Ontology to graph
In this module we provide different methods for projecting an ontology into a graph: The methods we provide are:
Ontology Projection
- class mowl.projection.base.ProjectionModel
Bases:
objectAbstract class for Ontology projection into a graph
- Parameters
ontology (
org.semanticweb.owlapi.model.OWLOntology) – The ontology to be processed.
- project(ontology)
Performs the ontology parsing.
- Returns
A list of triples where each triple is of the form \((head, relation, tail)\)
- Return type
List of
mowl.graph.edge.Edge
- class mowl.projection.base.Graph(edges)
Bases:
objectStores a graph in the form of an edgelist in which each edge is an instance of the class
mowl.graph.edge.Edge- Parameters
edges (
mowl.graph.edge.Edge) – A list of edges
All the methods will return a list of edges corresponding to the Edge class:
Edge
- class mowl.projection.edge.Edge(src, rel, dst, weight=1)
Bases:
object- src()
Getter method for _src attribute
- Return type
- rel()
Getter method for _rel attribute
- Return type
- dst()
Getter method for _dst attribute
- Return type
- weight()
Getter method for _weight attribute
- Return type
- static getEntitiesAndRelations(edges)
- Parameters
edges (
Edge) – list of edges- Returns
Returns a 2-tuple containing the list of entities (heads and tails) and the list of relations
- Return type
(Set of str, Set of str)
Subclass Hierarchy
- class mowl.projection.taxonomy.model.TaxonomyProjector(bidirectional_taxonomy: bool = False)
Bases:
ProjectionModelThis class will project the ontology considering only the axioms of the form \(A \sqsubseteq B\) where A and B are ontology classes.
- Parameters
ontology – The ontology to be processed.
bidirectional_taxonomy – If true then per each SubClass edge one SuperClass edge will be generated.
- project(ontology)
Performs the ontology parsing.
- Returns
A list of triples where each triple is of the form \((head, relation, tail)\)
- Return type
List of
mowl.graph.edge.Edge
Subclass Hierarchy With Relations
- class mowl.projection.taxonomyRels.model.TaxonomyWithRelsProjector(taxonomy=False, bidirectional_taxonomy: bool = False, relations=None)
Bases:
ProjectionModelThis class will project the ontology considering the following axioms:
\(A \sqsubseteq B\) will generate the triple \(\langle A, subClassOf, B \rangle\)
\(A \sqsubseteq \exists R. B\) will generate the triple \(\left\langle A, R, B \right\rangle\)
- Parameters
ontology – The ontology to be processed.
bidirectional_taxonomy – If true then per each SubClass edge one SuperClass edge will be generated.
- project(ontology)
Performs the ontology parsing.
- Returns
A list of triples where each triple is of the form \((head, relation, tail)\)
- Return type
List of
mowl.graph.edge.Edge
DL2Vec Graph
The DL2Vec graph follows the rules described in the paper Predicting candidate genes from phenotypes, functions, and anatomical site of expression (2020). The parsing rules are shown in the table below:
Condition 1 |
Condition 2 |
Triple(s) |
|---|---|---|
\(A \sqsubseteq Q R_{0} \ldots Q R_{m} D\) |
\(D := B_{1} \sqcup \ldots \sqcup B_{n} | B_{1} \sqcap \ldots \sqcap B_{n}\) |
\(\left\langle A, (R_{0}...R_{m}), B_i \right\rangle\) for \(i \in 1 \ldots n\) |
\(A \equiv Q R_{0} \ldots Q R_{m} D\) |
||
\(A \sqsubseteq B\) |
\(\left\langle A, SubClassOf, B \right\rangle\) |
|
\(A \equiv B\) |
\(\left\langle A, EquivalentTo, B \right\rangle\) |
- class mowl.projection.dl2vec.model.DL2VecProjector(bidirectional_taxonomy: bool = False)
Bases:
ProjectionModel- Parameters
ontology – The ontology to be processed.
bidirectional_taxonomy – If true then per each SubClass edge one SuperClass edge will be generated.
- project(ontology)
Performs the ontology parsing.
- Returns
A list of triples where each triple is of the form \((head, relation, tail)\)
- Return type
List of
mowl.graph.edge.Edge
OWL2Vec* Graph
The OWL2Vec* graph follows the rules described in the paper OWL2Vec*: embedding of OWL ontologies (2021). The parsing rules are shown in the table below:
Axiom of condition 1 |
Axiom or triple(s) of condition 2 |
Projected triple(s) |
|---|---|---|
\(A \sqsubseteq \square r . D\) |
\(D \equiv B\left|B_{1} \sqcup \ldots \sqcup B_{n}\right| B_{1} \sqcap \ldots \sqcap B_{n}\) |
\(\langle A, r, B\rangle\) |
or |
||
\(\square r . D \sqsubseteq A\) |
||
\(\exists r . \top \sqsubseteq A\) (domain) |
\(\top \sqsubseteq \forall r . B\) (range) |
\(\langle A, r, B_{i}\rangle\) for \(i \in 1, \ldots, n\) |
\(A \sqsubseteq \exists r .\{b\}\) |
\(B(b)\) |
|
\(r \sqsubseteq r^{\prime}\) |
\(\left\langle A, r^{\prime}, B\right\rangle\) has been projected |
|
\(r^{\prime} \equiv r^{-}\) |
\(\left\langle B, r^{\prime}, A\right\rangle\) has been projected |
|
\(s_{1} \circ \ldots \circ s_{n} \sqsubseteq r\) |
\(\langle A, s_1, C_1\rangle \ldots \langle C_n, s_n, B\rangle\) have been projected |
|
\(B \sqsubseteq A\) |
\(-\) |
\(\langle B, r d f s: s u b C l a s s O f, A\rangle\) |
\(\left\langle A, rdfs:subClassOf^{-}, B\right\rangle\) |
||
\(A(a)\) |
\(-\) |
\(\langle a, r d f: t y p e, A\rangle\) |
\(\left\langle A, r d f: t y p e^{-}, a\right\rangle\) |
||
\(r(a, b)\) |
\(-\) |
\(\langle a, r, b\rangle\) |
- class mowl.projection.owl2vec_star.model.OWL2VecStarProjector(bidirectional_taxonomy=False, only_taxonomy=False, include_literals=False)
Bases:
ProjectionModel- Parameters
ontology (
org.semanticweb.owlapi.model.OWLOntology) – The ontology to be processed.bidirectional_taxonomy (bool) – If true then per each SubClass edge one SuperClass edge will be generated. Default is False.
include_literals (bool) – If true the graph will also include triples involving data property assertions and annotations. Default is False.
only_taxonomy (bool) – If true, the projection will only include subClass edges
- project(ontology)
Performs the ontology parsing.
- Returns
A list of triples where each triple is of the form \((head, relation, tail)\)
- Return type
List of
mowl.graph.edge.Edge