A Python frontend to (Open Biomedical) Ontologies.
MIT License
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Published by althonos almost 2 years ago
LineageIterator.to_set
when starting from an empty set of entities.Published by althonos over 2 years ago
fastobo
dependecy to v0.12.1
Published by althonos over 3 years ago
pronto.pv.PropertyValue
is now an abstract class.pronto.parsers.RdfXmlParser
now ignores synonym Xrefs not inpronto.Entity.definition
documentation now lists return type aspronto.definition.Definition
as expected.pronto.utils.typechecked.disabled
is now reentrant and shouldlxml
instead of xml.etree
, which causedRdfXmlParser
.Published by althonos over 3 years ago
v3
.fastobo
dependency to v0.10.0
.Published by althonos about 4 years ago
pronto.entity
package not being included in source distribution.Published by althonos about 4 years ago
Ontology
.Relationships
view.__all__
attribute to all modules of the data model.RelationshipSet
container like TermSet
with shortcut attributes andRelationship
instances.Relationship.subproperties
and Relationship.superproperties
methodsRelationship
instance.Ontology.synonym_types
method to count (via SizedIterator
) and iterateOntology.get_synonym_type
method to retrieve a single synonym type by IDconsider
, disjoint_from
, disjoint_over
, equivalent_to
, replaced_by
transitive_over
and union_of
properties of Relationship
now returnRelationshipSet
.Term.subclasses
describing the performances ofAttributeError
with the setter of the Entity.synonyms
property.Published by althonos about 4 years ago
Entity.annotations
return a mutable set and add a setter.Term.relationship
erroneously updating the Ontology._lineage
cache.pronto.serializers._fastobo
handling is_a
clauses.Published by althonos about 4 years ago
frozendict
with immutabledict
(#90).fastobo
dependency to v0.9.0
to support inline comments.Published by althonos over 4 years ago
Term.subclasses
and Term.superclasses
.Term.equivalent_to
setter crashing with a NameError
.Entity.synonyms
setter not extracting synonym data.Published by althonos over 4 years ago
anti_symmetric
clauses in OBO typedefs.ResourceWarning
when creating Ontology
from file-handles not mappingPublished by althonos over 4 years ago
threads
parameter to Ontology
constructor to control the number ofis_a
pseudo-relationshipOntology
.Term.subclasses()
and Term.superclasses()
. (#84)fastobo
to v0.8
, which reduce memory footprint of identifiers,Xref
instantiation.idspace
clauses in their headers.TermSet
.nanoset
depency, which was not useful anymore in Python 3.8 and causedPublished by althonos over 4 years ago
Published by althonos over 4 years ago
Ontology
to outlive allTerm
s created from it.Term.id
property missing a return type annotation.Term.equivalent_to
not returning a TermSet
but a set of strings.SubclassesIterator
andSuperclassesIterator
to make both use the interal subclassing cache.Term.is_leaf
use internal subclassing cache to make it run inPublished by althonos over 4 years ago
TermSet.subclasses
and TermSet.superclasses
methods to query allTerm
.TermSet
class to the top-level pronto
module.Ontology
class.Term.consider
, Term.union_of
and Term.intersection_of
.cache
keyword argument for the Ontology
.SuperclassesIterator.to_set
being named to_self
because of a typo.fastobo
-backed serializer.Published by althonos over 4 years ago
with_self
to disable reflexivity of Term.subclasses
andTerm.superclasses
iterators.TermSet
class which stores a set of terms efficiently while providingTerm.subclasses
and Term.superclasses
to a dedicatedpronto.logic
submodule.contexter
requirement.Synonym.type
setter leading to a potential bug whentype
is None
.mypy
.fastobo
serializer crashing on namespace clauses because of a typefastobo
parsers using data version clauses as format version clauses.Published by althonos almost 5 years ago
fastobo
to v0.7.0
, switching parser implementation to use