perl-Data-Babel-Client-0.02-alt1.noarch.rpm


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Description

perl-Data-Babel-Client - A Client to access the Babel web service

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package filename perl-Data-Babel-Client-0.02-alt1.noarch.rpm
Package name perl-Data-Babel-Client
Package version 0.02
Package release alt1
Package architecture noarch
Package type rpm
Category Development/Perl
Homepage -
License -
Maintainer -
Download size 9.39 KB
Installed size 9.39 KB
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.

Alternatives

Package Version Architecture Repository
perl-Data-Babel-Client - - -

Requires

Name Value
/usr/share/perl5 -
perl(Class/AutoClass.pm) -
perl(Data/Dumper.pm) -
perl(HTTP/Request/Common.pm) -
perl(JSON.pm) -
perl(LWP/UserAgent.pm) -
perl(base.pm) -
rpmlib(PayloadIsLzma) -

Provides

Name Value
perl(Data/Babel/Client.pm) = 0.020
perl-Data-Babel-Client = 0.02-alt1

Download

Type URL
Mirror ftp.altlinux.org
Binary Package perl-Data-Babel-Client-0.02-alt1.noarch.rpm
Source Package perl-Data-Babel-Client-0.02-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-Data-Babel-Client rpm package:
    # sudo apt-get install perl-Data-Babel-Client

Files

Path
/usr/share/doc/perl-Data-Babel-Client-0.02/Changes
/usr/share/doc/perl-Data-Babel-Client-0.02/README
/usr/share/perl5/Data/
/usr/share/perl5/Data/Babel/Client.pm

See Also

Package Description
perl-Data-Beacon-0.3.1-alt1.noarch.rpm BEACON format validating parser and serializer
perl-Data-Beacon-scripts-0.3.1-alt1.noarch.rpm Data-Beacon scripts
perl-Data-BenchmarkResults-0.01-alt1.noarch.rpm perl module Data-BenchmarkResults
perl-Data-BiaB-0.10.3-alt1.noarch.rpm Analyze Band-in-a-Box data files
perl-Data-Binder-1-alt1.noarch.rpm perl module Data-Binder
perl-Data-BitMask-0.91-alt1.noarch.rpm bitmask manipulation
perl-Data-BitStream-0.08-alt1.noarch.rpm A class implementing a stream of bits and coding methods
perl-Data-Bitfield-0.04-alt1.noarch.rpm manage integers containing multiple bit fields
perl-Data-Bool-2.98014-alt1.noarch.rpm An interface to booleans as objects for Perl
perl-Data-Bucketeer-0.003-alt1.noarch.rpm sort data into buckets based on threshholds
perl-Data-Bvec-1.01-alt1.noarch.rpm a module to manipulate integer arrays as bit vectors and
perl-Data-CGIForm-0.5-alt1.noarch.rpm Form Data Interface
perl-Data-CHEF-1.01-alt1.noarch.rpm perl module Data-CHEF
perl-Data-COW-0.02-alt1.noarch.rpm perl module Data-COW
perl-Data-CPAN-DSLIP-Explain-0.04-alt1.noarch.rpm "decrypts" CPAN module DSLIP code
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