CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

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.

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

“…The information used for the annotation of the position is stored in CellBase (17), which collects it from different sources. The identifiers of single nucleotide polymorphism (SNP) are extracted from dbSNP (18).…”

“…Each line corresponds to a variant for which the following information is displayed: (i) genomic position (chromosome:position); (ii) allelic change (reference allele > alternative allele); (iii) the name of the gene affected by the variant; (iv) the allelic composition of each sample analyzed (0/0, 0/1 and 1/1 for the homozygote reference allele, the heterozygote and the homozygote alternative allele, respectively; ./. accounts for low quality or low coverage positions); (v) the SNP identifier in dbSNP (18) if the variant is an already known SNP; (vi) the MAF in the population derived from the 1000 genomes (22) and ESP (23) studies; (vii) the consequence type of the variant; (viii) the predicted pathologic effect of the variants according to Polyphen (19) or (ix) SIFT (20) indexes (if the variant has more than one pathologic consequence, the most deleterious value of the indexes is displayed here); and the phenotype extracted from CellBase (17) as annotated in HGMD (24), ClinVar (25) and UNIPROT (26). Columns can be customized by hiding or rearranging them by directly clicking on them or using the button ‘columns’ in the lower right corner of the panel.…”

“…The relevant information on genes, variants, features, etc. used for the prioritization is remotely stored (and kept updated) in CellBase (17) and is provided through highly efficient web services.…”

Big linked cancer data: Integrating linked TCGA and PubMed

“…In contrast, TopFed is an index-assisted approach particularly designed for Linked TCGA and makes use of the intelligent data distribution provided as input. 12 Using a lightweight index, TopFed is able to detect the contributing sources for each SPARQL query and can thus reduce the number of sources selected (without losing any recall) during the query federation. By selecting fewer sources than state-of-the-art approaches, our approach can compute the answer to queries significantly faster, leading to acceptable response times for the queries required to use our framework.…”

“…These Chromosome Bands (Ideograms) were downloaded from the Mapping and Sequencing Tracks Table in the Human Genome Assembly (GRCh37/hg19, Feb 2009), available at the UCSC Genome Browser 13 [11]. The coordinates and descriptions of the Proteincoding genes contained within this chromosome are retrieved from CellBase [12]. These genes are annotated using the HGNC Nomenclature [13] and the positions are indicated by start/stop attributes, and are shown in the subsequent track ( Fig.…”