How to access <owl:Axiom>?

[fsutter]

Hi,

Sorry for my rookie question: my classes have <owl:Axiom> sections.

A typical ex:
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://xxxxxxx/ID1"/>
        <owl:annotatedProperty rdf:resource="http://XXXXXXX/core#CONCEPT_hasMapping"/>
        <owl:annotatedTarget rdf:resource="http://id.nlm.nih.gov/mesh/D016584"/>
        <dcterm:source>IDMESH</dcterm:source>
        <rdfs:label>Panic Disorder</rdfs:label>
    </owl:Axiom>

I haven't found how to access and modify their content.

Many thanks in advance and kind regards,

fsutter

[Jiba]

Hi,

These axioms, used for annotating relations, can be accessed in Owlready as follows :

 * Old notations (still supported) : annotation[source, property, target]

where annotation is the annotation property (e.g. label in your example), and source, property and target are the annotatedSource, annotatedProperty and annotatedTarget.

 * New notation : AnnotatedRelation(source, property, target) object, and then use .annotation to access the various annotation (e.g. .label).

Access is both read and write.

Here is an example:


onto = get_ontology("http://example.org/onto.owl")

with onto:
  class C(Thing): pass
  class p(C >> int): pass

  c1 = C()
  c1.p = [1]

  comment[c1, p, 1] = ["comment"]

  a = AnnotatedRelation(c1, p, 1)
  a.comment = ["a comment on the relation"]
  a.label = ["relation label"]


Best regards,
Jiba

[fsutter]

Hi,

thanks for the reply.

Maybe I should better explain what I want to achieve:

In the file I've currently a lot of block like that:

    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://xxxxxxx/ID1"/>
        <owl:annotatedProperty rdf:resource="http://XXXXXXX/core#CONCEPT_hasMapping"/>
        <owl:annotatedTarget rdf:resource="http://id.nlm.nih.gov/mesh/D016584"/>
        <dcterm:source>IDMESH</dcterm:source>
        <rdfs:label>Panic Disorder</rdfs:label>
    </owl:Axiom>

And want to replace <owl:annotatedProperty rdf:resource="http://XXXXXXX/core#CONCEPT_hasMapping"/> depending of the value of dcterm:source

So I need two things:
* have a way to find all AnnotatedRelation with annotatedProperty == http://XXXXXXX/core#CONCEPT_hasMapping
* replace http://XXXXXXX/core#CONCEPT_hasMapping

I can access a specif disease with this code:

disease_ontology = get_ontology("class.owl").load()
disease = disease_ontology["ID1"]

But after I don't know how to continue.

Once again, sorry fo my stupid questions.

Thanks a lot

[Jiba]

Hi,

If you want to search for all such axioms, the best option is to use a SPARQL query. Here is an example:


onto = get_ontology("http://example.org/onto.owl")

with onto:
  class C(Thing): pass

  class p (C >> int): pass
  class p2(C >> int): pass

  c1 = C()
  c1.p = [1]

  comment[c1, p, 1] = "comment"

  a = AnnotatedRelation(c1, p, 1)
  a.comment = ["a comment on the relation"]
  a.label = ["relation label"]

l = default_world.sparql("""
SELECT ?source ?target {
  ?x owl:annotatedSource ?source .
  ?x owl:annotatedProperty onto:p .
  ?x owl:annotatedTarget ?target .
}
""")

for source, target in l:
  a = AnnotatedRelation(source, p, target)
  print(a, a.get_properties())
 

You can either use AnnotatedRelation to modify the axiom, or using more complex SPARQL queries to perform the modification, e.g.:


with onto:
  default_world.sparql("""
INSERT {
  ?x owl:annotatedProperty onto:p2 .
} WHERE {
  ?x owl:annotatedSource ?source .
  ?x owl:annotatedProperty onto:p .
  ?x owl:annotatedTarget ?target .
}
""")
  default_world.sparql("""
DELETE {
  ?x owl:annotatedProperty onto:p .
} WHERE {
  ?x owl:annotatedSource ?source .
  ?x owl:annotatedProperty onto:p .
  ?x owl:annotatedTarget ?target .
}
""")


Best regards,
Jiba