python - SPARQL:查询链接到一个 URL 但不链接到另一个 URL 的所有三元组

Question

从一个包含多种化合物声明的 RDF 文件中，我想为每种化合物创建一个 RDF 文件。

为了做到这一点，我开始寻找一个 SPARQL 查询，它可以隔离链接到某个 URL 的所有三元组，无论中间有多少节点。

我从一个非常有趣的 SPARQL 查询 ( https://stackoverflow.com/a/33290642/5433896 ) 开始，这样它会(希望)返回与我的数据集中的化学化合物 :d1 相关的所有三元组，但不是关于另一个化合物:d10:

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

但是，当我在简化的测试用例(python)上运行此命令时:

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))

我遇到了两个我想避免的错误:

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.

Answer 1

在添加我已经注意到的额外内容时，我找到了这个问题的答案。

由于 :d1 rdf:type :Compound 和 :d10 rdf:type :Compound，实际上有一条从 :d1 到:d10 因此关于 :d10 的三元组也最终出现在我的查询结果中 - 这当然不是我想要的。

查看查询，我认为添加一个附加约束是有意义的，即 ?child 不得为 :d10。并且，思考https://stackoverflow.com/a/33290642/5433896的海报的方式解释了他的查询，我还应该排除 ?someSubj 或 ?childPropVal 可以是 :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)
}

这从我的查询结果中删除了 :d10。太棒了!

但是错误ERROR:root:This Triple不应该出现在结果中! => 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。 仍然存在。

我删除了一些可能导致此问题的三元组，发现三元组 { Six_ring rdf:about="#six_ring-9"} 是仍然存在 # 的原因查询结果中的 Six_ring-9。因此，再次，rdf:type(隐含在 rdf:about 中)导致了问题。

理想情况下，我们需要在 SPARQL 中描述我们有兴趣知道链接到 :d1 的对象的 rdf:types 是什么(例如 :Compound 、:Six_Ring)，但不包括链接到这些对象类型的其他对象。这将解决我们最初通过查询检测到的两个问题。

所以这个查询解决了这个问题:

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)
}