This document is a request for comment on a set of proposed new REST services 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 set of straightforward REST (REpresentational State Transfer) services to commonly required information based on the data in GPMDB. These services 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 network-aware application.
The following statements refer to all methods and description given below:
Interface services give the programmer access to information about the current state of the REST interface.
input: none return: [ARRAY - string] a text description of the current REST interface
Example: find help information through the interface
http://gpmdb.thegpm.org/1/interface/help
input: none return: [ARRAY - string] the version number of the REST interface
Example: find the current REST interface version number
http://gpmdb.thegpm.org/1/interface/version
Peptide services give the programmer access of information about the peptides currently stored in GPMDB. All peptide services require an appropriate peptide amino acid sequence to identify the target peptide.
input: peptide sequence of interest
return: {HASH - string:int} of {accession number:number of observations} pairs
Example: retrieve the accession numbers and observations of SPSSVEPVADMLMGLFFR
http://gpmdb.thegpm.org/1/peptide/accessions/seq=SPSSVEPVADMLMGLFFR.
input: peptide sequence of interest return: [ARRAY - int] the total number of observations
Example: retrieve the total observations of SPSSVEPVADMLMGLFFR
http://gpmdb.thegpm.org/1/peptide/count/seq=SPSSVEPVADMLMGLFFR.
input: peptide sequence of interest
return: {HASH - int:int} of {parent ion charge:number of observations} pairs
Example: retrieve the total observations of SPSSVEPVADMLMGLFFR by parent ion charge
http://gpmdb.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR.
Protein services give the programmer access of information about the proteins currently stored in GPMDB. All protein services require an appropriate protein accession number to identify the protein sequence being queried.
input: accession number for the protein of interest return: [ARRAY - float] the log10(E) for the best observation of ACCESSION
Example: retrieve the lowest E value for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/best_e/acc=ENSMUSP00000026459.
input: accession number for the protein of interest return: [ARRAY - int] the total number of observations of ACCESSION
Example: retrieve the number of time ENSMUSP00000026459 has been observed
http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - float] the log10(E) for the best observation of ACCESSION
Example: retrieve a text description of ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/description/acc=ENSMUSP00000026459
input: accession number for the protein of interest
mass (Da) of the modification, e.g., phosphorylation = 80
list of residue types that may be modified, e.g., phosphorylation = STY
log10(E) of the maximum allowed expectation value for a valid observation
return: {HASH - int:int} of {modified site:number of observations} for ACCESSION
Example: retrieve the phosphorylated S, T or Y residues for YKL112W
http://gpmdb.thegpm.org/1/protein/modifications/acc=YKL112W&mod=80&res=STY&maxe=-2.0
Example: retrieve all acetylated residues for ENSP00000281111
http://gpmdb.thegpm.org/1/protein/modifications/acc=ENSP00000281111&mod=42&res=&maxe=-2.0
input: accession number for the protein of interest
peptide sequence in single letter code
return: {HASH - int:int} of {parent ion charge:number of observations} of SEQUENCE in ACCESSION
Example: retrieve the number of times LDATTVLSR was observed for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/peptide_count/acc=ENSMUSP00000026459&seq=LDATTVLSR
input: accession number for the protein of interest return: [ARRAY - string] of all peptides observed for ACCESSION
Example: retrieve the peptide sequences observed for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/peptide_sequences/acc=ENSMUSP00000026459
input: accession number for the protein of interest
return: {HASH - int:int} of the {parent ion charge:number of peptide observations} for ACCESSION
Example: retrieve the number of peptide observations by parent ion charge state for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/peptides_z/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - int] number of observations of peptides associated with ACCESSION
Example: retrieve the total number of peptide observations for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - string] the amino acid sequence of ACCESSION
Example: retrieve the protein sequence for ENSMUSP00000026459
http://gpmdb.thegpm.org/1/protein/sequence/acc=ENSMUSP00000026459
These services are being implemented in PERL, which provides most of the web page creation logic for the GPMDB system. The code is available at ftp://ftp.thegpm.org/repos/gpmdb_rest. The files currently available are as follows:
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.
| Reference name | Revision date | Document status | Stable URL |
|---|---|---|---|
| GPM-2012.06.11 | 2012.06.13 | draft specification | http://wiki.thegpm.org/wiki/GPMDB_REST |