SPARQL: querying all triples linked to one URL, but not to another

Question

From one RDF file containing statements about multiple chemical compounds, I would like to create one RDF file per chemical compound.

In order to do that, I started off looking for a SPARQL query that can isolate all triples linked to a certain URL, no matter how much nodes are in between.

I started off with a very interesting SPARQL query (https://stackoverflow.com/a/33290642/5433896) such that it would return (hopefully) all triples linked to a chemical compound :d1 in my dataset, but NOT about another compound :d10:

CONSTRUCT {
   :d1 ?prop ?val .
   ?child ?childProp ?childPropVal . 
   ?someSubj ?incomingChildProp ?child .
}
WHERE {
     :d1 ?prop ?val ;
         (:overrides|!:overrides)+ ?child . 
     ?child ?childProp ?childPropVal.
     ?someSubj ?incomingChildProp ?child. 
}

However, when I ran this on my simplified test case (python):

rdf = """<?xml version="1.0"?>


<!DOCTYPE rdf:RDF [
    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
    <!ENTITY owl11 "http://www.w3.org/2006/12/owl11#" >
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
    <!ENTITY owl11xml "http://www.w3.org/2006/12/owl11-xml#" >
    <!ENTITY carcinogenesis "http://dl-learner.org/carcinogenesis#" >
    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>


<rdf:RDF xmlns="http://dl-learner.org/carcinogenesis#"
     xml:base="http://dl-learner.org/carcinogenesis"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl11="http://www.w3.org/2006/12/owl11#"
     xmlns:carcinogenesis="http://dl-learner.org/carcinogenesis#"
     xmlns:owl11xml="http://www.w3.org/2006/12/owl11-xml#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
    <owl:Ontology rdf:about=""/>

    <owl:ObjectProperty rdf:about="#hasAtom">
        <rdfs:domain rdf:resource="#Compound"/>
        <rdfs:range rdf:resource="#Atom"/>
    </owl:ObjectProperty>

    <owl:ObjectProperty rdf:about="#hasBond">
        <rdfs:domain rdf:resource="#Compound"/>
        <rdfs:range rdf:resource="#Bond"/>
    </owl:ObjectProperty>

    <owl:ObjectProperty rdf:about="#hasStructure">
        <rdfs:domain rdf:resource="#Compound"/>
        <rdfs:range rdf:resource="#Structure"/>
    </owl:ObjectProperty>

    <owl:ObjectProperty rdf:about="#inBond">
        <rdfs:range rdf:resource="#Atom"/>
        <rdfs:domain rdf:resource="#Bond"/>
    </owl:ObjectProperty>

    <owl:DatatypeProperty rdf:about="#charge">
        <rdfs:domain rdf:resource="#Atom"/>
        <rdfs:range rdf:resource="&xsd;double"/>
    </owl:DatatypeProperty>

    <owl:DatatypeProperty rdf:about="#isMutagenic">
        <rdfs:domain rdf:resource="#Compound"/>
        <rdfs:range rdf:resource="&xsd;boolean"/>
    </owl:DatatypeProperty>

    <owl:Class rdf:about="#Atom"/>

    <owl:Class rdf:about="#Bond">
        <owl:disjointWith rdf:resource="#Structure"/>
        <owl:disjointWith rdf:resource="#Atom"/>
    </owl:Class>

    <owl:Class rdf:about="#Bond-7">
        <rdfs:subClassOf rdf:resource="#Bond"/>
    </owl:Class>

    <owl:Class rdf:about="#Carbon-22">
        <rdfs:subClassOf rdf:resource="#Carbon"/>
    </owl:Class>

    <owl:Class rdf:about="#Compound">
        <owl:disjointWith rdf:resource="#Structure"/>
        <owl:disjointWith rdf:resource="#Atom"/>
        <owl:disjointWith rdf:resource="#Bond"/>
    </owl:Class>

    <owl:Class rdf:about="#Six_ring">
        <rdfs:subClassOf rdf:resource="#Ring"/>
    </owl:Class>

    <owl:Class rdf:about="#Ring">
        <rdfs:subClassOf rdf:resource="#Structure"/>
    </owl:Class>

    <owl:Class rdf:about="#Structure">
        <owl:disjointWith rdf:resource="#Atom"/>
    </owl:Class>

    <Compound rdf:about="#d1">
        <hasBond rdf:resource="#bond1"/>
        <hasAtom rdf:resource="#d1_2"/>
        <hasAtom rdf:resource="#d1_3"/>
        <hasStructure rdf:resource="#six_ring-1"/>
        <isMutagenic rdf:datatype="&xsd;boolean">false</isMutagenic>
    </Compound>

    <Bond-7 rdf:about="#bond1">
        <inBond rdf:resource="#d1_3"/>
        <inBond rdf:resource="#d1_2"/>
    </Bond-7>

    <Carbon-22 rdf:about="#d1_2">
        <charge rdf:datatype="&xsd;double">-0.133</charge>
    </Carbon-22>

    <Carbon-22 rdf:about="#d1_3">
        <charge rdf:datatype="&xsd;double">-0.0030</charge>
    </Carbon-22>

    <Six_ring rdf:about="#six_ring-1"/>

    <Compound rdf:about="#d10">
        <hasBond rdf:resource="#bond40"/>
        <hasAtom rdf:resource="#d10_12"/>
        <hasAtom rdf:resource="#d10_13"/>
        <isMutagenic rdf:datatype="&xsd;boolean">false</isMutagenic>
        <hasStructure rdf:resource="#six_ring-9"/>
    </Compound>

    <Bond-1 rdf:about="#bond40">
        <inBond rdf:resource="#d10_12"/>
        <inBond rdf:resource="#d10_13"/>
    </Bond-1>

    <Six_ring rdf:about="#six_ring-9"/>

    <Nitrogen-32 rdf:about="#d10_12">
        <charge rdf:datatype="&xsd;double">-0.313</charge>
    </Nitrogen-32>

    <Nitrogen-32 rdf:about="#d10_13">
        <charge rdf:datatype="&xsd;double">-0.313</charge>
    </Nitrogen-32>

</rdf:RDF>
"""

# Inspired by https://stackoverflow.com/a/33290642/5433896:

sparql_query = """CONSTRUCT {
   :d1 ?prop ?val .
   ?child ?childProp ?childPropVal . 
   ?someSubj ?incomingChildProp ?child .
}
WHERE {
     :d1 ?prop ?val ;
         (:overrides|!:overrides)+ ?child . 
     ?child ?childProp ?childPropVal.
     ?someSubj ?incomingChildProp ?child. 
}
"""

# Trying this query out:
import rdflib
import logging
logger = logging.getLogger()
logger.setLevel("INFO")

graph = rdflib.Graph()
graph.parse(data=rdf, format='xml')
result = graph.query(sparql_query)
for s, p, o in result:
    print(s, p, o)
    if s.endswith('#d10') or s.endswith('#bond40') or s.endswith('#six_ring-9') or s.endswith('#d10_12') or s.endswith('#d10_13'):
        logging.error('This triple should not be in the results! => {0} {1} {2}.'.format(s, p, o))

I get two errors that I want to avoid:

ERROR:root:This triple should not be in the results! => http://dl-learner.org/carcinogenesis#six_ring-9 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dl-learner.org/carcinogenesis#Six_ring.

ERROR:root:This triple should not be in the results! => http://dl-learner.org/carcinogenesis#d10 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dl-learner.org/carcinogenesis#Compound.

score 2 · Accepted Answer · edited Jun 18 '19 at 16:22

I found out the answer to this question when adding extra things I had already noticed.

Since :d1 rdf:type :Compound and :d10 rdf:type :Compound, there is actually a path from :d1 to :d10 and therefore triples about :d10 also end up in my query results - which is of course not what I wanted.

Looking at the query, I thought it would make sense to add an additional constraint that ?child mustn't be :d10. And, thinking about the way the poster of https://stackoverflow.com/a/33290642/5433896 explained his query, I should also exclude that ?someSubj or ?childPropVal can be :d10:

CONSTRUCT {
   :d1 ?prop ?val .
   ?child ?childProp ?childPropVal . 
   ?someSubj ?incomingChildProp ?child .
}
WHERE {
     :d1 (:overrides|!:overrides)+ ?child . 
     ?child ?childProp ?childPropVal.
     ?someSubj ?incomingChildProp ?child.
     FILTER (?child != :d10)
     FILTER (?childPropVal != :d10)
     FILTER (?someSubj != :d10)
}

This removed :d10 from my query results. Great!

But the error ERROR:root:This triple should not be in the results! => http://dl-learner.org/carcinogenesis#six_ring-9 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dl-learner.org/carcinogenesis#Six_ring. remains.

I played with removal of some plausible triples causing this issue and found out that the triple { Six_ring rdf:about="#six_ring-9" } is the cause of still having #six_ring-9 in the query results. So, again, rdf:type (implied in rdf:about) is causing the problem.

Ideally, we would need describe in SPARQL that we are interested to know what the rdf:types are of objects linked to :d1 (e.g. :Compound, :Six_Ring), but NOT what other objects are also linked to those object types. That would solve BOTH problems we initially detected with the query.

So this query solves the issue:

CONSTRUCT {
   :d1 ?prop ?val .
   ?child ?childProp ?childPropVal . 
   ?someSubj ?incomingChildProp ?child .
}
WHERE {
     :d1 (:overrides|!:overrides)+ ?child . 
     ?child ?childProp ?childPropVal.
     ?someSubj ?incomingChildProp ?child.
     FILTER (?incomingChildProp != rdf:type)
}

SPARQL: querying all triples linked to one URL, but not to another

1 Answers1