| Type: | Package |
| Title: | Query the 'UniProtKB' REST API |
| Version: | 1.0.5 |
| Maintainer: | Guillaume Voisinne <voisinne@gmail.com> |
| Description: | Retrieve protein information from the 'UniProtKB' REST API (see https://www.uniprot.org/help/api_queries). |
| License: | GPL-3 |
| URL: | https://github.com/VoisinneG/queryup |
| BugReports: | https://github.com/VoisinneG/queryup/issues |
| Depends: | R (≥ 2.10) |
| Imports: | httr, jsonlite, utils |
| Suggests: | covr, knitr, xml2, rmarkdown, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.1.2 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-06-05 12:46:10 UTC; rstudio |
| Author: | Guillaume Voisinne
 [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2023-06-05 18:30:02 UTC |
Accessory function used to build the query url
Description
Accessory function used to build the query url
Usage
build_query_url(
query = NULL,
base_url = "https://rest.uniprot.org/uniprotkb/",
columns = c("accession", "id", "gene_names", "organism_name", "reviewed"),
format = "json"
)
Arguments
query |
list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes") |
base_url |
The base url for the UniProt REST API |
columns |
names of UniProt data columns to retrieve. |
format |
format of the response provided by the UniProt API |
Value
the query url
Accessory function removing invalid values from a query
Description
Accessory function removing invalid values from a query
Usage
clean_query(query, df)
Arguments
query |
list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes") |
df |
data.frame with invalid values (in column "value") and corresponding query field (in column "field"). |
Value
the input query without the invalid values
Retrieve data from UniProt using UniProt's REST API
Description
Retrieve data from UniProt using UniProt's REST API
Usage
get_uniprot_data(
query = NULL,
base_url = "https://rest.uniprot.org/uniprotkb/",
columns = c("accession", "id", "gene_names", "organism_id", "reviewed")
)
Arguments
query |
list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes"). See 'query_fields' for available query fields. |
base_url |
The base url for the UniProt REST API |
columns |
names of UniProt data columns to retrieve. Examples include "accession", "id", "gene_names", "keyword", "sequence". See 'return_fields' for available return fields. |
Value
a list with the following items :
- url
the query url
- status
the http status code for the request
- messages
messages returned by the REST API
- content
a data.frame containing the query results
Examples
#Getting gene names, keywords and protein sequences for a set of UniProt IDs.
ids <- c("P22682", "P47941")
cols <- c("accession", "id", "gene_names", "keyword", "sequence")
query = list("accession_id" = ids)
df <- get_uniprot_data(query = query, columns = cols)$content
df
Accessory function retrieving invalid values from messages returned by the UniProt API.
Description
Accessory function retrieving invalid values from messages returned by the UniProt API.
Usage
parse_messages(messages)
Arguments
messages |
character string containing the error messages returned by UniProt API |
Value
a data.frame with invalid values (in column "value") and corresponding query field (in column "field"). NULL if no invalid values are identified.
Available query fields.
Description
Query fields that can be used to generate queries using 'queryup' along with associated examples and description.
Usage
query_fields
Format
A data frame with 44 rows and 3 variables:
- field
Name of the query field
- example
Example query (as appearing in the query url)
- description
Description of the example query
Source
https://www.uniprot.org/help/query-fields
Retrieve data from UniProt using UniProt's REST API.
Description
Retrieve data from UniProt using UniProt's REST API.
To avoid non-responsive queries, they are split into
smaller queries with at most max_keys items per query field.
Not that it works only with queries where items within query fields are
collapsed with '+OR+' and different
query fields are collapsed with '+AND+' (see query_uniprot())
Usage
query_uniprot(
query = NULL,
base_url = "https://rest.uniprot.org/uniprotkb/",
columns = c("accession", "id", "gene_names", "organism_id", "reviewed"),
max_keys = 200,
updateProgress = NULL,
show_progress = TRUE
)
Arguments
query |
list of keys corresponding to UniProt's query fields. For example : query = list("gene_exact" = c("Pik3r1", "Pik3r2"), "organism_id" = c("10090", "9606"), "reviewed" = "true"). See 'query_fields' for available query fields. |
base_url |
The base url for the UniProt REST API |
columns |
names of UniProt data columns to retrieve. Examples include "accession", "id", "genes", "keywords", "sequence". See 'return_fields' for available return fields. |
max_keys |
maximum number of field items submitted |
updateProgress |
used to display progress in shiny apps |
show_progress |
Show progress bar |
Value
a data.frame
Examples
# Get the UniProt entries of all proteins encoded by gene Pik3r1
ids <- c("P22682", "P47941")
query = list("accession_id" = ids)
df <- query_uniprot(query = query)
head(df)
Available return fields ("columns").
Description
Return fields that can be retrieved using 'queryup' along with their label (column "Label") as appearing in the retrieved data.frame.
Usage
return_fields
Format
A data frame with 287 rows and 2 variables:
- field
Name of the returned field
- label
Label of the corresponding column in the retrieved data.frame
Source
https://www.uniprot.org/help/return_fields
Information for 1000 UniProt entries from the organism Mus musculus
Description
Entry names and other attributes of 1000 UniProt entries in Mus musculus.
Usage
uniprot_entries
Format
A data frame with 1000 rows and 5 variables:
- Entry
UniProt entry accession id
- Entry Name
UniProt entry name
- Gene Names
Gene names
- Organism (ID)
Taxon ID
- Reviewed
Swiss-Prot review status