Line 50: | Line 50: | ||
Example: list PTM information linked to base 8925354 on Chromosome 1 | Example: list PTM information linked to base 8925354 on Chromosome 1 | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/dna/1/8925354 http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/dna/1/8925354] |
===GET /grch37/ensembl_70/dna/CHR/POS/mod=MOD => [{OBJECT1},{OBJECT2},...]=== | ===GET /grch37/ensembl_70/dna/CHR/POS/mod=MOD => [{OBJECT1},{OBJECT2},...]=== | ||
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Example: list acetylation modification information linked to base 8925354 on Chromosome 1 | Example: list acetylation modification information linked to base 8925354 on Chromosome 1 | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/dna/1/8925354/mod=Acetyl http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70b/dna/1/8925354/mod=Acetyl] |
Line 69: | Line 69: | ||
Example: list modification changes caused by the variant base A at position 8925354 on Chromosome 1 (no change) | Example: list modification changes caused by the variant base A at position 8925354 on Chromosome 1 (no change) | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/dna/1/8030998/snp=A http://openslice.fenyolab.org/rest.dna_ptm/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) | Example: list modification changes caused by the variant base C at position 8925354 on Chromosome 1 (removes modification) | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/dna/1/8030998/snp=C http://openslice.fenyolab.org/rest.dna_ptm/g2pdb/grch37/ensembl_70/dna/1/8030998/snp=C] |
==/protein/ services== | ==/protein/ services== | ||
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Example: retrieve the PTM mappings for ENSP00000234590 | Example: retrieve the PTM mappings for ENSP00000234590 | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/protein/ENSP00000234590 http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/protein/ENSP00000234590]. |
===GET /grch37/ensembl_70/protein/ACC/mod=MOD => [{OBJECT1},{OBJECT2},...]]=== | ===GET /grch37/ensembl_70/protein/ACC/mod=MOD => [{OBJECT1},{OBJECT2},...]]=== | ||
Line 96: | Line 96: | ||
Example: retrieve the ubiquitinylation mappings for ENSP00000234590 | Example: retrieve the ubiquitinylation mappings for ENSP00000234590 | ||
- | [http:// | + | [http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/protein/ENSP00000234590/mod=GlyGly http://openslice.fenyolab.org/rest.dna_ptm/grch37/ensembl_70/g2pdb/protein/ENSP00000234590/mod=GlyGly]. |
==Source code== | ==Source code== |
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 auto-curated post-translational modification acceptor sites mapped to their associated genomic codons (in chromosome coordinates) stored in a MongoDB database. The current version has mappings for the best human STY-phosphorylation, K-ubiquitinylation and K-acetylation acceptor sites found using the data available in the GPMDB system. 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 use "http://openslice.fenyolab.org/rest.dna_ptm" as their base URL. A redirect service for these methods is also available at the base URL "http://rest.thegpm.org/2/g2pdb" for the same methods. These methods are new and they in no way affect version 1 methods, which only access the main production data system GPMDB. The existing methods in version 1 (described here) will remain in place, with the same URLs and output JSON formatting.
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://openslice.fenyolab.org/rest.dna_ptm/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://openslice.fenyolab.org/rest.dna_ptm/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://openslice.fenyolab.org/rest.dna_ptm/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://openslice.fenyolab.org/rest.dna_ptm/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://openslice.fenyolab.org/rest.dna_ptm/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
These services and for creating g2pDB were implemented in Python. The code is available at ftp://ftp.thegpm.org/projects/g2pDB/human/code.
The information used to construct g2pDB can be found at ftp://ftp.thegpm.org/projects/g2pDB. The data directories are as follows:
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 | 2015.03.04 | draft specification | http://g2pdb.org/rest |