BioThingsClient

This is an R package that provides access to the BioThings APIs:

• Chemicals
• Taxons
• Variants
• Genes

As new APIs are added, this package will be updated to provide access to them. If there is a new API and the package still hasn't been updated, you can create a new configuration object that will allow you to access such new API.

Installation

Installing from GitHub

install.packages("devtools")
library(devtools)
install_github("biothings/BioThingsClient.R")

Usage

The package is intended to be simple to use, without the need to instantiate a class object (though you can! Particularly if you have an updated API configuration). For a given API and relevant id, the user can make requests from the API as follows:

Accessing the MyGene API

library(BioThingsClient.R)
gene_client <- BioThingsClient("gene")
btGet(gene_client, "1017")
# or:
btGet("gene", "1017")
# or:
btGet("gene", "c("9606", "10030")")

Accessing the Taxonomy API

library(BioThingsClient.R)
taxon_client <- BioThingsClient("taxon")
btGet(taxon_client, "9606")
# or:
btGet("taxon", "9606")

Accessing the MyVariant API

library(BioThingsClient.R)
variant_client <- BioThingsClient("variant")
btGet(variant_client, "chr7:g.140453134T>C")

Accessing the MyChem API

library(BioThingsClient.R)
chem_client <- BioThingsClient("chem")

Viewing available clients and endpoints

library(BioThingsClient.R)
biothings_clients

Accessing endpoints of the APIs with the query method:

btQuery("chem", "drugbank.name:celecoxib")

btQuery("variant", c("rs58991260", "rs2500"))

Existing Issues

There are some issues with requesting data frames for certain APIs and endpoints. Some chemical responses are so large that fromJSON will hang. Others have so many fields that the data frame will be heavily nested and hard to use. We recommend avoid requesting data frames without specifying certain fields.