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- | [[File:Rest_gpmdb.png|center|GPMDB REST API | + | [[File:Rest_gpmdb.png|center|GPMDB REST API channel 2]] |
- | The purpose of this document is to define a set of straightforward [http://en.wikipedia.org/wiki/Representational_state_transfer REST (REpresentational State Transfer)] services to commonly required information based on the data in g2pDB | + | The purpose of this document is to define a set of straightforward [http://en.wikipedia.org/wiki/Representational_state_transfer REST (REpresentational State Transfer)] services to commonly required information based on the data in the novel database g2pDB. g2pDB is a collection of post-translational modification acceptor site mappings to the human genome stored in a MongoDB database. 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. |
- | The methods described here belong the | + | The methods described here belong the channel 2 (i.e., they use http://rest.thegpm.org/2 as there base URL). These methods are new and they are not meant to be a replacement for version 1, which accesses GPMDB. The existing methods in version 1 (described [http://wiki.thegpm.org/wiki/GPMDB_REST here]) will remain in place, with the |
same URLs and output JSON formatting. | same URLs and output JSON formatting. | ||
+ | |||
+ | Note: these methods are made available through rest.thegpm.org for convenience. The methods listed here are redirects to the original site for these methods, which uses the base URL "http://openslice.fenyolab.org/rest.dna_ptm" for these methods. | ||
==Conventions== | ==Conventions== | ||
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#rest.pl - provides an interface between Apache CGI calls and the database layer; | #rest.pl - provides an interface between Apache CGI calls and the database layer; | ||
#g2pdb_rest.pl - a PERL module for most requests; | #g2pdb_rest.pl - a PERL module for most requests; | ||
+ | |||
+ | ==Data sources== | ||
+ | The information used to construct g2pDB can be found at [ftp://ftp.thegpm.org/projects/g2pDB ftp://ftp.thegpm.org/projects/g2pDB]. The following data directories are current available: | ||
+ | |||
+ | #[ftp://ftp.thegpm.org/projects/g2pDB/human/ptm_listings human/ptm_listings] - contains the files mapping the three PTM types in proteome and genome coordinates; and | ||
+ | #[ftp://ftp.thegpm.org/projects/g2pDB/human/gff human/gff] human/gff] - contains the corresponding GFF genome feature annotation files. | ||
==Comments and suggestions== | ==Comments and suggestions== |
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 the novel database g2pDB. g2pDB is a collection of post-translational modification acceptor site mappings to the human genome stored in a MongoDB database. 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.
The methods described here belong the channel 2 (i.e., they use http://rest.thegpm.org/2 as there base URL). These methods are new and they are not meant to be a replacement for version 1, which accesses GPMDB. The existing methods in version 1 (described here) will remain in place, with the same URLs and output JSON formatting.
Note: these methods are made available through rest.thegpm.org for convenience. The methods listed here are redirects to the original site for these methods, which uses the base URL "http://openslice.fenyolab.org/rest.dna_ptm" for these methods.
Contents |
The following statements refer to all methods and description given below:
Interface services give the programmer access to information about the current state of the REST interface.
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/interface/help
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 give access to PTM-linked information about particular genomic locations.
input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome return: ARRAY of 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/grch37/ensembl_70/dna/1/8925354
input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome, MOD = modification return: ARRAY of 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/g2pd/grch37/ensembl_70b/dna/1/8925354/mod=Acetyl
input: CHR = human chromosome 1-22, MT, X, or Y), POS = base position on chromosome, BASE = variant base return: ARRAY of 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 (no change)
http://rest.thegpm.org/2/g2pdb/grch37/ensembl_70/dna/1/8030998/snp=A
Example: list modification changes caused by the variant base C at position 8925354 on Chromosome 1 (removes modification)
http://rest.thegpm.org/2/g2pdb/grch37/ensembl_70/dna/1/8030998/snp=C
Peptide services access to all of the genomic mapping information associated with PTMs for a particular protein.
input: ACC = ENSEMBL protein accession number return: ARRAY of PTM mapping information objects
Example: retrieve the PTM mappings for ENSP00000234590
http://rest.thegpm.org/2/g2pdb/grch37/ensembl_70/protein/ENSP00000234590.
input: ACC = ENSEMBL protein accession number, MOD = modification return: ARRAY of PTM mapping information objects for MOD only
Example: retrieve the ubiquitinylation mappings for ENSP00000234590
http://rest.thegpm.org/2/grch37/ensembl_70/g2pdb/protein/ENSP00000234590/mod=GlyGly.
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:
The information used to construct g2pDB can be found at ftp://ftp.thegpm.org/projects/g2pDB. The following data directories are current available:
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-2014.11.27 | 2014.11.27 | draft specification | http://g2pdb.org/rest |