AliasServer Perl API


Introduction

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).


Using Perl

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,


Methods

Aliases(id_list, taxid_list, input_type, output_type, one_option)
This is the main method of the API.
It allow to retrieve aliases of an identifier in a given specie (species identified by his NCBI TaxID).
The result is stored in a hash table.

Example : to obtain all SwissProt accession number and SwissProt identifier corresponding to the systematic name YMR039C in S. cerevisiae (TaxId=4932)

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( )
Return the list of species available in AliasServer in a hash table.
Each result contains the species name and the NCBI TaxID (useful in other methods).

my $sorn=$soap->Species_List(); %tab=%{$sorn->result}; foreach my $v (keys %tab) { print $tab{$v}{'name'}." - ".$tab{$v}{'taxid'}."\n"; }
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( )
Return the list of available alias type in AliasServer in a hash table

my $sorn=$soap->Type_List(); %tab=%{$sorn->result}; foreach my $v (keys %tab) { print "-> ".$v."\n"; }
-> SYSTEMATIC
-> UNIGENE
-> GENBANK_AC
-> SGD_ID
-> GENE_NAME
-> TIGR_LOCUS
-> REFSEQ
-> SWISSPROT_AC
-> CRC64
-> SWISSPROT_ID
-> HGNC_ID
-> PID
   ............. 


Species_available_type(taxid)
Return the list of identifier type available for a given specie.
The result is stored in a hash table.

Example : to obtain all available identifier type for H. sapiens (TaxId=9606)

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)
Return all available aliases for a given species in tabular format.

my $sorn=$soap->All_aliases("2097");
print $sorn->result ;