In biothings/biothings_client.R: BioThings Client (https://github.com/biothings/BioThingsClient.R)

The BioThings APIs provide query and retrieve annoation of genes, variants, chemicals and taxons.

Package Usage

This package has S4 methods for accessing each API, as well as an R6 class that is extensible so that as other APIs are made, a configuration can be passed and used to query and retrieve annotation from said APIs. The S4 methods are also extensible by providing a configuration object like the included biothings_clients configuration, and then using the btGet, btQuery, btMetadata and btFields methods.

Annotations

Each API (gene, taxon, variant and chemical - when this was written) has a set of methods for getting annotations. Additionally, there are the generic btGet method.

Example: btGet

These methods can be used with a defined BioThingsClient class object or with just the name of a client from the biothings_clients object.

With a defined BioThings object (see next example for output):

> gene_client <- BioThingsClient("gene")
> # Suppress messages
> slot(gene_client, "verbose") <- FALSE
> btGet(gene_client, "1017")
> btGet(gene_client, c("1017","1018","ENSG00000148795"))

Without (output trimmed):

> btGet(gene_client, "1017") # btGet("gene", "1017") is equivalent
[[1]]
[[1]]$`_id`
[1] "1017"

[[1]]$`_score`
[1] 22.32558
...(trimmed for space)

> btGet(gene_client, c("1017","1018","ENSG00000148795"))
[[1]]
[[1]]$`_id`
[1] "1017"

[[1]]$`_score`
[1] 22.32558
...(trimmed for space)


[[2]]
[[2]]$`_id`
[1] "1018"
...(trimmed for space)

Users can also specify fields and the type of return object. However, due to the size of some API responses, the default is a list (denoted by "records") and we recommend only requesting "data.frame" when also specifing fields. Requesting "data.frame" will generally return a data frame, though it might be heavily nested and hard to use. So again, specify fields for the best results when requesting a data frame.

> btGet(gene_client, c("1017","1018","ENSG00000148795"),
        fields = c("symbol","name","taxid","entrezgene"),
        return.as = "data.frame")
   _id   _score entrezgene                                           name  symbol
1 1017 22.32558       1017                      cyclin dependent kinase 2    CDK2
2 1018 22.32596       1018                      cyclin dependent kinase 3    CDK3
3 1586 23.35202       1586 cytochrome P450 family 17 subfamily A member 1 CYP17A1
  taxid           query
1  9606            1017
2  9606            1018
3  9606 ENSG00000148795

Queries

The APIs also have query endpoints, so a user can provide query terms and receive annotations in that form. The btQuery method is generic and rely on input of a key for the biothings_clients or a BioThings object configuration for specification of which API to use. Just like the generic annotation methods, these methods can be used with an updated or customized configuration.

Example: btQuery

btQuery:

> btQuery(gene_client, "sp2")
[[1]]
[[1]]$max_score
[1] 457.1937

[[1]]$took
[1] 5

[[1]]$total
[1] 10

[[1]]$hits
[[1]]$hits[[1]]
[[1]]$hits[[1]]$`_id`
[1] "6668"
...(output trimmed)

btQuery for multiple ids:

> genes <- c('1053_at', '117_at', '121_at', '1255_g_at', '1294_at')
> btQuery(gene_client, genes, scopes=c("symbol", "reporter", "accession"),
        fields = c("entrezgene", "uniprot"), species = "human",
        returnall = TRUE)
Finished
$response
$response[[1]]
$response[[1]]$`_id`
[1] "5982"

$response[[1]]$`_score`
[1] 22.32529

$response[[1]]$entrezgene
[1] 5982

$response[[1]]$uniprot
$response[[1]]$uniprot$`Swiss-Prot`
[1] "P35250"
...(output trimmed)

Example: Using fetch_all parameter

Some queries return thousands of results. Use fetch_all to get all of them.

> faquery <- btQuery(gene_client, '_exists_:pdb', fetch_all = TRUE,
                     fields = 'pdb')
Getting additional records. Took: 536
Getting additional records. Took: 484
Getting additional records. Took: 301
Getting additional records. Took: 300
Getting additional records. Took: 409
Getting additional records. Took: 538
Getting additional records. Took: 225
Getting additional records. Took: 147
Getting additional records. Took: 46
> str(faquery)
List of 8176
 $ :List of 3
  ..$ _id   : chr "23211"
  ..$ _score: num 1.55
  ..$ pdb   : chr "2CQE"
 $ :List of 3
  ..$ _id   : chr "5888"
  ..$ _score: num 1.55
  ..$ pdb   : chr [1:6] "1B22" "1N0W" "5H1B" "5H1C" ...
...(output trimmed)

Metadata and Metadata Fields

Users can also retrieve information about metadata for an API with btMetadata:

> btMetadata("gene") # Equivalent to btMetadata(gene_client)
[[1]]
[[1]]$source
NULL

[[1]]$stats
[[1]]$stats$entrez_retired
[1] 201591

[[1]]$stats$ensembl_prosite
[1] 725969

[[1]]$stats$ensembl_pfam
[1] 1174908

[[1]]$stats$entrez_gene
[1] 19752422
...(output trimmed)

As well as metadata fields with btFields:

> btFields("gene") # Beware, produces a lot of output

biothings/biothings_client.R documentation built on Jan. 8, 2020, 9:33 p.m.