Line 17: | Line 17: | ||
#all bases are expressed in single letter code (A, C, T, G); | #all bases are expressed in single letter code (A, C, T, G); | ||
#modifications allowed are "Phospho", "Acetyl" or "GlyGly" (ubiquitinyl); | #modifications allowed are "Phospho", "Acetyl" or "GlyGly" (ubiquitinyl); | ||
- | #genome coordinates refer to Genome Reference Consortium Human genome | + | #genome coordinates refer to Genome Reference Consortium Human genome builds (GRCh37 and GRCh38); |
- | #protein accession numbers use ENSEMBL | + | #protein accession numbers use ENSEMBL numbers for the appropriate build; |
#all return values are in [http://en.wikipedia.org/wiki/JSON JSON] notation ([http://www.ietf.org/rfc/rfc4627.txt RFC 4627]) as either an ARRAY or OBJECT; and | #all return values are in [http://en.wikipedia.org/wiki/JSON JSON] notation ([http://www.ietf.org/rfc/rfc4627.txt RFC 4627]) as either an ARRAY or OBJECT; and | ||
#protein post-translational modifications currently covered in g2pDB are S,T & Y phosphorylation (MOD=Phospho), lysine ubiquitinylation (MOD=GlyGly) and lysine acetylation (MOD=Acetyl). | #protein post-translational modifications currently covered in g2pDB are S,T & Y phosphorylation (MOD=Phospho), lysine ubiquitinylation (MOD=GlyGly) and lysine acetylation (MOD=Acetyl). | ||
+ | |||
+ | ==Available sequence builds== | ||
+ | |||
+ | The protein and genome sequence dependent information requires the specification of particular ENSEMBL and GRCh sequence assemblies. The assemblies currently available are as follows: | ||
+ | |||
+ | # /grch37/ensembl_70; and | ||
+ | # /grch38/ensembl_76. | ||
+ | |||
+ | The /grch38/ensembl_78 build will be made available on April 15, 2015. | ||
==/interface/ services== | ==/interface/ services== |
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 most reproducible 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 services are available to anyone involved in computational, biological or biomedical research. We, the providers, retain the right to block access by any user or system that we feel is using the information or infrastructure inappropriately.
The methods described here use "http://openslice.fenyolab.org/g2pdb" 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.
Anyone interested in direct access to the production database of experimental results that was used to construct g2pDB should look at the GPMDB REST API.
Contents |
The following statements refer to all methods and description given below:
The protein and genome sequence dependent information requires the specification of particular ENSEMBL and GRCh sequence assemblies. The assemblies currently available are as follows:
The /grch38/ensembl_78 build will be made available on April 15, 2015.
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://openslice.fenyolab.org/g2pdb/grch37/ensembl_70/
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/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://openslice.fenyolab.org/g2pdb/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/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://openslice.fenyolab.org/g2pdb/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/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://openslice.fenyolab.org/g2pdb/grch37/ensembl_70/g2pdb/protein/ENSP00000234590/mod=GlyGly.
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 |