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#!
Wikidata queries, initially lifted over from the gn3 gene-alias code (that was written in Racket).
Note you can take a SPARQL query and push it into https://query.wikidata.org/. E.g. generate a query and
copy paste into the query service:
scheme@(guile-user) [3]> (display (wikidata-query-geneids "Shh"))
```
SELECT DISTINCT ?wikidata_id
WHERE {
?wikidata_id wdt:P31 wd:Q7187;
wdt:P703 ?species .
VALUES (?species) { (wd:Q15978631 ) ( wd:Q83310 ) ( wd:Q184224 ) } .
?wikidata_id rdfs:label "Shh"@en .
}
```
It is possible to run queries through curl with
```
curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="
SELECT DISTINCT ?alias
WHERE {
wd:Q24420953 rdfs:label ?name ;
skos:altLabel ?alias .
FILTER(LANG(?name) = \"en\" && LANG(?alias) = \"en\").
}"
```
!#
(define-module (gn db sources wikidata)
#:export (wikidata-query-geneids
wikidata-query-gene-aliases
)
)
(define ps-encoded-by "ps:P702")
(define wdt-instance-of "wdt:P31")
(define wdt-in-taxon "wdt:P703")
(define wd-human "wd:Q15978631")
(define wd-mouse "wd:Q83310")
(define wd-rat "wd:Q184224")
(define wd-gene "wd:Q7187")
(define wd-shh-rat "wd:Q24420953")
(define (wikidata-query-geneids gene_name)
"SPARQL query to get the wikidata identifiers pointing to genes of listed species, e.g. 'Shh'"
(string-append
"SELECT DISTINCT ?wikidata_id
WHERE {
?wikidata_id " wdt-instance-of " " wd-gene ";
" wdt-in-taxon " ?species .
VALUES (?species) { (" wd-human " ) ( " wd-mouse" ) ( " wd-rat" ) } .
?wikidata_id rdfs:label \"" gene_name "\"@en .}"))
(define (wikidata-query-gene-aliases wikidata_id)
"SPARQL query to get a list of gene aliases based on a wikidata identifier, e.g. for Q24420953. This
version supports the expanded id only, so <http://www.wikidata.org/entity/Q24420953> including the <,>."
(string-append
"SELECT DISTINCT ?stripped_alias
WHERE { " wikidata_id " rdfs:label ?name ;
skos:altLabel ?alias .
BIND (STR(?alias) AS ?stripped_alias) .
FILTER(LANG(?name) = \"en\" && LANG(?alias) = \"en\").}"))
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