G2PDB REST

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Revision as of 22:09, 26 November 2014

The purpose of this document is to define a set of straightforward REST (REpresentational State Transfer) services to commonly required information based on the data in g2pDB, a collection of post-translational modification acceptor site mappings to the human genome. 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 1 Conventions 2 /interface/ services 2.1 GET /help => [ARRAY] 2.2 GET /interface/version => [ARRAY] 3 /dna/ services 3.1 GET /dna/CHR/POS => {OBJECT} 3.2 GET /dna/CHR/POS/mod=MOD => [ARRAY] 3.3 GET /dna/CHR/POS/snp=BASE => {OBJECT} 4 /protein/ services 4.1 GET /protein/ACC => {OBJECT} 4.2 GET /protein/ACC/mod=MOD => [ARRAY] 5 Source code 6 Comments and suggestions 7 Revision date and status

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/2";
2. all bases are expressed in single letter code (A, C, T, G);
3. modifications allowed are "Phospho", "Acetyl" or "GlyGly" (ubiquitinyl);
4. protein accession numbers use ENSEMBL 70; and
5. 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 /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/2/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/2/interface/version

/dna/ services

Dna services give access to PTM-linked information about particular genomic locations.

GET /dna/CHR/POS => {OBJECT}

 input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome 
return: {OBJECT} objects containing text description of all modification linked to the specified base

Example: list PTM information linked to base 8925354 on Chromosome 1

http://rest.thegpm.org/2/g2pdb/dna/1/8925354

GET /dna/CHR/POS/mod=MOD => [ARRAY]

 input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome, MOD = modification
return: {OBJECT} objects containing text description of the specified modification linked to the specified base

Example: list acetylation modification information linked to base 8925354 on Chromosome 1

http://rest.thegpm.org/2/g2pdb/dna/1/8925354/mod=Acetyl

GET /dna/CHR/POS/snp=BASE => {OBJECT}

 input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome, BASE = variant base 
return: {OBJECT} objects containing text description of modifications changed by the variant BASE

Example: list modification changes caused by the variant base A at position 8925354 on Chromosome 1

http://rest.thegpm.org/2/g2pdb/dna/1/8030998/snp=A

/protein/ services

Peptide services access to all of the genomic mapping information associated with PTMs for a particular protein.

GET /protein/ACC => {OBJECT}

 input: ACC = ENSEMBL protein accession number
return: {OBJECT} of PTM mapping information

Example: retrieve the PTM mappings for ENSP00000234590

http://rest.thegpm.org/2/g2pdb/protein/ENSP00000234590.

GET /protein/ACC/mod=MOD => [ARRAY]

 input: ACC = ENSEMBL protein accession number, MOD = modification
return: {OBJECT} of PTM mapping information for MOD only

Example: retrieve the ubiquitinylation mappings for ENSP00000234590

http://rest.thegpm.org/2/g2pdb/protein/ENSP00000234590/mod=GlyGly.

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/g2p_rest. The files currently available are as follows:

1. rest.pl - provides an interface between Apache CGI calls and the database layer;
2. g2pdb_rest.pl - a PERL module for most requests;

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-2014.11.26	2014.11.26	final specification	http://wiki.thegpm.org/wiki/G2PDB_REST