Adding a relationship between two terms

[neobernad]

Hi,

According to the docs I can see how I could create a relationship, however I do not manage to link two terms with a relationship. I would like to achieve something like:

ms: Ontology = pronto.Ontology.from_obo_library("ms.obo")
rel_is_a: Relationship = ms.get_relationship("is_a")
ms['MS:1000031'].relationships.set(rel_is_a, ms['MS:1001792'])

Is this possible somehow?

Thanks,
José Antonio

[althonos]

Hi @neobernad

currently there's no recommended way of doing it, mostly because I haven't taken the time to write a custom mapping class for the Term.relationship attribute that would perform a validation step on its arguments. Because of this, I use frozendicts for the time being, which you can't edit.

Note that is_a is not considered as a normal relationship by the way: OBO relationships are semantically equivalent to OWL AnnotationProperty or ObjectProperty, while is_a is actually the subClassOf defined in the RDF schema. It is being exposed as a relationship for convenience with OBO, but actually it's handled differently.

I'm currently refactoring some parts of the parser interface, but I'll try to see what I can do before the next release.

[althonos]

However, if for the time being you really really need that feature, you can achieve that by fondling with pronto's internals (this is not guaranteed to work in the next versions but should at least work now).

Subclasses

ont: Ontology = pronto.Ontology()
ont.create_term("ONT:001")
ont.create_term("ONT:002")

ont._inheritance["ONT:001"].sub.add("ONT:002")   # register ONT:002 as a subclass of ONT:001
ont._inheritance["ONT:002"].sup.add("ONT:001")   # register ONT:001 as a superclass of ONT:002

Note that you must do both, otherwise Term.subclasses or Term.superclasses is bound to break.

Relationships

ont: Ontology = pronto.Ontology()
ont.create_term("ONT:001")
ont.create_term("ONT:002")
better_than = ont.create_relationship("better_than")

ont["ONT:002"].relationships = {better_than: {"ONT:001"}}

Same, if you want to be semantically coherent, you'd need to take into account whether the relation is symmetric etc.

[neobernad]

Hi @althonos!

Thanks for the solution and your quick response, it worked for me, I really needed to establish the relationships.

[althonos]

Hi @neobernad ,

v2.2.0 was released, and I changed the way to manage subclasses and superclasses. is_a relationship is soft-deprecated, and adding new subclasses to a term is done with the object given by the subclasses or superclasses method:

ont: Ontology = pronto.Ontology()
t1 = ont.create_term("ONT:001")
t2 = ont.create_term("ONT:002")

t1.superclasses().add(t2)     # these two lines are equivalent,
t2.subclasses().add(t1)       # only call one of them.

For relationships, the snippet I wrote in the previous answer is the recommended way for now.

[neobernad]

Hello @althonos,

Thank you so much, this is really helpful. I will do it this way now!