GPMDB REST

This document is a request for comment on a proposed new SOAP interface for GPMDB. The RFC process began on June 11, 2012 and will end on September 10, 2012.

The purpose of the RFC is to define a straightforward SOAP (Simple Object Access Protocol) interface to commonly required information based on the data in GPMDB. This interface will provide simple, non-SQL methods to extract this information and make it available over the Internet to anyone wishing to use it as part of a SOAP-aware application.

Contents 1 Conventions 2 Methods 2.1 gpmdbProteinBestExpect(string accession) 2.2 gpmdbProteinCount(string accession) 2.3 gpmdbProteinDescription(string accession) 2.4 gpmdbProteinPeptideCount(string accession, string sequence) 2.5 gpmdbProteinPeptideSequences(string accession) 2.6 gpmdbProteinPeptidesCharges(string accession) 2.7 gpmdbProteinPeptidesTotal(string accession) 2.8 gpmdbProteinSequence(string accession) 2.9 gpmdbVersion() 3 Interface parameters 4 Comments and suggestions 5 Revision date and status

Conventions

The following statements refer to all methods and description given below:

1. all protein and peptide sequences are expressed in single letter code;
2. all methods have the prefix "gpmdb" followed by a description name;
3. protein accession numbers use the same format as normally used in GPMDB; and
4. all "tuples" are returned as comma-separated text strings.

Methods

gpmdbProteinBestExpect(string accession)

 input: string, accession number for the protein of interest
return: string, the log10(E) for the best observation of the referenced protein

gpmdbProteinCount(string accession)

 input: string, accession number for the protein of interest
return: string, the total number of observations of the referenced protein

gpmdbProteinDescription(string accession)

 input: string, accession number for the protein of interest
return: string, the log10(E) for the best observation of the referenced protein

gpmdbProteinPeptideCount(string accession, string sequence)

 input: string, accession number for the protein of interest
        string, peptide sequence in single letter code
return: string, a comma-separated tuple of the number of observations of the sequence 
                in the referenced protein, by parent ion charge state

gpmdbProteinPeptideSequences(string accession)

 input: string, accession number for the protein of interest
return: string, a comma-separated tuple of all peptides observed for the referenced protein

gpmdbProteinPeptidesCharges(string accession)

 input: string, accession number for the protein of interest
return: string, a comma-separated tuple of the number of peptide observations 
                of the referenced protein, by parent ion charge state.

gpmdbProteinPeptidesTotal(string accession)

 input: string, accession number for the protein of interest
return: string, number of observations of peptides associated with the reference protein

gpmdbProteinSequence(string accession)

 input: string, accession number for the protein of interest
return: string, the single-letter amino acid sequence of the referenced protein

gpmdbVersion()

 input: none
return: string, the version number of the SOAP interface

Interface parameters

  uri = "http://db8.thegpm.org/GPMDB"
proxy = "http://db8.thegpm.org/soap/gpmdb_soap.pl"

These parameters are used to set up a SOAP interface for programming. For example, in PERL:

my $soap = SOAP::Lite
           ->uri("http://db8.thegpm.org/GPMDB")
           ->proxy("http://db8.thegpm.org/soap/gpmdb_soap.pl");

Comments and suggestions

Any one interested in making suggestions or commenting on the ideas in this document should send them by email to Ron Beavis, rbeavis@thegpm.org.

Revision date and status

Reference name	Revision date	Document status	Stable URL
GPM-2012.06.11	2012.06.11	draft specification	n/a to draft