Relationship¶

class pronto.Relationship[source]¶

A relationship, constitute the edges of the ontology graph.

Also sometimes refered as typedefs, relationship types, properties or predicates. Formally equivalent to a property (either ObjectProperty or AnnotationProperty) in OWL2.

classmethod __class_getitem__(params)¶

Parameterizes a generic class.

At least, parameterizing a generic class is the main thing this method does. For example, for some generic class Foo, this is called when we do Foo[int] - there, with cls=Foo and params=int.

However, note that this method is also called when defining generic classes in the first place with class Foo(Generic[T]): ....

__eq__(other: Any) → bool¶: Return self==value.

__ge__(other)¶: Return self>=value.

__gt__(other)¶: Return self>value.

__hash__()¶: Return hash(self).

__le__(other)¶: Return self<=value.

__lt__(other)¶: Return self<value.

__repr__()¶: Return repr(self).

add_synonym(description: str, scope: str | None = None, type: SynonymType | None = None, xrefs: Iterable[Xref] | None = None) → Synonym¶

Add a new synonym to the current entity.

Parameters:

description (str) – The alternate definition of the entity, or a related human-readable synonym.
scope (str or None) – An optional synonym scope. Must be either EXACT, RELATED, BROAD or NARROW if given.
type (SynonymType or None) – An optional synonym type. Must be declared in the header of the current ontology.
xrefs (iterable of Xref, or None) – A collections of database cross-references backing the origin of the synonym.

Raises:

ValueError – when given an invalid synonym type or scope.

Returns:

Synonym – A new synonym for the terms. The synonym is already added to the Entity.synonyms collection.

property alternate_ids: Set[str]¶

A set of alternate IDs for this entity.

Type:: set of str

property annotations: Set[PropertyValue]¶

Annotations relevant to the entity.

Type:: set of PropertyValue

property anonymous: bool¶

Whether or not the entity has an anonymous id.

Semantics of anonymous entities are the same as B-Nodes in RDF.

Type:: bool

property builtin: bool¶

Whether or not the entity is built-in to the OBO format.

pronto uses this tag on the is_a relationship, which is the axiomatic to the OBO language but treated as a relationship in the library.

Type:: bool

property comment: str | None¶

A comment about the current entity.

Comments in comment clauses are guaranteed to be conserved by OBO parsers and serializers, unlike bang comments. A non None comment is semantically equivalent to a rdfs:comment in OWL2. When parsing from OWL, several RDF comments will be merged together into a single comment clause spanning over multiple lines.

Type:: str or None

property consider: _S¶

A set of potential substitutes for an obsolete term.

An obsolete entity can provide one or more entities which may be appropriate substitutes, but needs to be looked at carefully by a human expert before the replacement is done.

See also

replaced_by, which provides a set of entities suitable for automatic replacement.

Type:: EntitySet

property created_by: str | None¶

The name of the creator of the entity, if any.

This property gets translated to a dc:creator annotation in OWL2, which has very broad semantics. Some OBO ontologies may instead use other annotation properties such as the ones found in Information Interchange Ontology, which can be accessed in the annotations attribute of the entity, if any.

Type:: str or None

property creation_date: datetime | None¶

The date the entity was created.

Type:: datetime or None

property definition: Definition | None¶

The definition of the current entity.

Definitions in OBO are intended to be human-readable text describing the entity, with some additional cross-references if possible.

Example

>>> hp = pronto.Ontology.from_obo_library("hp.obo")
>>> term = hp["HP:0009882"]
>>> term.name
'Short distal phalanx of finger'
>>> str(term.definition)
'Short distance from the end of the finger to the most distal...'
>>> sorted(term.definition.xrefs)
[Xref('HPO:probinson'), Xref('PMID:19125433')]

Type:: Definition or None

property disjoint_from: _S¶

The entities declared as disjoint from this entity.

Two entities are disjoint if they have no instances in common. Two entities that are disjoint cannot share any subentities, but the opposite is not always true.

Type:: EntitySet

property equivalent_to: _S¶

The entities declared as equivalent to this entity.

Type:: EntitySet

property id: str¶

The OBO identifier of the entity.

Identifiers can be either prefixed (e.g. MS:1000031), unprefixed (e.g. part_of) or given as plain URLs. Identifiers cannot be edited.

Type:: str

property name: str | None¶

The name of the entity.

Names are formally equivalent to rdf:label in OWL2. The OBO format version 1.4 made names optional to improve OWL interoperability, as labels are optional in OWL.

Type:: str or None

property namespace: str | None¶

The namespace this entity is defined in.

Type:: str or None

property obsolete: bool¶

Whether or not the entity is obsolete.

Hint

All OBO entities can be made obsolete through a boolean flag, and map to one or several replacements. When querying an obsolete entity, pronto will not attempt to perform any kind of replacement itself

>>> ms = pronto.Ontology.from_obo_library("ms.obo")
>>> term = ms["MS:1001414"]
>>> term
Term('MS:1001414', name='MGF scans')
>>> term.obsolete
True

To always get the up-to-date, non-obsolete entity, you could use the following snippet, going through a term replacement if there is no ambiguity

>>> while term.obsolete:
...     if len(term.replaced_by) != 1:
...         raise ValueError(f"no replacement for {term.id}")
...     term = term.replaced_by.pop()
>>> term
Term('MS:1000797', name='peak list scans')