GPMDB REST

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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 ended on September 10, 2012. This version (1.0) of the interface is complete and adopted.

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.

Contents

Conventions

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

  1. all GETs are made to the base URL "http://rest.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 return values are in JSON notation (RFC 4627) as either an ARRAY or OBJECT.

/interface/ services

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

GET /interface/help => [ARRAY]

 input: none
return: [ARRAY - "string"] a text description of the current REST interface

Example: find help information through the interface

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

GET /interface/version => [ARRAY]

 input: none
return: [ARRAY - "string"] the version number of the REST interface

Example: find the current REST interface version number

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

/model/ services

Model services give access to information about a calculated model for a particular data set.

GET /model/metadata/gpm=GPM => {OBJECT}

 input: a GPM model accession number (GPMddddddddddd)
return: {OBJECT - "string":{"string":"string"}}} objects containing text descriptions of how, when and what was modeled

Example: list sample, analytical parameters and result values for the data set GPM10100159682

http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682

GET /model/proteins/gpm=GPM => [ARRAY]

 input: a GPM model accession number (GPMddddddddddd)
return: [ARRAY - "string"} accession numbers for primary proteins in the model

Example: list proteins found in GPM10100159682

http://rest.thegpm.org/1/model/proteins/gpm=GPM10100159682

GET /model/protein_modifications/gpm=GPM&acc=ACC => [ARRAY]

 input: a GPM model accession number (GPMddddddddddd)
        accession number for the protein of interest (ACC)
return: [ARRAY - "string"] all residue modifications assigned to ACC, as specified in RFC GPM-2011.12.14 §2.3.

Example: list residue modifications found in GPM10100159682 for the protein ENSP00000324804

http://rest.thegpm.org/1/model/protein_modifications/gpm=GPM10100159682&acc=ENSP00000324804

GET /model/protein_peptides/gpm=GPM&acc=ACC => {OBJECT}

 input: a GPM model accession number (GPMddddddddddd)
        accession number for the protein of interest (ACC)
return: {OBJECT - "string":int} peptide sequence : ×observed for peptide sequences assigned to ACC

Example: list peptides found in GPM10100159682 for the protein ENSP00000324804

http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804

GET /model/protein_polymorphisms/gpm=GPM&acc=ACC => [ARRAY]

 input: a GPM model accession number (GPMddddddddddd)
        accession number for the protein of interest (ACC)
return: [ARRAY - "string"] all residue polymorphisms assigned to ACC, as specified in RFC GPM-2011.12.14 §2.5.

Example: list residue polymorphisms found in GPM10100159682 for the protein ENSP00000331514

http://rest.thegpm.org/1/model/protein_polymorphisms/gpm=GPM10100159682&acc=ENSP00000331514

GET /model/protein_sequence/gpm=GPM&acc=ACC => [ARRAY]

 input: a GPM model accession number (GPMddddddddddd)
        accession number for the protein of interest (ACC)
return: [ARRAY - "string"] the sequence of protein ACC identified in the model.

Example: get the protein sequence of ENSP00000331514 found in GPM10100159682

http://rest.thegpm.org/1/model/protein_sequence/gpm=GPM10100159682&acc=ENSP00000331514


/peptide/ services

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.

GET /peptide/accessions/seq=SEQUENCE => {OBJECT}

 input: peptide sequence of interest
return: {OBJECT - "string":int} of {accession number:number of observations} pairs

Example: retrieve the accession numbers and observations of SPSSVEPVADMLMGLFFR

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

GET /peptide/count/seq=SEQUENCE => [ARRAY]

 input: peptide sequence of interest
return: [ARRAY - int] the total number of observations

Example: retrieve the total observations of SPSSVEPVADMLMGLFFR

http://rest.thegpm.org/1/peptide/count/seq=SPSSVEPVADMLMGLFFR.

GET /peptide/count_z/seq=SEQUENCE => {OBJECT}

 input: peptide sequence of interest
return: {OBJECT - "string":int} of {parent ion charge:number of observations} pairs

Example: retrieve the total observations of SPSSVEPVADMLMGLFFR by parent ion charge

http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR.

/protein/ services

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.

GET /protein/best_e/acc=ACCESSION => [ARRAY]

 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://rest.thegpm.org/1/protein/best_e/acc=ENSMUSP00000026459.

GET /protein/count/acc=ACCESSION => [ARRAY]

 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://rest.thegpm.org/1/protein/count/acc=ENSMUSP00000026459

GET /protein/description/acc=ACCESSION => [ARRAY]

 input: accession number for the protein of interest
return: [ARRAY - "string"] text description of the protein ACCESSION

Example: retrieve a text description of ENSMUSP00000026459

http://rest.thegpm.org/1/protein/description/acc=ENSMUSP00000026459

GET /protein/evidence/acc=ACCESSION => {OBJECT}

 input: accession number for the protein of interest
return: {OBJECT - "string":"string"} evidence code information about status of the protein

Example: retrieve the evidence codes for ENSMUSP00000026459

http://rest.thegpm.org/1/protein/evidence/acc=ENSMUSP00000026459

GET /protein/keyword/key=KEYWORD(&filter=FILTER) => {OBJECT}

 input: a keyword in a protein description
        a string to filter the accession numbers (default = "human")
return: {OBJECT - "string":"string"} information about the proteins matching the keyword

Example: list human proteins with the keyword "actinin"

http://rest.thegpm.org/1/protein/keyword/key=actinin

GET /protein/modifications/acc=ACCESSION&mod=MODMASS&res=LIST&maxe=MAXEXPECT => {OBJECT}

 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: {OBJECT - "string":int} of {modified site:number of observations} for ACCESSION

Example: retrieve the phosphorylated S, T or Y residues for YKL112W

http://rest.thegpm.org/1/protein/modifications/acc=YKL112W&mod=80&res=STY&maxe=-2.0

Example: retrieve all acetylated residues for ENSP00000281111

http://rest.thegpm.org/1/protein/modifications/acc=ENSP00000281111&mod=42&res=&maxe=-2.0

GET /protein/omega/acc=ACCESSION&seq=SEQUENCE(,SEQUENCE2,...) => {OBJECT}

 input: accession number for the protein of interest
        comma separated list of peptide sequences in single letter code
return: {OBJECT - "string":[{"string":[float,float,float,float]}]}
        {"ACCESSION":[{"SEQUENCE":[ω(z=1),ω(z=2),ω(z=3),ω(z=4)]}]}
 added: 2013-05-05

Example: retrieve the omega peptide frequencies for LDATTVLSR and AAQASAAPK observed for ENSMUSP00000026459

http://rest.thegpm.org/1/protein/omega/acc=ENSMUSP00000026459&seq=LDATTVLSR,AAQASAAPK

GET /protein/peptide_count/acc=ACCESSION&seq=SEQUENCE => {OBJECT}

 input: accession number for the protein of interest
        peptide sequence in single letter code
return: {OBJECT - "string":int} of {parent ion charge:number of observations} of SEQUENCE in ACCESSION

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

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

GET /protein/peptide_sequences/acc=ACCESSION => [ARRAY]

 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://rest.thegpm.org/1/protein/peptide_sequences/acc=ENSMUSP00000026459

GET /protein/peptides_z/acc=ACCESSION => {OBJECT}

 input: accession number for the protein of interest
return: {OBJECT - "string":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://rest.thegpm.org/1/protein/peptides_z/acc=ENSMUSP00000026459

GET /protein/peptides_total/acc=ACCESSION => [ARRAY]

 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://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459

GET /protein/polymorphisms/acc=ACCESSION => [ARRAY of OBJECT "string":int]

 input: accession number for the protein of interest
return: [ARRAY - OBJECT "string":int] an array of observed polymorphisms and the number of observations for the protein ACCESSION

Example: retrieve a summary of amino acid polymorphisms found for ENSMUSP00000026459

http://rest.thegpm.org/1/protein/polymorphisms/acc=ENSMUSP00000026459

GET /protein/sequence/acc=ACCESSION => [ARRAY]

 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://rest.thegpm.org/1/protein/sequence/acc=ENSMUSP00000026459

Source code

These services are being implemented in PERL, the language that is used to provide 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:

  1. rest.pl - provides an interface between Apache CGI calls and the database layer;
  2. gpmdb_rest.pl - a PERL module for most requests;
  3. gpm_rest.pl - a PERL module for "model" requests; and
  4. rest_client.pl - a demonstration command-line client that provides examples of how to use the services with PERL.

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-2012.6.11 2013.05.05 final specification http://icex.ca/ice.0.m
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