class pronto.Entity[source]

An entity in the ontology graph.

With respects to the OBO semantics, an Entity is either a term or a relationship in the ontology graph. Any entity has a unique identifier as well as some common properties.

__eq__(other: Any) → bool[source]

Return self==value.


Return self<value.


Return self<=value.


Return self>value.


Return self>=value.


Return hash(self).


Return repr(self).

property alternate_ids

A set of alternate IDs for this entity.


frozenset of str

property annotations

Annotations relevant to the entity.


frozenset of PropertyValue

property anonymous

Whether or not the entity has an anonymous id.

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



property builtin

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.



property comment

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.


str or None

property created_by

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.


str or None

property creation_date

the date the entity was created.


datetime or None

property definition

the textual 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.


str or None

property id

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.



property name

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.


str or None

property namespace

the namespace this entity is defined in.


str or None

property obsolete

whether or not the entity is obsolete.



property subsets

the subsets containing this entity.


frozenset of str

property synonyms

a set of synonyms for this entity.


frozenset of Synonym

property xrefs

a set of database cross-references.

Xrefs can be used to describe an analogous entity in another vocabulary, such as a database or a semantic knowledge base.


frozenset of Xref

add_synonym(description: str, scope: Optional[str] = None, type: Optional[pronto.synonym.SynonymType] = None, xrefs: Optional[Iterable[pronto.xref.Xref]] = None) → pronto.synonym.Synonym[source]

Add a new synonym to the current entity.

  • 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.


ValueError – when given an invalid synonym type or scope.


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