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- | 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 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. | + | 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 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. The details of the construction of the database and REST interface have been published ([https://doi.org/10.1021/acs.jproteome.5b01018 doi:10.1021/acs.jproteome.5b01018]). |
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. | 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 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. The details of the construction of the database and REST interface have been published (doi:10.1021/acs.jproteome.5b01018).
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 the following base URLs:
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:
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_70/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 linked to the canonical BASE
at the given position, followed by 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)
Note: First and second ARRAYs are identical due to no change as a result of variant base
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)
Note: Second ARRAY is empty due to removal of modification as a result of the variant base
http://openslice.fenyolab.org/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:
A preliminary web site that shows the contents of g2pDB for a particular gene, transcript or protein is 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 | 2015.10.26 | draft specification | http://g2pdb.org/rest |