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.

__eq__(other: Any) → bool[source]

Return self==value.

__lt__(other)[source]

Return self<value.

__le__(other)[source]

Return self<=value.

__gt__(other)[source]

Return self>value.

__ge__(other)[source]

Return self>=value.

__hash__()[source]

Return hash(self).

__repr__()[source]

Return repr(self).

property alternate_ids

A set of alternate IDs for this entity.

Type

set of str

property annotations

Annotations relevant to the entity.

Type

set 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.

Type

bool

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.

Type

bool

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.

Type

str or None

property consider

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

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

The date the entity was created.

Type

datetime or None

property definition

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

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

The entities declared as equivalent to this entity.

Type

EntitySet

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

str

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.

Type

str or None

property namespace

The namespace this entity is defined in.

Type

str or None

property obsolete

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')

See also

consider and replaced_by, storing some replacement options for an obsolete entity.

Type

bool

property relationships

The links from an entity to other entities.

This property returns an object that maps a Relationship to an EntitySet (either a TermSet for Term.relationships, or a RelationshipSet for Relationship.relationships).

Hint

The mapping is mutable, so relationships can be created or removed using the usual interface of a MutableMapping.

Example

Get the MS:1000004 term (sample mass) from the Mass Spectrometry ontology:

>>> ms = pronto.Ontology.from_obo_library("ms.obo")
>>> sample_mass = ms["MS:1000004"]

Then use the relationships property to get the relevant unit from the Unit Ontology:

>>> sorted(sample_mass.relationships.keys())
[Relationship('has_units', name='has_units')]
>>> sample_mass.relationships[ms.get_relationship('has_units')]
TermSet({Term('UO:0000021', name='gram')})
Type

Relationships

property replaced_by

A set of of replacements for an obsolete term.

An obsolete entity can provide one or more replacement that can safely be used to automatically reassign instances to non-obsolete classes.

See also

consider, which provides a set of entities suitable for replacement but requiring expert curation.

Type

EntitySet

property subsets

The subsets containing this entity.

Type

frozenset of str

property synonyms

A set of synonyms for this entity.

Type

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.

Type

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.

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.