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authorPjotr Prins2023-07-10 09:59:53 -0500
committerPjotr Prins2023-07-10 09:59:53 -0500
commit8ddd7f80f15943f9a48ac760babff9da9f95c043 (patch)
tree17a7156924fad85792f9e4f545b7d0b7d69e277c /gn3-guile/web/webserver.scm
parent64f83e0e726790f140b6cbbc6e1aaee3997280d1 (diff)
downloadgenenetwork3-8ddd7f80f15943f9a48ac760babff9da9f95c043.tar.gz
Trying SPARQL
Diffstat (limited to 'gn3-guile/web/webserver.scm')
-rwxr-xr-xgn3-guile/web/webserver.scm41
1 files changed, 36 insertions, 5 deletions
diff --git a/gn3-guile/web/webserver.scm b/gn3-guile/web/webserver.scm
index e19cfd7..7ce2a9a 100755
--- a/gn3-guile/web/webserver.scm
+++ b/gn3-guile/web/webserver.scm
@@ -13,6 +13,7 @@
(srfi srfi-1)
(srfi srfi-26)
(web http)
+ (web client)
(web request)
(web response)
(web uri)
@@ -56,12 +57,42 @@
(,(mk-url "mouse")."Get information on mouse")
(,(mk-url "datasets")."Get a list of datasets")))))
+(define (sparql-species)
+ "
+PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
+PREFIX gn: <http://genenetwork.org/>
+PREFIX hgnc: <http://bio2rdf.org/hgnc:>
+PREFIX homologene: <https://bio2rdf.org/homologene:>
+PREFIX kegg: <http://bio2rdf.org/ns/kegg#>
+PREFIX molecularTrait: <http://genenetwork.org/molecular-trait/>
+PREFIX nuccore: <https://www.ncbi.nlm.nih.gov/nuccore/>
+PREFIX omim: <https://www.omim.org/entry/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX phenotype: <http://genenetwork.org/phenotype/>
+PREFIX pubchem: <https://pubchem.ncbi.nlm.nih.gov/>
+PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+PREFIX uniprot: <http://purl.uniprot.org/uniprot/>
+PREFIX up: <http://purl.uniprot.org/core/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+CONSTRUCT {
+ ?s ?p ?o
+} WHERE {
+ ?s rdf:type gn:species .
+ ?s ?p ?o .
+}"
+ )
+
+;; curl "https://sparql.genenetwork.org/sparql?default-graph-uri=&query=prefix+gn%3A+%3Chttp%3A%2F%2Fgenenetwork.org%2F%3E+%0D%0A%0D%0ASELECT+distinct+*+WHERE+%7B%3Fu++gn%3AbinomialName+%3Fo%7D&format=application%2Fsparql-results%2Bjson"|jq
(define (get-species)
- '(("Mus_musculus" . (("id" . "mouse" )
- ("api" . "https://genenetwork.org/api/v2/mouse/")))
- ("Rattus_norvegicus" . (("id" . "rat")
- ("api" . "https://genenetwork.org/api/v2/rat/")))
- ))
+ (http-get "http://sparql.genenetwork.org/sparql?default-graph-uri=&query=")
+ )
(define (get-species-api-str)
(scm->json-string #("https://genenetwork.org/api/v2/mouse/"