To make this entire database accessible to researchers, a RESTful Web Service API has been implemented. This API contains several methods designed to facilitate researchers query and obtain regulatory information from a single database saving a lot of time.

General structure of the implemented RESTful call is:

ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/<category>/<subcategory>/id/<resource>?filters

Sections in braquets are parameters, so they are variable entities:

Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/tfbs

As is explained in this documentation, this REST call will get all transcription factor binding sites (TFBSs) related to the gene BRCA2 in human.

Note: All sections in URL must be in lower case!

Regulatory category refers to regulatory elements, such transcription factors and microRNAs.

URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/regulatory/<subcategory>/id/<resource>

tf:
URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/regulatory/tf/tf1, tf2/<resource|action>
Format: HGNC Symbol, Ensembl gene, Ensembl TF Name.
Resources or actions:

• info: Returns information about this transcription factor (TF).
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/info
  Output columns:

• tfbs: Get all TFBSs for this TF.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/tfbs
  Output columns: TF name, target gene name, chromosome, start, end, cell type, sequence, score.

• target_gene: Get all genes regulated by this TF.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/target_gene
  Output columns: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.

• gene: Get the corresponding gene for this TF.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/gene
  Output columns: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.

• pwm: Get all position weight matrices associated to this TF.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/tf/USF1/pwm
  Output columns: TF Name, type, frequency_matrix, description, source, length, jaspar_accession.

mirna_mature:
URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/regulatory/mirna_mature/mirna_mature1, mirna_mature2/<resource>
Format: miRBase name/identifier.
Resources or actions:

• info: Returns information about a miRNA mature.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149-3p/info
  Output columns: miRBase accession, miRBase ID, sequence.

• gene: Get the gene associated to this miRNA mature.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149-3p/gene
  Output columns: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.

• mirna_gene: Get the miRNA gene information associated to this miRNA mature.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149-3p/mirna_gene
  Output columns: miRBase accession, miRBase ID, status, sequence, source.

• target_gene: Get all genes that are regulated by this miRNA mature.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149/target_gene
  Output columns: Ensembl gene, external name, external name source, biotype, status, chromosome, start, end, strand, source, description.

• target: Get all binding sites associated to this miRNA.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149/target
  Output columns: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.

• disease: Get all diseases related with this miRNA.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_mature/hsa-miR-149-3p/disease
  Output columns: miRBase ID, disease name, pubmed ID, description.

mirna_gene:
URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/regulatory/mirna_gene/mirna_gene1, mirna_gene2/<resource|action>
Format: miRBase name/identifier.
Resources or actions:

• info: Returns information about a miRNA gene.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/hsa-mir-149/info
  Output columns: miRBase accession, miRBase ID, status, sequence, source.

• target: Get all binding sites associated to this miRNA.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/hsa-mir-149/target
  Output columns: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.

• disease: Get all diseases related with this miRNA.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/hsa-mir-149/disease
  Output columns: miRBase ID, disease name, pubmed ID, description.

Genomic category makes reference to the coordinates necessary to place a position or a region in the genome. Using these coordinates, the user can query our database to retrieve any regulatory information within a position or region.

URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/genomic/<subcategory>/id/<resource|action>

• region:
  URL pattern:
  ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/genomic/region/region1, region2/<resource|action>
  Chr. region format: chr:start-end (i.e.: 7:245000-501560). Use the same start and end to indicate a position.
  Resources or actions:

• tfbs: Returns all TFBSs located in the specified region.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/region/16:3698105-3801105/tfbs
  Output columns: TF name, target gene name, chromosome, start, end, cell type, sequence, score.

• mirna_binding_site: Returns all miRNA binding sites located in the specified region.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/region/16:3698105-3801105/mirna_binding_site
  Output columns: TF name, target gene name, chromosome, start, end, cell type, sequence, score.

Feature category involve all elements which have a defined location on the genome.

URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/feature/<subcategory>/id/<resource|action>

gene:
URL pattern:
ws.bioinfo.cipf.es/cellbase/rest/<version>/<species>/feature/gene/gene1, gene2/<resource|action>
Gene format: we accept all id formats.
Resources or actions:

• tfbs: Returns all TFBSs located in the specified gene.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/tfbs
  Output columns: TF name, target gene name, chromosome, start, end, cell type, sequence, score.

• mirna_target: Get all microRNA target sites for this gene.
  Example: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/mirna_target
  Output columns: miRBase ID, gene target name, chromosome, start, end, strand, pubmed ID, source.

Today, the vast majority of programming languages can handle URLs, what makes RENATO Web Services API fully accessible in a programmatic way. Here we present an example of usage in Perl. The code below extracts the related diseases of a miRNA gene simply using the URL structure described avobe.

renato_example_code.pl

#!/usr/bin/perl -w
use strict;
 
## load LWP library and create UserAgent object
use LWP::Simple;
my $browser = LWP::UserAgent->new;
 
## define the query URL
my $url = 'http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/regulatory/mirna_gene/hsa-mir-149/disease';
 
## send request
my $response = $browser->get($url);
 
## check the outcome
if ($response->is_success) {
	print $response->content;
}else {
	print "Error getting $url \n Error: ".$response->status_line."\n";
}