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Data-Babel-Client-0.02
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/ Data::Babel::Client

NAME

Data::Babel::Client - A Client to access the Babel web service.

VERSION

Version 0.02

SYNOPSIS

    use Data::Babel::Client;
    my $bc=new BabelClient;

    # Get a list of valid id types: each element is a two-element array containing the literal type and an English description
    my @idtypes=$bc->idtypes;
    my %idtypes=map {($_->[0],$_->[1])} @idtypes;         # convert to hash form

    # Translate some Entrez gene ids to various types; $table contains an array of arrays
    my %args=(input_type=>'gene_entrez',
              input_ids=>[2983,1829,589,20383,293883],
              output_types=>[qw(protein_ensembl peptide_pepatlas reaction_ec function_go gene_symbol_synonym)]);
    my $table=$bc->translate(%args);

Description

BabelClient.pm provides access to the babel web service. The Babel web service provides translations between biological identifiers of various types. For example, given a list of Entrez gene ids, it can provide the corresponding Ensembl gene ids, UniProt protien ids, and so forth. The full list of available identifiers, and accompanying English descriptions, can be obtained by making a call to the 'idtypes' method.

This web service client provides two calls, idtypes() and translate(). Both of these calls mimic calls of the same names found in Data::Babel, which also provides full documentation. It is intended that the API's of the corresponding calls be exactly the same.

The main method is 'translate'. It makes a request to the web service to translate identifiers. The parameters to translate are: - input_type: a string describing the type of the input identifiers. This type must match exactly with one of the values returned by the 'idtypes' method. - input_ids: a listref containing the actual identifiers to be translated. - output_types: a listref containing the output types desired, ie, the translations from 'input_type'. For example, if you have a list of Uniprot ids and you would like to know what are the corresponding Ensembl gene ids, gene symbols, and associated OMIM numbers, you would pass the list [qw(gene_ensembl gene_symbol function_omim)]

As mentioned, the method 'idtypes' provides a list of all valid id types for use in the 'translate' method (for both 'input_type' and 'output_type'). The 'idtypes' method takes no parameters.

NOTE: not all translations are 1-to-1. Many of the translations will return more than one output value for a given input value. For example, there are multiple Affymetrix probeset ids for many genes. In this case, there will be one row for each unique combination of return values, so if there were six Affymetrix probe ids for a given Entrez gene id, there would be six rows in the returned array for that Entrez gene id, with the value for the Entrez gene id repeated in each row. Were you to request two non-unique translations to a call to 'translate', the returned array would contain all the different combinations of values, one on each row. In this way the returned array can grow in size so as to overwhelm the capabilities of the server, the web, and so forth, and caution must be used in making requests to the server.

Location of the web service:

The current URL for the web service is http://babel.gdxbase.org/cgi-bin/translate.cgi. It is encoded into this client, but can be overridden by passing the named argument 'base_url' into the constructor, as in:

    my $bc=new BabelClient(base_url=>'http://some.other.url');

This assumes, of course, that there is another instance of the web service at the location mentioned.

SUBROUTINES/METHODS

translate()

$table=translate(\%args)

%args:

inputs_ids:

an arrayref containing the ids you want translated. They must all be of the type specified by $args{input_types}.

input_type:

a string describing the type of the inputs. Must be one of the known values. For a list of known (legal) values, use the idtypes() function.

output_types

a list (ARRAY ref) of desired output types. Similarly to $args{input_type}, each value must be one of the known (legal) types, as obtained by a call to idtypes().

return value

translate() returns an array (or arrayref) to a table of translated values. Each row in the table contains one column for the passed-in input, and one column for each output_type desired, in the order that they were passed in.

idtypes()

$table=idtypes()

idtypes() takes no arguments. It returns a table containing a list of all the legal identifier types. Each row in the table is a 2-element arrayref; the first element is the actual idtype, and the second element is a short description of the idtype.

AUTHOR

Victor Cassen, <vcassen at systemsbiology.org>

BUGS

Please report any bugs or feature requests to bug-data-babel-client at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Data-Babel-Client. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Data::Babel::Client

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2010 Victor Cassen.

This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.