New Protein Data REST API

There is a greater need than ever to integrate large-scale biological data with known annotations and disseminate this information to an increasingly diverse research community. To address this need, our Protein Function group has introduced a new API that provides access to key biological data from UniProt and Large Scale Studies data mapped to UniProt. The Protein REST API service also serves as a bridge between genomic and protein data, enabling users to retrieve genome coordinates for protein sequences. 

Protein REST API features

With the new API, it is now possible to retrieve the following: 

• UniProtKB proteins and isoform by accession, IDs and cross-references 
• Sequence feature annotations for canonical as well as isoform protein sequences 
• Genomic coordinate mappings for protein sequences 
• Peptide evidence mapped from proteomics resources (PeptideAtlas, EPD, MaxQB) 
• UniProtKB annotated variants and variants from large scale studies (1000 Genomes, ExAC, ESP and COSMIC) 

Each service has been implemented to seamlessly extend our existing programmatic capabilities. You can access information about a single entry or multiple entries depending upon whether you are interested in a specific entry or a broader set of entries. 

Documentation

The REST API documentation is generated using the documentation framework Swagger and is available in the Proteins REST API documentation page on the EMBL-EBI website.

REST Web Services and methods

Resource: http://www.ebi.ac.uk/proteins/api

Description: 

1) Proteins 

/proteins 

• Get list of UniProt entries  

/accession 

• Get UniProt entry by accession 

/accession/isoform 

• Get UniProt isoform entries from parent normal entry accession  

/db/{dbtype}:{dbid} 

• Get UniProt entries by UniProt cross reference and its ID 

2) Features 

/features 

• Get features of list of UniProt entries 

/features/type/{type} 

• Search for features of given type and search terms. 

/features/{accession} 

• Get UniProt features by accession 

3) Coordinates 

/coordinates 

• query for entries with genomic location 

/coordinates/{accession} 

• Get genome coordinates by accession 

/coordinates/{taxonomy}/location/{gstart}-{gend} 

• Get genome coordinate by genome location 

4) Proteomics  

/proteomics 

• Get proteomics peptides of list of UniProt accessions

/proteomics/{accession} 

• Get proteomics peptides mapped to UniProt by accession 

5) Variation 

/variation 

• Get variation by search  

/variation/{accession} 

• Get UniProt variation features by accession.

We welcome your feedback!

We hope you will find the new Protein REST service useful and easy to use. You can send us feedback on the new service through our website, or submit it directly to our Protein REST API user survey.