SPARQL chunks and queries

André Ourednik - https://ourednik.info

2022-06-01

This package allows you to query SPARQL endpoints in two different ways:

1. Run SPARQL chunks in Rmarkdown files.
2. Use inline functions to send SPARQL queries to a user-defined endpoint and retrieve data in dataframe form (sparql2df) or list form (sparql2list).

Endpoints can be reached from behind corporate firewalls on Windows machines thanks to automatic proxy detection. See Execute SPARQL chunks in R Markdown.

Use

To use the full potential of the package you need to load the library and tell knitr that a SPARQL engine exists:

Once you have done so, you can run SPARQL chunks:

Chunks

Retrieve a data frame

output.var: the name of the data.frame you want to store the results in

endpoint: the URL of the SPARQL endpoint

autoproxy: whether or not try to use the automatic proxy detection

Example 1 (Swiss administration endpoint)

```{sparql output.var="queryres_csv", endpoint="https://lindas.admin.ch/query"}
PREFIX schema: <http://schema.org/>
SELECT * WHERE {
  ?sub a schema:DataCatalog .
  ?subtype a schema:DataType .
}
```

Example 2 (Uniprot endpoint)

Note the use of attempt at automatic proxy detection.

```{sparql output.var="tes5", endpoint="https://sparql.uniprot.org/sparql", autoproxy=TRUE}
PREFIX up: <http://purl.uniprot.org/core/>
SELECT ?taxon
FROM <http://sparql.uniprot.org/taxonomy>
WHERE {
    ?taxon a up:Taxon .
} LIMIT 500
```

Example 3 (WikiData endpoint):

```{sparql output.var="res.df", endpoint="https://query.wikidata.org/sparql"}
SELECT DISTINCT ?item ?itemLabel ?country ?countryLabel ?linkTo ?linkToLabel
WHERE {
    ?item wdt:P1142 ?linkTo .
    ?linkTo wdt:P31 wd:Q12909644 .
    VALUES ?type { wd:Q7278  wd:Q24649 }
    ?item wdt:P31 ?type .
    ?item wdt:P17 ?country .
    MINUS { ?item wdt:P576 ?abolitionDate }
    SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en" . }
}
```

Retrieve a list

output.var: the name of the list you want to store the results in

endpoint: the URL of the SPARQL endpoint

output.type : when set to “list”, retrieves a list (tree structure) instead of a dataframe

autoproxy: whether or not try to use the automatic proxy detection

```{sparql output.var="queryres_list", endpoint="https://lindas.admin.ch/query", output.type="list"}
PREFIX schema: <http://schema.org/>
SELECT * WHERE {
  ?sub a schema:DataCatalog .
  ?subtype a schema:DataType .
}
```

Inline code

The inline functions sparql2df and sparql2list both have the same pair of arguments: a SPARQL endpoint and a SPARQL query. Queries can be multi-line:

endpoint <- "https://lindas.admin.ch/query"
query <- "PREFIX schema: <http://schema.org/>
  SELECT * WHERE {
  ?sub a schema:DataCatalog .
  ?subtype a schema:DataType .
}"

Retrieve a data frame

result_df <- sparql2df(endpoint,query)

The same but with attempt at automatic proxy detection:

result_df <- sparql2df(endpoint,query,autoproxy=TRUE)

Retrieve a list

result_list <- sparql2list(endpoint,query)

The same but with attempt at automatic proxy detection:

result_list <- sparql2list(endpoint,query,autoproxy=TRUE)