GPMDB REST

Revision as of 15:58, 13 June 2012

This document is a request for comment on a proposed new REST 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 REST (REpresentational State Transfer) 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 an network-aware application.

Conventions

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

1. all GETs are made to the base URL "http://gpmdb.thegpm.org/1";
2. all protein and peptide sequences are expressed in single letter code;
3. protein accession numbers use the same format as normally used in GPMDB; and
4. all "tuples" are returned as comma-separated text strings.

/interface/ methods

Interface methods give the programmer access to information about the current state of the REST interface.

GET /interface/help

 input: none
return: a text description of the current REST interface

Example: find help information through the interface

http://gpmdb.thegpm.org/1/interface/help

GET /interface/version

 input: none
return: the version number of the REST interface

Example: find the current REST interface version number

http://gpmdb.thegpm.org/1/interface/version

/peptide/ methods

Peptide methods give the programmer access of information about the peptides currently stored in GPMDB. All peptide methods require an appropriate peptide amino acid sequence to identify the target peptide.

GET /peptide/accessions/seq=SEQUENCE

 input: sequence of the protein of interest
return: a tuple of (accession number:number of observation) pairs

Example: retrieve the accession numbers and observations of SPSSVEPVADMLMGLFFR

http://gpmdb.thegpm.org/1/peptide/accessions/seq=SPSSVEPVADMLMGLFFR.

/protein/ methods

Protein methods give the programmer access of information about the proteins currently stored in GPMDB. All protein methods require an appropriate protein accession number to identify the protein sequence being queried.

GET /protein/best_e/acc=ACCESSION

 input: accession number for the protein of interest
return: 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.

GET /protein/count/acc=ACCESSION

 input: accession number for the protein of interest
return: 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

GET /protein/description/acc=ACCESSION

 input: accession number for the protein of interest
return: 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

GET /protein/modifications/acc=ACCESSION&mod=MODMASS&res=LISTOFRESIDUES&maxe=MAXIMUMEXPECTION

 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: a tuple of modificatied site in ACCESSION in the format pos1:num1,pos2:num2, ...
        where: pos1 is the protein coordinate of the first modified site; and
               num1 is the number of times modified pos1 has been observed

Example: retrieve the phosphorylated S, T or Y residues for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/modifications/acc=ENSMUSP00000026459&mod=80&res=STY&maxe=-2.0

Example: retrieve all acetylated residues for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/modifications/acc=ENSMUSP00000026459&mod=42&res=&maxe=-2.0

GET /protein/peptide_count/acc=ACCESSION&seq=SEQUENCE

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

Example: retrieve the number of times LDATTVLSR was observed for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/peptide_count/acc=ENSMUSP00000026459&seq=LDATTVLSR

GET /protein/peptide_sequences/acc=ACCESSION

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

Example: retrieve the peptide sequences observed for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/peptide_sequences/acc=ENSMUSP00000026459

GET /protein/peptides_z/acc=ACCESSION

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

Example: retrieve the number of peptide observations by parent ion charge state for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/peptides_z/acc=ENSMUSP00000026459

GET /protein/peptides_total/acc=ACCESSION

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

Example: retrieve the total number of peptide observationsfor ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459

GET /protein/sequence/acc=ACCESSION

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

Example: retrieve the protein sequence for ENSMUSP00000026459

http://gpmdb.thegpm.org/1/protein/sequence/acc=ENSMUSP00000026459

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.

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