Entity¶
-
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.-
property
anonymous
¶ Whether or not the entity has an anonymous id.
Semantics of anonymous entities are the same as B-Nodes in RDF.
- Type
-
property
builtin
¶ Whether or not the entity is built-in to the OBO format.
pronto
uses this tag on theis_a
relationship, which is the axiomatic to the OBO language but treated as a relationship in the library.- Type
-
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 nonNone
comment
is semantically equivalent to ardfs:comment
in OWL2. When parsing from OWL, several RDF comments will be merged together into a singlecomment
clause spanning over multiple lines.
-
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 theannotations
attribute of the entity, if any.
-
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.
- Type
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.- Type
-
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.
-
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.
-
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.
- Parameters
description (
str
) – The alternate definition of the entity, or a related human-readable synonym.scope (
str
orNone
) – An optional synonym scope. Must be either EXACT, RELATED, BROAD or NARROW if given.type (
SynonymType
orNone
) – An optional synonym type. Must be declared in the header of the current ontology.xrefs (iterable of
Xref
, orNone
) – 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 theEntity.synonyms
collection.
-
property