Overview

During the last years the advances of high-throughput technologies have produced an unprecedented growth 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 most of the times. Some of the most common problems are: a) information is spread out in many small repositories and databases, b) lack of standards between different repositories, c) unsupported databases, d) specific and unconnected information, etc. All these problems make very difficult: a) to integrate or join many different sources into only one database to work or analyze experiments; b) to access and query this information in programmatically way.

To cope with all these problems we have developed a relational database that contains the most relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. About one hundred tables have been well designed and normalized into one database. We have integrated the most relevant repositories such as Ensembl, Uniprot, Omim, COSMIC, IntAct, HapMap, Reactome, and other. The information integrated covers:

  • Core features: genes, transcripts, exons, proteins, genome sequence, etc.
  • Regulatory: Jaspar TFBS, miRNA targets, CTCF, Open chromatin, etc.
  • Functional annotation: OBO ontologies (Gene Ontology, Human Disease Ontology), etc.
  • Genomic variation: dbSNP, HapMap, 1000Genome project, COSMIC, etc.
  • Systems biology: IntAct , Biogrid, Reactome, gene co-expression, etc.

To make this entire database accessible to researchers, an exhaustive RESTful Web service API has been implemented. This API contains about 100 methods that will facilitate researchers to query and obtain different biological information from a single database saving a lot of time. Another benefit is that researchers can make easily queries about different biological topics and link all this information together as all information is integrated.

Currently Homo sapiens, Mus musculus and other species are available and many others will be included soon. Results are offered in plain text or JSON format, making all this information accessible to both software or web applications.

Members

Head of the Department: Joaquin Dopazo
Project Manager: Ignacio Medina
Bioinformatician: Ignacio Medina, Luz Garcia, Marta Bleda
Scientific Programmer: Ignacio Medina
Software Developer: Alejandro de MarĂ­a, Francisco Salavert, Roberto Alonso