/ 
Bio-DB-NextProt-0.01
River stage zero No dependents
/ Bio::DB::NextProt

NAME

Bio::DB::NextProt - Object interface to NextProt REST API.

SYNOPSIS

my $np = Bio::DB::NextProt->new();

my @result_1 = $np->search_cv(-query => "kinase#");

my @result_2 = $np->get_isoform_info(-id => "NX_O00142-2");

my @result_3 = $np->get_protein_cv_info(-id => "PTM-0205", -format => "html");

DESCRIPTION

The module allows the dynamic retrieval of information from the NextProt Database through its API service. All the information below was extracted from the API webpage. For the moment the results obtained from the API are in pure HTML, XML or JSON, so you will have to parse them yourself.

Search functionalities

Search Protein

Search proteins matching the query or search proteins for which the filter is true. Available filter values are: structure, disease, expression, mutagenesis or proteomics. Note: only one filter parameter at a time is possible for the moment.

@result = $np->search_protein(-query => "kinase");
@result = $np->search_protein(-query => "kinase", -filter => "disease");

Control Vocabulary Terms

Search control vocabulary terms matching the query or search control vocabulary terms in the category specified by the filter. Available filter values are: enzyme, go, mesh, cell, domain, family, tissue, metal, pathway, disease, keyword, ptm, subcell. Note: only one category at a time is possible.

@result = $np->search_cv(-query => "colon");
@result = $np->search_cv(-query => "colon", -filter => "keyword");

Format:

Output format maybe in JSON (default), HTML or XML.

@result = $np->search_protein(-query => "kinase", -filter => "disease", -format => "html");

Find information by protein entry

Protein ID

ID is neXtProt identifier. Retrieve gene name as well as main identifier and isoform sequences

@result = $np->get_protein_info(-query => "NX_P13051");

Post-translational modifications

For each isoform of the specified entry, retrieve all post-translational modifications.

@result = $np->get_protein_info(-query => "NX_P13051", -retrieve => "ptm");

Variant

For each isoform of the specified entry, retrieve all variants.

@result = $np->get_protein_info(-query => "NX_P13051", -retrieve => "variant");

Localisation

For each isoform of the specified entry, retrieve all subcellular location.

@result = $np->get_protein_info(-query => "NX_P13051", -retrieve => "localisation");

Expression

Retrieve all expression information by tissue for the specified entry.

@result = $np->get_protein_info(-query => "NX_P13051", -retrieve => "expression");

Format:

Output format maybe in JSON (default), HTML or XML.

@result = $np->get_protein_info(-query => "NX_P13051", -retrieve => "expression", -format => "html");

Find information by isoform

Protein ID

ID is neXtProt identifier. Retrieve gene name as well as main identifier and isoform sequences

@result = $np->get_isoform_info(-query => "NX_O00142-2");

Post-translational modifications

For each isoform of the specified entry, retrieve all post-translational modifications.

@result = $np->get_isoform_info(-query => "NX_P01116-2", -retrieve => "ptm");

Variant

For each isoform of the specified entry, retrieve all variants.

@result = $np->get_isoform_info(-query => "NX_P01116-2", -retrieve => "variant");

Localisation

For each isoform of the specified entry, retrieve all subcellular location.

@result = $np->get_isoform_info(-query => "NX_P01116-2", -retrieve => "localisation");

Find information by controlled vocabulary term

Protein ID

ID is neXtProt identifier. Retrieve the accession, the name and the category of the CV term.

@result = $np->get_protein_cv_info(-query => "PTM-0205");

Protein List

List all the proteins associated with the term in neXtProt.

@result = $np->get_protein_cv_info(-query => "PTM-0205", -retrieve => "proteins");

Format:

Output format maybe in JSON (default), HTML or XML.

@result = $np->get_protein_cv_info(-query => "PTM-0205", -retrieve => "proteins", -format => "html");

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live

AUTHOR - Felipe da Veiga Leprevost

Email leprevost@cpan.org