CRN-KG: OntoRXN@blazegraph

Chemical Reaction Network Knowledge Graphs based on the OntoRXN ontology.
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Current namespace:

Blazegraph database instance for OntoRXN-based knowledge graphs.

Graphs in a Blazegraph instance are segregated by namespace. Go to the "Namespaces" tab to switch between provided KG examples [click here].

Through the adapted Blazegraph workbench you can:

  • Issue SPARQL queries on example KGs (Query tab).
  • Navigate through data entities (Explore tab).
  • Change the current namespace (Namespaces tab).

    • This webapp provides access to three knowledge graphs based on OntoRXN, which can be selected at the Namespaces tab.

    • · kg_pf. Peroxyformate decomposition: simple mechanism with many calculations per molecule, carried out at different solvents.
    • · kg_indole. Indole decomposition: larger network computed through the automated mechanism discovery tool AutoMeKin.
    • · kg_cycoct. Stereoselective carbon dioxide fixation over an epoxy alcohol derivative.
    Go to the Query tab to access a dropdown with example queries.

    All graphs:
    · Recover core stage-based network structure.

    Peroxyformate (KG_PF):
    · Get stage energies grouped by solvent.

    Indole (KG_Indole):
    · Fetch fragments from the species appearing on stages and get their frequency of appearance.

    Epoxy alcohol (KG_CyCOct):
    · Get parameters for partition function and free energy recalculation.
    · Map stages to the corresponding calculations.
    · Fetch reactions for every step in the network by selecting the corresponding species.

    This webapp provides access to three knowledge graphs based on OntoRXN, which can be selected at the Namespaces tab.

    • · kg_pf. Peroxyformate decomposition: simple mechanism with many calculations per molecule, carried out at different solvents.
    • · kg_indole. Indole decomposition: larger network computed through the automated mechanism discovery tool AutoMeKin.
    • · kg_cycoct. Stereoselective carbon dioxide fixation over an epoxy alcohol derivative.

    Recover core network (any KG) 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
SELECT ?stepX (GROUP_CONCAT(?stgX) AS ?stgL) (SAMPLE(?stgY) AS ?stgTS)
WHERE {
?stepX rxn:hasNode ?stgX .
OPTIONAL {?stepX rxn:hasTS ?stgY}
}
GROUP BY ?stepX

    query 2 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
PREFIX gc: <http://purl.org/gc/>
SELECT DISTINCT ?stgX ?solvX (SUM(?G) as ?Gsum)
  (SUM(?Eel) as ?Eelec) (SAMPLE(?nameX) AS ?name) (SAMPLE(?epsX) as ?eps)
WHERE {
  ?stgX rxn:hasSpecies ?spcX .
  ?spcX rxn:hasCalculation ?calcX .
  ?calcX gc:hasResult / rxn:hasElecEnergy / gc:hasValue ?Eel .
  ?calcX gc:hasResult / rxn:hasGibbsFreeEnergy / gc:hasValue ?G .
  ?calcX rxn:hasSolvent ?solvX .
  ?calcX gc:hasResult / rxn:hasSolventPolarity / gc:hasValue ?epsX .
  OPTIONAL {?stgX rxn:hasAnnotation ?nameX}
}
GROUP BY ?stgX ?solvX
ORDER BY ?stgX ?solvX

    query 3 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
SELECT DISTINCT ?spcX (COUNT(?stgX) as ?Ncount) (SAMPLE(?labX) as ?lab)
(GROUP_CONCAT(?nameX) AS ?stages)
WHERE {
  ?stgX rxn:hasSpecies ?spcX .
  ?spcX rxn:hasCalculation ?calcX .
  ?calcX rxn:hasAnnotation ?labelX .
  BIND(STRBEFORE(?labelX,';') AS ?labX) .
  OPTIONAL {?stgX rxn:hasAnnotation ?nameX}
}
GROUP BY ?spcX
ORDER BY DESC(?Ncount)
LIMIT 5

    query 4 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
PREFIX gc: <http://purl.org/gc/>
SELECT DISTINCT ?calcX ?Eel ?molmass ?moi ?symmnumb ?freqlist
WHERE {
  ?calcX gc:hasResult / rxn:hasElecEnergy / gc:hasValue ?Eel .
  OPTIONAL{?calcX gc:hasResult / rxn:hasMolMass / gc:hasValue ?molmass} .
  OPTIONAL{?calcX gc:hasResult / rxn:hasMomentInertia / gc:hasValue ?moi} .
  OPTIONAL{?calcX gc:hasResult / rxn:hasFreqList / gc:hasValue ?freqlist} .
  OPTIONAL{?calcX rxn:hasSymmetryNumber ?symmnumb}
  }
ORDER BY ?calcX

    query 5 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
PREFIX gc: <http://purl.org/gc/>
SELECT DISTINCT ?stgX (SAMPLE(?nameX) AS ?name) (GROUP_CONCAT(?calcX ; separator=';') AS ?calcList)
WHERE {
  ?stgX rxn:hasSpecies ?spcX .
  ?spcX rxn:hasCalculation ?calcX .
  OPTIONAL {?stgX rxn:hasAnnotation ?nameX}
}
GROUP BY ?stgX
ORDER BY ?stgX

    query 6 

    PREFIX rxn: <http://www.semanticweb.com/OntoRxn#>
PREFIX gc: <http://purl.org/gc/>
SELECT DISTINCT ?stepX ?stgX ?stgTS
        (GROUP_CONCAT(?spcName ; separator='+') as ?spcNode)
WHERE {
  ?stepX rxn:hasNode ?stgX .
  ?stgX rxn:hasSpecies ?spcX .
  ?spcX rxn:hasCalculation ?calcX .
  ?calcX rxn:hasAnnotation ?noteX .
  BIND(STRBEFORE(?noteX,';') AS ?spcName) .
  ?stepX rxn:hasTS ?stgTS
}
GROUP BY ?stepX ?stgX ?stgTS
ORDER BY ?stepX
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      Namespaces


      Download VoID description of all namespaces

      Create namespace

      There are a number of features to enable. There's full documentation here. You must select "Use" after you have created the KB.


      A quick reference is below:


      1. o PropertyGraph: Select triples.

      2. o RDF + SPARQL with named graphs: Select quads mode.

      3. o Support for Reification Done Right (RDR). Select rdr mode.


      (Inference disabled - inference is not compatible with quads or isolatable indices.)