The miRGate API allows programmers to access miRGate data in a programmatic way, through a RESTful Web Service. Using this service, the server can be accessed from multiple programming languages, allowing researchers to wire miRGate results to their experiments. At this time, the API offers the gene retrieval operations, including data source listing, catalog listing and query execution.
Like any RESTful Web Service, operations are performed via web queries with a well-defined URL structure. The server API is located at http://mirgate.bioinfo.cnio.es/ResT
Lists all data source that the server can access at this moment. The URL is:
http://mirgate.bioinfo.cnio.es/ResT/API/
Executing a query on a data source is performed via:
http://mirgate.bioinfo.cnio.es/ResT/API/{organism}/{datasource}/{query}
All possible values for {organism} and {datasource}, can be obtained form the previous link at http://mirgate.bioinfo.cnio.es/ResT/API/
In the case of constrained query data API, the {query} must be a valid id of the catalog. This URL could be an example:
http://mirgate.bioinfo.cnio.es/ResT/API/human/miRNA_gene_predictions/hsa-miR-1/TP53
Getting the available namespaces for conversion of genesets is done via the gene_info source
http://mirgate.bioinfo.cnio.es/ResT/API/rat/gene_info/Nfkbib
http://mirgate.bioinfo.cnio.es/ResT/API/mouse/gene_info/ILMN_1238558
http://mirgate.bioinfo.cnio.es/ResT/API/human/gene_info/ENSG00000106077
For miRNAs miRNA_info, accepts serveral namespaces :
For miRNA names : http://mirgate.bioinfo.cnio.es/ResT/API/human/miRNA_info/hsa-miR-329
For miRNA accesions : http://mirgate.bioinfo.cnio.es/ResT/API/rat/miRNA_info/MIMAT0012831
For Probes : http://mirgate.bioinfo.cnio.es/ResT/API/mouse/miRNA_info/A_54_P2281
Getting predictions for miRNA/Gene of interest are available through several methods:
For a miRNA and a gene : gene_miRNA_predictions or miRNA_gene_predictions: http://mirgate.bioinfo.cnio.es/ResT/API/human/miRNA_gene_predictions/hsa-miR-1/TP53
For just a gene : gene_predictions: http://mirgate.bioinfo.cnio.es/ResT/API/rat/gene_predictions/Mapkapk5
For a miRNA : miRNA_predictions: http://mirgate.bioinfo.cnio.es/ResT/API/rat/miRNA_predictions/MIMAT0000858
In the case of predictions a filtering, method is also possible. This URL could be an example:
http://mirgate.bioinfo.cnio.es/ResT/API/human/gene_miRNA_predictions/ABCD1/MIMAT0007883/Rnahybrid
Getting the available experimentally confirmed targets :
For a miRNA and a gene : gene_miRNA_confirmed or miRNA_gene_confirmed: http://mirgate.bioinfo.cnio.es/ResT/API/human/miRNA_gene_confirmed/hsa-miR-1/ABHD11
For just a gene : gene_confirmed: http://mirgate.bioinfo.cnio.es/ResT/API/human/gene_confirmed/ABHD11
For a miRNA : miRNA_confirmed: http://mirgate.bioinfo.cnio.es/ResT/API/mouse/miRNA_confirmed/MIMAT0000246
Script to print Basic Information about miRGateDB. Download from here.
1
2 #
3 #
4 # Created by Eduardo Andres Leon .
5 # Copyright (c) 2015 CNIO. All rights reserved.
6 # eandres@cnio.es
7
8 #!/usr/bin/perl
9 $|=1;
10 use strict;
11 use XML::LibXML;
12
13 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API";
14
15 my $parser = XML::LibXML->new();
16 my $xmldoc = $parser->parse_file($SourceListingURL);
17
18 #######################################################Listing basic information stored in miRGate Database#################################################################
19
20 print "\nmiRGate contains information for " . scalar(@{$xmldoc->findnodes('/miRGate/organism/commonName')}) . " organisms :\n\n";
21 foreach my $organism ($xmldoc->findnodes('/miRGate/organism/commonName')) {
22 print "For " .$organism->textContent() ." contains " .scalar(@{$xmldoc->findnodes('/miRGate/organism/'.$organism->textContent().'/method')}) . " different sources:\n";
23 foreach my $method ($xmldoc->findnodes('/miRGate/organism/'.$organism->textContent().'/method')) {
24 foreach my $met ($method->childNodes()){
25 if($met and $met->localname){
26 print "\t". $met->localname .": " . $met->textContent."\n" if ($met->localname eq "name");
27 }
28 }
29 }
30 }
31 print "\n";
32
33 ##############################################################################################################################################################################
34
35 __END__
Script to retrieve all sources to make query with. Download from here.
1 #
2 # Created by Eduardo Andres Leon .
3 # Copyright (c) 2015 CNIO. All rights reserved.
4 # eandres@cnio.es
5
6 #!/usr/bin/perl
7 $|=1;
8 use strict;
9 use XML::LibXML;
10
11 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API";
12
13 my $parser = XML::LibXML->new();
14 my $xmldoc = $parser->parse_file($SourceListingURL);
15
16
17 #######################################################How to make questions to miRGate Database##############################################################################
18
19 print "\nmiRGate contains " . scalar(@{$xmldoc->findnodes('/miRGate/sources/source_name')}) . " different sources :\n\n";
20 foreach my $source ($xmldoc->findnodes('/miRGate/sources/source_name')) {
21 print "\t". $source->textContent() ."\n";
22 }
23 print "\n";
24 ##############################################################################################################################################################################
25
26 __END__
Script to retrieve all experimentally validated targets from a couple of genes of interest. Download from here.
1
2 #
3 # Created by Eduardo Andres Leon .
4 # Copyright (c) 2015 CNIO. All rights reserved.
5 # eandres@cnio.es
6
7 #!/usr/bin/perl
8 $|=1;
9 use strict;
10 use XML::LibXML;
11
12 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API";
13
14 my $parser = XML::LibXML->new();
15 my $xmldoc = $parser->parse_file($SourceListingURL);
16
17 #######################################################Example : retrieve experimentally validated information about my genes of interest#####################################
18
19 my $parser = XML::LibXML->new();
20
21 my $working_organism="human";
22 my @genes_of_interest=("TP53","TBCCD1");
23
24 #Using the source gene_confirmed
25 my $source="gene_confirmed";
26 foreach my $gene (@genes_of_interest){
27 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API/$working_organism/$source/$gene";
28 my $xmldoc = $parser->parse_file($SourceListingURL);
29 print "There is/are " . scalar(@{$xmldoc->findnodes('/miRGate/search/results/result')}) . " experimentally validated experiments for $gene\n\n";
30 my $cont=1;
31 foreach my $confirmed_data ($xmldoc->findnodes('/miRGate/search/results/result')) {
32 print $cont ." )";
33 foreach my $confirmed_attr ($confirmed_data->childNodes()){
34 if($confirmed_data){
35 print "\t ". $confirmed_attr->localname .": " . $confirmed_attr->textContent."\n" ;
36 }
37 }
38 $cont++;
39 print "\n";
40
41 }
42 }
43 ##############################################################################################################################################################################
44
45 __END__
Script to obtained all predictions stored in miRGate for two genes and three miRNAs. Download from here.
1 #
2 # Created by Eduardo Andres Leon .
3 # Copyright (c) 2015 CNIO. All rights reserved.
4 # eandres@cnio.es
5
6 #!/usr/bin/perl
7 $|=1;
8 use strict;
9 use XML::LibXML;
10
11 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API";
12
13 my $parser = XML::LibXML->new();
14 my $xmldoc = $parser->parse_file($SourceListingURL);
15
16
17 ####################################################### Example : retrieve predicctions about my genes and miRNAs of interest #####################################
18
19 my $parser = XML::LibXML->new();
20
21 my $working_organism="human";
22 my @genes_of_interest=("TP53","TBCCD1");
23 my @miRNAs_of_interest=("hsa-miR-1","hsa-miR-605","hsa-miR-195-5p");
24
25 #Using the source miRNA_gene_predictions
26
27 my $source="miRNA_gene_predictions";
28 foreach my $gene (@genes_of_interest){
29 foreach my $miRNA (@miRNAs_of_interest){
30 my $SourceListingURL = "http://mirgate.bioinfo.cnio.es/ResT/API/$working_organism/$source/$miRNA/$gene";
31 my $xmldoc = $parser->parse_file($SourceListingURL);
32 print "There is/are " . scalar(@{$xmldoc->findnodes('/miRGate/search/results/result')}) . " predictions for $miRNA and $gene\n\n";
33 my $cont=1;
34 foreach my $predicted_data ($xmldoc->findnodes('/miRGate/search/results/result')) {
35 print $cont ." )";
36 foreach my $pred_attr ($predicted_data->childNodes()){
37 if($pred_attr){
38 print "\t ". $pred_attr->localname .": " . $pred_attr->textContent."\n" ;
39 }
40 }
41 $cont++;
42 print "\n";
43
44 }
45 }
46 }
47 ##############################################################################################################################################################################
48
49 __END__