AliasServer API is a web service to use the AliasServer system from your program via SOAP protocol.
This guide explains how to use the AliasServer API for searching and retrieve alias(es) of a given protein
from the AliasServer database located at the Bioinformatic Center of Bordeaux (CBiB).
You need to install the following packages:
Here's a first example in Perl language
extracting all aliases of the recA protein in Mycoplasma genitalium
#!/usr/bin/perl
use SOAP::Lite;
my $soap = SOAP::Lite
-> readable(1)
-> uri('urn:alias')
-> proxy('http://cbi.labri.fr/outils/cgi-bin/ultim/alias.pl');
my $sorn=$soap->Aliases('recA','2097','all','all','F');
%tab=%{$sorn->result};
foreach my $v (keys %tab) {
print $v." : ".$tab{$v}."\n"; }
|
The output will be :
SWISSPROT_ID : RECA_MYCGE, SYSTEMATIC : MG339, GENE_NAME : recA, PIR_ID : E64237, GI : 12045198, REFSEQ : NP_073009.1, SWISSPROT_AC : P47581,Q49512, CRC64 : 0957B712CD2125C0, |
| Aliases(id_list, taxid_list, input_type, output_type, one_option) |
my $sorn=$soap->Aliases('YMR039C','4932','SYSTEMATIC','SWISSPROT_AC,SWISSPROT_ID','F');
%tab=%{$sorn->result};
foreach my $v (keys %tab) {
print $v." : ".$tab{$v}."\n"; }
|
SWISSPROT_ID : SUB1_YEAST, SWISSPROT_AC : P54000, |
| Species_List( ) |
|
Mycoplasma gallisepticum str. R - 233150 SARS coronavirus - 248485 Helicobacter pylori str. J99 - 85963 Schizosaccharomyces pombe - 4896 Bacillus subtilis subsp. subtilis str. 168 - 224308 Onion yellows phytoplasma - 100379 Arabidopsis thaliana - 3702 Mycoplasma mobile 163K - 267748 Helicobacter pylori str. 26695 - 85962 Drosophila melanogaster - 7227 Listeria monocytogenes - 169963 Mycoplasma genitalium - 2097 ............. |
| Type_List( ) |
|
-> SYSTEMATIC -> UNIGENE -> GENBANK_AC -> SGD_ID -> GENE_NAME -> TIGR_LOCUS -> REFSEQ -> SWISSPROT_AC -> CRC64 -> SWISSPROT_ID -> HGNC_ID -> PID ............. |
| Species_available_type(taxid) |
my $sorn=$soap->Species_available_type("9606");
foreach my $v (keys %{$sorn->result})
{ print "-> ".$v."\n"; }
|
-> SWISSPROT_ID -> HGNC_ID -> PIR_ID -> GI -> UNIGENE -> TREMBL_AC -> GENE_NAME -> TREMBL_ID -> REFSEQ -> SWISSPROT_AC -> CRC64 |
| All_aliases(taxid) |
my $sorn=$soap->All_aliases("2097");
print $sorn->result ;
|