Line 7: | Line 7: | ||
The following statements refer to all methods and description given below: | The following statements refer to all methods and description given below: | ||
- | #all GETs are made to the base URL "http://gpmdb.thegpm.org"; | + | #all GETs are made to the base URL "http://gpmdb.thegpm.org/1"; |
#all protein and peptide sequences are expressed in [[Amino acid symbols|single letter code]]; | #all protein and peptide sequences are expressed in [[Amino acid symbols|single letter code]]; | ||
#protein accession numbers use the same format as normally used in GPMDB; and | #protein accession numbers use the same format as normally used in GPMDB; and | ||
#all "tuples" are returned as comma-separated text strings. | #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. | Interface methods give the programmer access to information about the current state of the REST interface. | ||
- | ===GET | + | ===GET /interface/help=== |
input: none | input: none | ||
return: a text description of this interface | return: a text description of this interface | ||
- | ===GET | + | ===GET /interface/version=== |
input: none | input: none | ||
- | return: the version number of the | + | return: the version number of the REST interface |
- | == | + | ==/protein/ methods== |
Protein methods give the programmer access of information about the proteins currently stored in GPMDB. All | Protein methods give the programmer access of information about the proteins currently stored in GPMDB. All | ||
Line 32: | Line 32: | ||
queried. | queried. | ||
- | ===GET | + | ===GET /protein/best_e/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
return: the log10(E) for the best observation of ACCESSION | return: the log10(E) for the best observation of ACCESSION | ||
- | ===GET | + | ===GET /protein/count/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
return: the total number of observations of ACCESSION | return: the total number of observations of ACCESSION | ||
- | ===GET | + | ===GET /protein/description/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
return: the log10(E) for the best observation of ACCESSION | return: the log10(E) for the best observation of ACCESSION | ||
- | ===GET | + | ===GET /protein/modifications/acc=ACCESSION&mod=MODMASS&res=LISTOFRESIDUES&maxe=MAXIMUMEXPECTION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
Line 57: | Line 57: | ||
num1 is the number of times modified pos1 has been observed | num1 is the number of times modified pos1 has been observed | ||
- | ===GET | + | ===GET /protein/peptide/count/acc=ACCESSION&seq=SEQUENCE=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
Line 64: | Line 64: | ||
in ACCESSION, by parent ion charge state | in ACCESSION, by parent ion charge state | ||
- | ===GET | + | ===GET /protein/peptide/sequences/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
return: a comma-separated tuple of all peptides observed for ACCESSION | return: a comma-separated tuple of all peptides observed for ACCESSION | ||
- | ===GET | + | ===GET /protein/peptides_z/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
Line 75: | Line 75: | ||
of ACCESSION, by parent ion charge state. | of ACCESSION, by parent ion charge state. | ||
- | ===GET | + | ===GET /protein/peptides_total/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
return: number of observations of peptides associated with the reference protein | return: number of observations of peptides associated with the reference protein | ||
- | ===GET | + | ===GET /protein/sequence/acc=ACCESSION=== |
input: accession number for the protein of interest | input: accession number for the protein of interest |
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
input: none return: the version number of the REST interface
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
input: accession number for the protein of interest return: the total number of observations of ACCESSION
input: accession number for the protein of interest return: the log10(E) for the best observation of ACCESSION
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
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
input: accession number for the protein of interest return: a comma-separated tuple of all peptides observed for 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.
input: accession number for the protein of interest return: number of observations of peptides associated with the reference protein
input: accession number for the protein of interest return: the single-letter amino acid sequence of the referenced protein
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 | n/a to draft |