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+ | [[File:Rest_gpmdb.png|center|GPMDB REST API v.1]] | ||
This document is a request for comment on a set of proposed new REST services for GPMDB. The RFC process began on June 11, 2012 and ended on September 10, 2012. This version (1.0) of the interface is complete and adopted. | This document is a request for comment on a set of proposed new REST services for GPMDB. The RFC process began on June 11, 2012 and ended on September 10, 2012. This version (1.0) of the interface is complete and adopted. | ||
- | + | These 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 the RFC 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 GPMDB. 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 purpose of the RFC 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 GPMDB. 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. | ||
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[http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682 http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682] | [http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682 http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682] | ||
+ | |||
+ | ===GET /db/metadata/gpm=GPM => {OBJECT}=== | ||
+ | |||
+ | input: a GPM model accession number (GPMddddddddddd) | ||
+ | return: {OBJECT - "string":"string"} metadata abstract text stored in GPMDB | ||
+ | |||
+ | Example: list metadata abstract text information for the data set GPM10100159682 | ||
+ | |||
+ | [http://rest.thegpm.org/1/db/metadata/gpm=GPM10100159682 http://rest.thegpm.org/1/db/metadata/gpm=GPM10100159682] | ||
===GET /model/proteins/gpm=GPM => [ARRAY]=== | ===GET /model/proteins/gpm=GPM => [ARRAY]=== | ||
Line 78: | Line 88: | ||
[http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804 http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804] | [http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804 http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804] | ||
- | ===GET /model/ | + | ===GET /model/protein_savs/gpm=GPM&acc=ACC => [ARRAY]=== |
input: a GPM model accession number (GPMddddddddddd) | input: a GPM model accession number (GPMddddddddddd) | ||
accession number for the protein of interest (ACC) | accession number for the protein of interest (ACC) | ||
- | return: [ARRAY - "string"] all | + | return: [ARRAY - "string"] all single amino acid variants (SAVs) assigned to ACC, as specified in [http://wiki.thegpm.org/wiki/Nomenclature_for_the_description_of_protein_sequence_modifications#.28:p..29_Specifying_amino_acid_residue_changes_caused_by_nucleic_acid_sequence_variants RFC GPM-2011.12.14 §2.5]. |
+ | NOTE: this method was originally "protein_polymorphisms", which still functions as a URL. | ||
- | Example: list | + | Example: list SAVs found in GPM10100159682 for the protein ENSP00000331514 |
- | [http://rest.thegpm.org/1/model/ | + | [http://rest.thegpm.org/1/model/protein_savs/gpm=GPM10100159682&acc=ENSP00000331514 http://rest.thegpm.org/1/model/protein_savs/gpm=GPM10100159682&acc=ENSP00000331514] |
===GET /model/protein_sequence/gpm=GPM&acc=ACC => [ARRAY]=== | ===GET /model/protein_sequence/gpm=GPM&acc=ACC => [ARRAY]=== | ||
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[http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR]. | [http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR]. | ||
+ | |||
+ | ===GET /peptide/xx/acc=ACCESSION&pos=1-N&w=n => {OBJECT}=== | ||
+ | |||
+ | input: peptide sequence of interest | ||
+ | return: {OBJECT - "string":int} of {protein coordinate:number of observations} pairs for select modifications | ||
+ | |||
+ | "xx" can be any of the following: | ||
+ | # "pf"- S/T/Y phosphorylation; | ||
+ | # "af"- K acetylation; | ||
+ | # "uf"- K ubiquitination; | ||
+ | # "di"- R dimethylation; | ||
+ | # "ox"- P/K oxidation; | ||
+ | # "su"- K sumoylation; | ||
+ | # "nq"- N/Q deamidation; | ||
+ | # "ol"- S/T O-linked glycosylation; | ||
+ | # "ct"- R citrulination; | ||
+ | # "sc"- K succinylation; | ||
+ | # "qc"- Q cyclization; and | ||
+ | # "gl"- E gamma-carboxylation. | ||
+ | |||
+ | Example: retrieve the total observations of phosphorylation for ENSP00000384660 | ||
+ | |||
+ | [http://gpmdb.thegpm.org/1/peptide/pf/acc=ENSP00000384660&pos=1-706&w=n http://gpmdb.thegpm.org/1/peptide/pf/acc=ENSP00000384660&pos=1-706&w=n]. | ||
==/protein/ services== | ==/protein/ services== | ||
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[http://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459 http://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459] | [http://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459 http://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459] | ||
- | ===GET /protein/ | + | ===GET /protein/savs/acc=ACCESSION => [ARRAY of OBJECT "string":int]=== |
input: accession number for the protein of interest | input: accession number for the protein of interest | ||
- | return: [ARRAY - OBJECT "string":int] an array of observed | + | return: [ARRAY - OBJECT "string":int] an array of observed single amino acid variants (SAVs) and the number of observations for the protein ACCESSION |
+ | NOTE: this method was originally "/protein/polymorphisms", which still functions as a URL. | ||
- | Example: retrieve a summary of | + | Example: retrieve a summary of SAVs found for ENSMUSP00000026459 |
- | [http://rest.thegpm.org/1/protein/ | + | [http://rest.thegpm.org/1/protein/savs/acc=ENSMUSP00000026459 http://rest.thegpm.org/1/protein/savs/acc=ENSMUSP00000026459] |
===GET /protein/sequence/acc=ACCESSION => [ARRAY]=== | ===GET /protein/sequence/acc=ACCESSION => [ARRAY]=== | ||
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==Comments and suggestions== | ==Comments and suggestions== | ||
Any one interested in making suggestions or commenting on the ideas in this document should send them by email to [mailto:rbeavis@thegpm.org Ron Beavis, rbeavis@thegpm.org]. | Any one interested in making suggestions or commenting on the ideas in this document should send them by email to [mailto:rbeavis@thegpm.org Ron Beavis, rbeavis@thegpm.org]. | ||
+ | |||
+ | ==Manuscripts and Presentations== | ||
+ | A manuscript describing this API has been published: [http://www.ncbi.nlm.nih.gov/pubmed/25697819 The GPMDB REST Interface], David Fenyö; Ronald C. Beavis, Bioinformatics 2015; doi: 10.1093/bioinformatics/btv107. | ||
+ | |||
+ | A poster presenting the API was shown at the US HUPO Conference (2015) in Tempe. You can download a PDF of the presentation [http://www.thegpm.org/present/rest_tempe.pdf here]. | ||
==Revision date and status== | ==Revision date and status== | ||
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|- align="center" | |- align="center" | ||
| GPM-2012.6.11 | | GPM-2012.6.11 | ||
- | | | + | | 2015.02.19 |
| final specification | | final specification | ||
| [http://icex.ca/ice.0.m http://icex.ca/ice.0.m] | | [http://icex.ca/ice.0.m http://icex.ca/ice.0.m] | ||
|} | |} |
This document is a request for comment on a set of proposed new REST services for GPMDB. The RFC process began on June 11, 2012 and ended on September 10, 2012. This version (1.0) of the interface is complete and adopted.
These 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 the RFC is to define a set of straightforward REST (REpresentational State Transfer) services to commonly required information based on the data in GPMDB. 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 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/1/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/1/interface/version
Model services give access to information about a calculated model for a particular data set.
input: a GPM model accession number (GPMddddddddddd) return: {OBJECT - "string":{"string":"string"}}} objects containing text descriptions of how, when and what was modeled
Example: list sample, analytical parameters and result values for the data set GPM10100159682
http://rest.thegpm.org/1/model/metadata/gpm=GPM10100159682
input: a GPM model accession number (GPMddddddddddd) return: {OBJECT - "string":"string"} metadata abstract text stored in GPMDB
Example: list metadata abstract text information for the data set GPM10100159682
http://rest.thegpm.org/1/db/metadata/gpm=GPM10100159682
input: a GPM model accession number (GPMddddddddddd) return: [ARRAY - "string"} accession numbers for primary proteins in the model
Example: list proteins found in GPM10100159682
http://rest.thegpm.org/1/model/proteins/gpm=GPM10100159682
input: a GPM model accession number (GPMddddddddddd) accession number for the protein of interest (ACC) return: [ARRAY - "string"] all residue modifications assigned to ACC, as specified in RFC GPM-2011.12.14 §2.3.
Example: list residue modifications found in GPM10100159682 for the protein ENSP00000324804
http://rest.thegpm.org/1/model/protein_modifications/gpm=GPM10100159682&acc=ENSP00000324804
input: a GPM model accession number (GPMddddddddddd) accession number for the protein of interest (ACC) return: {OBJECT - "string":int} peptide sequence : ×observed for peptide sequences assigned to ACC
Example: list peptides found in GPM10100159682 for the protein ENSP00000324804
http://rest.thegpm.org/1/model/protein_peptides/gpm=GPM10100159682&acc=ENSP00000324804
input: a GPM model accession number (GPMddddddddddd) accession number for the protein of interest (ACC) return: [ARRAY - "string"] all single amino acid variants (SAVs) assigned to ACC, as specified in RFC GPM-2011.12.14 §2.5.
NOTE: this method was originally "protein_polymorphisms", which still functions as a URL.
Example: list SAVs found in GPM10100159682 for the protein ENSP00000331514
http://rest.thegpm.org/1/model/protein_savs/gpm=GPM10100159682&acc=ENSP00000331514
input: a GPM model accession number (GPMddddddddddd) accession number for the protein of interest (ACC) return: [ARRAY - "string"] the sequence of protein ACC identified in the model.
Example: get the protein sequence of ENSP00000331514 found in GPM10100159682
http://rest.thegpm.org/1/model/protein_sequence/gpm=GPM10100159682&acc=ENSP00000331514
input: a comma-separated list of protein accession numbers return: [OBJECT - "string":"string"] the accession numbers and associated binomial species names.
Example: get the species associated with the protein accession numbers ENSMUSP00000026459, ENSP00000339186, gi|240103100|, and sp|ALBU_BOVIN|
Peptide services give the programmer access of information about the peptides currently stored in GPMDB. All peptide services require an appropriate peptide amino acid sequence to identify the target peptide.
input: peptide sequence of interest return: {OBJECT - "string":int} of {accession number:number of observations} pairs
Example: retrieve the accession numbers and observations of SPSSVEPVADMLMGLFFR
http://rest.thegpm.org/1/peptide/accessions/seq=SPSSVEPVADMLMGLFFR.
input: peptide sequence of interest return: [ARRAY - int] the total number of observations
Example: retrieve the total observations of SPSSVEPVADMLMGLFFR
http://rest.thegpm.org/1/peptide/count/seq=SPSSVEPVADMLMGLFFR.
input: peptide sequence of interest return: {OBJECT - "string":int} of {parent ion charge:number of observations} pairs
Example: retrieve the total observations of SPSSVEPVADMLMGLFFR by parent ion charge
http://rest.thegpm.org/1/peptide/count_z/seq=SPSSVEPVADMLMGLFFR.
input: peptide sequence of interest return: {OBJECT - "string":int} of {protein coordinate:number of observations} pairs for select modifications
"xx" can be any of the following:
Example: retrieve the total observations of phosphorylation for ENSP00000384660
http://gpmdb.thegpm.org/1/peptide/pf/acc=ENSP00000384660&pos=1-706&w=n.
Protein services give the programmer access of information about the proteins currently stored in GPMDB. All protein services require an appropriate protein accession number to identify the protein sequence being queried.
input: accession number for the protein of interest return: [ARRAY - float] the log10(E) for the best observation of ACCESSION
Example: retrieve the lowest E value for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/best_e/acc=ENSMUSP00000026459.
input: accession number for the protein of interest return: [ARRAY - int] the total number of observations of ACCESSION
Example: retrieve the number of time ENSMUSP00000026459 has been observed
http://rest.thegpm.org/1/protein/count/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - "string"] text description of the protein ACCESSION
Example: retrieve a text description of ENSMUSP00000026459
http://rest.thegpm.org/1/protein/description/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: {OBJECT - "string":"string"} evidence code information about status of the protein
Example: retrieve the evidence codes for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/evidence/acc=ENSMUSP00000026459
input: a keyword in a protein description a string to filter the accession numbers (default = "human") return: {OBJECT - "string":"string"} information about the proteins matching the keyword
Example: list human proteins with the keyword "actinin"
http://rest.thegpm.org/1/protein/keyword/key=actinin
input: accession number for the protein of interest mass (Da) of the modification, e.g., phosphorylation = 80 list of residue types that may be modified, e.g., phosphorylation = STY log10(E) of the maximum allowed expectation value for a valid observation return: {OBJECT - "string":int} of {modified site:number of observations} for ACCESSION
Example: retrieve the phosphorylated S, T or Y residues for YKL112W
http://rest.thegpm.org/1/protein/modifications/acc=YKL112W&mod=80&res=STY&maxe=-2.0
Example: retrieve all acetylated residues for ENSP00000281111
http://rest.thegpm.org/1/protein/modifications/acc=ENSP00000281111&mod=42&res=&maxe=-2.0
input: accession number for the protein of interest comma separated list of peptide sequences in single letter code return: {OBJECT - "string":[{"string":[float,float,float,float]}]} {"ACCESSION":[{"SEQUENCE":[ω(z=1),ω(z=2),ω(z=3),ω(z=4)]}]} added: 2013-05-05
Example: retrieve the omega peptide frequencies for LDATTVLSR and AAQASAAPK observed for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/omega/acc=ENSMUSP00000026459&seq=LDATTVLSR,AAQASAAPK
input: accession number for the protein of interest peptide sequence in single letter code return: {OBJECT - "string":int} of {parent ion charge:number of observations} of SEQUENCE in ACCESSION
Example: retrieve the number of times LDATTVLSR was observed for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/peptide_count/acc=ENSMUSP00000026459&seq=LDATTVLSR
input: accession number for the protein of interest return: [ARRAY - "string"] of all peptides observed for ACCESSION
Example: retrieve the peptide sequences observed for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/peptide_sequences/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: {OBJECT - "string":int} of the {parent ion charge:number of peptide observations} for ACCESSION
Example: retrieve the number of peptide observations by parent ion charge state for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/peptides_z/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - int] number of observations of peptides associated with ACCESSION
Example: retrieve the total number of peptide observations for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/peptides_total/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - OBJECT "string":int] an array of observed single amino acid variants (SAVs) and the number of observations for the protein ACCESSION
NOTE: this method was originally "/protein/polymorphisms", which still functions as a URL.
Example: retrieve a summary of SAVs found for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/savs/acc=ENSMUSP00000026459
input: accession number for the protein of interest return: [ARRAY - "string"] the amino acid sequence of ACCESSION
Example: retrieve the protein sequence for ENSMUSP00000026459
http://rest.thegpm.org/1/protein/sequence/acc=ENSMUSP00000026459
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/gpmdb_rest. The files currently available 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.
A manuscript describing this API has been published: The GPMDB REST Interface, David Fenyö; Ronald C. Beavis, Bioinformatics 2015; doi: 10.1093/bioinformatics/btv107.
A poster presenting the API was shown at the US HUPO Conference (2015) in Tempe. You can download a PDF of the presentation here.
Reference name | Revision date | Document status | Stable URL |
---|---|---|---|
GPM-2012.6.11 | 2015.02.19 | final specification | http://icex.ca/ice.0.m |