspondence may also be addressed to Joaquin Dopazo. Tel: +34 96 328 96 80 (ext 1007); Fax: +34 96 328 97 01; Email: jdopazo@cipf.es The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.