How to query

SPARQL endpoint

At https://nubbekg.aksw.org/sparql you will find the SPARQL endpoint for nubbekg. The backend is provided by OpenLink Virtuoso, while the frontend is provided by YASGUI.

Rates and limitations

You can make a limited number of connections. The settings can be seen below:

        ResultSetMaxRows           = 25000
        MaxQueryExecutionTime      =   600  (seconds)
        MaxQueryCostEstimationTime =   400  (seconds)
        Connection limit           =    10  (parallel connections per IP address

ATTENTION: The result size is currently limited to 25000 rows. This way partial results are displayed as complete ones and there won't be a HTTP error.

SPARQL example queries

The following query gives you formula, name, weight and smile of a compound:

PREFIX nubbe:  <http://nubbekg.aksw.org/ontology#>
PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?formula ?name ?smiles ?weight WHERE {

  ?compound a                       nubbe:Compound ;
            nubbe:molecularFormula  ?formula ;
            nubbe:commonName        ?name ;
            nubbe:smiles            ?smiles ;
            nubbe:hasDescriptors    ?descr .
  ?descr    nubbe:molecularWeight   ?weight }

LIMIT 100

The following query gives you formula and weight of a compound where the weight is between 320.00 and 320.20:

PREFIX nubbe:  <http://nubbekg.aksw.org/ontology#>
PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:  <http://www.w3.org/2001/XMLSchema#>

SELECT DISTINCT ?formula ?weight WHERE {

  ?compound a                       nubbe:Compound ;
            nubbe:molecularFormula  ?formula ;
            nubbe:hasDescriptors    ?descr .
  ?descr    nubbe:molecularWeight   ?weight .

FILTER (?weight > 320.00 && ?weight < 340.00)
}
LIMIT 100

It is also possible to query without YASGUI, but with a self written script that connects to our endpoint. Below is a example in python with SPARQLWrapper:

from SPARQLWrapper import SPARQLWrapper, JSON

sparql = SPARQLWrapper(
    "https://nubbekg.aksw.org/sparql"
)
sparql.setReturnFormat(JSON)

sparql.setQuery(
    """
    PREFIX nubbe:  <http://nubbekg.aksw.org/ontology#>
    PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

    #Get the Name, Smiles, molecular formula, species and bioactivity of the first 100 compounds

    SELECT DISTINCT  ?formula ?name ?smiles ?species ?bioactivity
    WHERE
        { ?compound a             					nubbe:Compound ;
                    nubbe:molecularFormula  		?formula ;
                    nubbe:commonName      			?name ;
                    nubbe:smiles         		    ?smiles ;
                    nubbe:wasSubjectedTo  			?bioanalysis .
        ?compound 	 nubbe:partOfSpecies/rdfs:label ?species .
        ?bioanalysis nubbe:revealed/rdfs:label 		?bioactivity
        }
    LIMIT   100
    """
)

try:
    ret = sparql.queryAndConvert()

    for r in ret["results"]["bindings"]:
        print(r)
except Exception as e:
    print(e)

You can check out a real simple tutorial for SPARQL here: