README.md

In lgatto/UniProt.REST: R Interface to UniProt REST API

Important This package is currently unmaintained and hasn't kept up with changes in UniProt itself. Please use the UniProt.ws package instead.

An R Interface to UniProt REST API

The UniProt.RES package is an R interface to UniProt's Proteins REST API, giving access to key biological data from UniProt and data from Large Scale Studies data mapped to UniProt.

The Proteins REST API

The Proteins REST API provides access to key biological data from UniProt and data from Large Scale Studies data mapped to UniProt. The services provide sequence feature annotations from UniProtKB, variation data from UniProtKB and mapped from Large Scale data sources (1000 Genomes, ExAC and COSMIC), proteomics data mapped from Large Scale sources (PeptideAtlas, MaxQB and EPD) and genome coordinate mappings.

The API:

Proteins

    get /proteins
        get list of UniProt entries
    get /proteins/{accession}
        get UniProt entry by accession
    get /proteins/{accession}/isoforms
        get UniProt isoform entries from parent normal entry accession
    get /proteins/{dbtype}:{dbid}
        get UniProt entries by uniprot cross reference and its id

library("UniProt.REST")

## 
## This is 'UniProt.REST' version 0.1.0

ac <- "P27361"
acs <- c("P27361", "P38398")

UniProtProtein(ac)

## A Protein retrieved from 'UnitProt.REST'
##  Available data for P27361:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence keyword feature evidence sequence

UniProtProteins(acs) ## works also as UniProtProtein(ac)

## $entry
## A Protein retrieved from 'UnitProt.REST'
##  Available data for P38398:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence keyword feature evidence sequence
## 
## $entry
## A Protein retrieved from 'UnitProt.REST'
##  Available data for P27361:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence keyword feature evidence sequence

UniProtProteinIsoforms(ac)

## $entry
## A Protein retrieved from 'UnitProt.REST'
##  Available data for P27361-3:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence sequence
## 
## $entry
## A Protein retrieved from 'UnitProt.REST'
##  Available data for P27361-2:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence sequence
## 
## $entry
## A Protein retrieved from 'UnitProt.REST'
##  Available data for P27361-1:
##   accession name protein gene organism reference comment dbReference
##   proteinExistence sequence

Variation

    get /variation
        get variation by search
    get /variation/{accession}
        get UniProt variation features by accession

Features

    get /features
        get features of list of UniProt entries.
    get /features/type/{type}
        Search for features of given type and search terms.
    get /features/{accession}
        get UniProt features by accession

Antigen

    get /antigen
        Get antigen of list of UniProt accessions.
    get /antigen/{accession}
        Get antigens mapped to UniProt by accession

Proteomics

    get /proteomics
        Get proteomics peptides of list of UniProt accessions.
    get /proteomics/{accession}
        Get proteomics peptides mapped to UniProt by accession

Proteomes

    get /proteomes
        Search Proteomes
    get /proteomes/genecentric/{upid}
        fetch proteome gene centric proteins by proteome upid
    get /proteomes/proteins/{upid}
        fetch proteome proteins by proteome upid
    get /proteomes/{upid}
        fetch proteome by proteome upid

Coordinates

    get /coordinates
        query for entries with genomic location
    get /coordinates/{accession}
        Get Genome Coordinates by accession.
    get /coordinates/{dbtype}:{dbid}
        get by database cross reference: Ensembl, CCDS, HGNC or RefSeq
    get /coordinates/{taxonomy}/{chromosome}:{gstart}-{gend}
        get genome coordinate by genome locatio

lgatto/UniProt.REST documentation built on May 21, 2019, 6:04 a.m.