| Line 47: | Line 47: | ||
return: the total number of observations of ACCESSION | return: the total number of observations of ACCESSION | ||
| - | Example: [http://gpmdb.thegpm.org/1 | + | Example: [http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459 http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459] |
===GET /protein/description/acc=ACCESSION=== | ===GET /protein/description/acc=ACCESSION=== | ||
| Line 54: | Line 54: | ||
return: the log10(E) for the best observation of ACCESSION | return: the log10(E) for the best observation of ACCESSION | ||
| - | Example: [http://gpmdb.thegpm.org/1 | + | Example: [http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459 http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459] |
===GET /protein/modifications/acc=ACCESSION&mod=MODMASS&res=LISTOFRESIDUES&maxe=MAXIMUMEXPECTION=== | ===GET /protein/modifications/acc=ACCESSION&mod=MODMASS&res=LISTOFRESIDUES&maxe=MAXIMUMEXPECTION=== | ||
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.
The following statements refer to all methods and description given below:
Interface methods give the programmer access to information about the current state of the REST interface.
input: none return: a text description of this interface
Example: http://gpmdb.thegpm.org/1/interface/help.
input: none return: the version number of the REST interface
Example: http://gpmdb.thegpm.org/1/interface/version.
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.
input: accession number for the protein of interest return: the log10(E) for the best observation of ACCESSION
Example: http://gpmdb.thegpm.org/1/protein/best_e/acc=ENSMUSP00000026459.
input: accession number for the protein of interest return: the total number of observations of ACCESSION
Example: http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: the log10(E) for the best observation of ACCESSION
Example: http://gpmdb.thegpm.org/1/protein/count/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: 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: http://gpmdb.thegpm.org/1/protein/count/acc=ENSMUSP00000026459
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: http://gpmdb.thegpm.org/1/peptide_count/acc=ENSMUSP00000026459&seq=
input: accession number for the protein of interest return: a comma-separated tuple of all peptides observed for ACCESSION
Example: http://gpmdb.thegpm.org/1/protein/sequences/acc=ENSMUSP00000026459
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: http://gpmdb.thegpm.org/1/protein/peptides_z/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: number of observations of peptides associated with the reference protein
Example: http://gpmdb.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: the single-letter amino acid sequence of the referenced protein
Example: http://gpmdb.thegpm.org/1/protein/sequence/acc=ENSMUSP00000026459
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 | 2012.06.11 | draft specification | http://wiki.thegpm.org/wiki/GPMDB_REST |