Title:	A SPARQL Client for R
Version:	0.1.0
Description:	Provides a client for running SPARQL queries directly from R. SPARQL (short for SPARQL Protocol and RDF Query Language) is a query language used to retrieve and manipulate data stored in RDF (Resource Description Framework) format.
License:	GPL-3
URL:	https://github.com/sib-swiss/sparqlr
BugReports:	https://github.com/sib-swiss/sparqlr/issues
Depends:	R (≥ 4.1.0)
Imports:	dplyr, httr2, purrr, rlang, stringr, tibble, tidyr
Suggests:	knitr, lintr, rcmdcheck, rmarkdown, styler, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
Config/testthat/edition:	3
Encoding:	UTF-8
RoxygenNote:	7.3.3
NeedsCompilation:	no
Packaged:	2026-04-02 09:12:39 UTC; rengler
Author:	Marco Pagni [aut], Robin Engler [aut, cre], SIB Swiss Institute of Bioinformatics [cph]
Maintainer:	Robin Engler <robin.engler@sib.swiss>
Repository:	CRAN
Date/Publication:	2026-04-08 14:10:08 UTC

Convert a 2-column tibble into a multi-line SPARQL prefix string.

Description

Convert a 2-column tibble into a multi-line SPARQL prefix string.

Usage

as_sparql_prefix(prefixes)

Arguments

Convert the style of IRIs from "long" or "short" into another form.

Description

Convert the style of IRIs in all columns of a tibble.

Usage

convert_iri_style(
  t,
  prefixes,
  iri_style = c("short", "long", "mdlink", "html"),
  replace_in_literal = FALSE
)

Arguments

Value

An copy of the input tibble t where the IRI style was modified.

Examples

# Create a sample tibble with long-form IRIs.
data <- tibble::tibble(
  composer = c(
    "<http://www.wikidata.org/entity/Q254>",
    "<http://www.wikidata.org/entity/Q255>",
    "<http://www.wikidata.org/entity/Q1268>"
  ),
  country = c(
    "<http://www.wikidata.org/entity/Q701614>",
    "<http://www.wikidata.org/entity/Q131964>",
    "<http://www.wikidata.org/entity/Q34266>"
  ),
  label = c(
    "Wolfgang Amadeus Mozart - http://example.org/Mozart",
    "Ludwig van Beethoven - http://example.org/Beethoven",
    "Frederic Chopin - http://example.org/Chopin)"
  )
)

# Define prefixes long-to-short correspondence.
prefixes <- tibble::tibble(
  short = c("wde", "ex"),
  long = c("http://www.wikidata.org/entity/", "http://example.org/")
)

# Convert IRIs to short form.
convert_iri_style(data, prefixes, iri_style = "short")

# Convert IRIs to markdown link format.
convert_iri_style(data, prefixes, iri_style = "mdlink")

# Convert IRIs to HTML link format.
convert_iri_style(data, prefixes, iri_style = "html")

# Also apply conversion to string literals.
convert_iri_style(
  data, prefixes,
  iri_style = "short",
  replace_in_literal = TRUE
)

# Apply different IRI styles to different columns.
convert_iri_style(
  data, prefixes,
  iri_style = c("short", "short", "mdlink"),
  replace_in_literal = TRUE
)

Create a function to replace IRI styles in strings.

Description

Returns a function to replace IRI styles in strings.

Usage

iri_replacement_function(iri_style, prefixes, replace_in_literal)

Arguments

Value

A function that replaces IRIs according to the specified style.

Load SPARQL prefixes from a text file.

Description

Extracts the list of PREFIXes from a SPARQL query file, and returns it as a tibble object.

Usage

load_prefixes_from_file(path)

Arguments

Value

A tibble with short and long columns.

Examples

# Load a query file
file_path <- system.file("extdata", "example_select.rq", package = "sparqlr")
prefixes <- load_prefixes_from_file(file_path)

Load a SPARQL query from a file.

Description

Reads a SPARQL query from a file and returns it as a single multi-line string. Optionally removes comment lines (lines starting with a '#' character).

Usage

load_query_from_file(path, remove_comments = FALSE)

Arguments

Value

A character string containing the loaded SPARQL query.

Examples

# Load a query file
file_path <- system.file("extdata", "example_select.rq", package = "sparqlr")
query <- load_query_from_file(file_path, remove_comments = TRUE)
cat(query)

Parse an HTTP response with content type "application/n-triples".

Description

Parse an HTTP response with content type "application/n-triples".

Usage

parse_construct_response(response)

Arguments

Parse an HTTP response with content type "application/sparql-results+json".

Description

Parse an HTTP response with content type "application/sparql-results+json".

Usage

parse_select_response(response)

Arguments

Convert a SPARQL SELECT query result into a tibble.

Description

Converts the result of a parsed SPARQL SELECT query (a list object) into an R tibble.

Usage

query_result_to_tibble(query_result, na_value = NA)

Arguments

Convert an individual RDF term to an R string.

Description

Convert an individual RDF term to an R string.

Usage

rdf_term_to_string(value, na_value = NA)

Arguments

Run a SPARQL CONSTRUCT query.

Description

Executes a SPARQL CONSTRUCT query and returns the results as a list containing two tibbles: one for edges (triples with IRIs) and one for nodes with properties. IRIs can be formatted in different styles using the iri_style argument.

Usage

sparql_construct(
  endpoint,
  query,
  prefixes = NULL,
  request_method = c("POST", "GET"),
  http_extra_params = list(),
  verbose = FALSE
)

Arguments

Value

        A list with two tibbles: `edges` and `nodes`.

Examples

# Load a SPARQL construct query from an example file.
query <- system.file(
  "extdata", "example_construct.rq",
  package = "sparqlr"
) |> load_query_from_file()

# Run the SPARQL query on the specified endpoint.
sparql_construct(
  endpoint = "https://query.wikidata.org/sparql",
  query = query
)

Run a SPARQL DESCRIBE query.

Description

Executes a SPARQL DESCRIBE query and returns the results tibble with 3 columns: subject, predicate, object.

IRIs can be formatted in different styles using the iri_style argument.

Usage

sparql_describe(
  endpoint,
  query,
  prefixes = NULL,
  request_method = c("POST", "GET"),
  http_extra_params = list(),
  verbose = FALSE
)

Arguments

Value

        A list with two tibbles: `edges` and `nodes`.

Examples

query <- "
# Retrieve all 'useful descriptions' associated with the 'cats' resource.
DESCRIBE <http://www.wikidata.org/entity/Q146>
"
endpoint <- "https://query.wikidata.org/sparql"

# Run the SPARQL query on the specified endpoint.
sparql_describe(endpoint, query)

# Same as above, but converting prefixes to their short form.
prefixes <- tibble::tibble(
  short = c("wd", "w3"),
  long = c(
    "http://www.wikidata.org/entity/",
    "http://www.w3.org/2000/01/rdf-schema#"
  )
)
sparql_describe(endpoint, query, prefixes = prefixes)

Run a SPARQL SELECT query.

Description

Run a SPARQL query, either SELECT, CONSTRUCT or DESCRIBE and return the results as a tibble. Returned column names are the same as SPARQL variables. Detection of column types relies on R built-in methods, not RDF data types.

In the HTTP request, the "application/sparql-results+json" MIME type is used, which is supported by most SPARQL endpoints.

Usage

sparql_select(
  endpoint,
  query,
  prefixes = NULL,
  request_method = c("POST", "GET"),
  http_extra_params = list(),
  verbose = FALSE
)

Arguments

Value

A tibble with the query results or NULL if the query returns nothing.

Examples

# Define the SPARQL query to run.
query <- "
# Query classical music composers and their country of origin.
SELECT ?composer ?composerLabel ?country ?countryLabel WHERE {

  ?composer wdt:P106 wd:Q36834 ;     # Occupation: composer
            wdt:P101  wd:Q9730 .     # Field of work: classical music

  OPTIONAL { ?composer wdt:P27 ?country . }  # country of citizenship

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language '[AUTO_LANGUAGE],en' .
  }
}
"

# Run the SPARQL query on the specified endpoint.
sparql_select(
  endpoint = "https://query.wikidata.org/sparql",
  query = query
)

# Same as above, but converting prefixes to their short form.
prefixes <- tibble::tibble(
  short = c("wde"),
  long = c("http://www.wikidata.org/entity/")
)
sparql_select(
  endpoint = "https://query.wikidata.org/sparql",
  query = query,
  prefixes = prefixes
)

Mix colors using subtractive color mixing.

Description

Combines multiple hex colors using subtractive color mixing, which simulates how pigments mix in the physical world (e.g., mixing paints). The function takes the minimum RGB value across all input colors for each channel, resulting in progressively darker colors as more colors are combined.

Usage

subtractive_mix(hex_colors)