https://github.com/lgatto/uniprot.rest

R Interface to UniProt REST API
https://github.com/lgatto/uniprot.rest

Last synced: about 2 months ago
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R Interface to UniProt REST API

• Host: GitHub
• URL: https://github.com/lgatto/uniprot.rest
• Owner: lgatto
• Created: 2016-12-27T13:07:45.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-03-01T10:20:44.000Z (about 7 years ago)
• Last Synced: 2025-01-20T22:55:21.372Z (3 months ago)
• Language: R
• Size: 13.7 KB
• Stars: 2
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md

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README

        
**Important** This package is currently unmaintained and hasn't kept

up with changes in UniProt itself. Please use the

[`UniProt.ws`](https://bioconductor.org/packages/release/bioc/html/UniProt.ws.html)

package instead.

[![codecov](https://codecov.io/gh/lgatto/UniProt.REST/branch/master/graph/badge.svg)](https://codecov.io/gh/lgatto/UniProt.REST)

# 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](https://www.ebi.ac.uk/proteins/api/doc/swagger/)

> 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

```{r}

library("UniProt.REST")

ac <- "P27361"

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

UniProtProtein(ac)

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

UniProtProteinIsoforms(ac)

```

### 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