All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.1.3 - 2019-11-10


  • Handling of some clauses in FastoboParser.

  • OboSerializer occasionaly missing lines between term and typedef frames.


  • Missing docstrings to some Entity properties.

1.1.2 - 2019-10-30


  • RdfXMLParser crashing on entities with rdf:label elements without literal content.

1.1.1 - 2019-10-29


  • pronto.serializers module not being embedded in Wheel distribution.

1.1.0 - 2019-10-24


  • Entity.add_synonym method to create a new synonym and add it to an entity.

  • @roundrepr now adds a minimal docstring to the generated __repr__ method.

  • Ontology caches subclassing relationships to greatly improve performance of Term.subclasses.


  • Entity subclasses now store their id directly to improve performance.

  • Term.subclasses and Term.superclasses use collections.deque instead of queue.Queue as a LIFO structure since thread-safety is not needed.

  • chardet result is now used even when prediction confidence is under 100% to detect encoding of the handle passed to Ontology.


  • SynonymType comparison implementation.

  • Synonym.type getter crashing on type not being None.

  • RdfXMLParser crashing on synonymtypedefs without scope specifiers.

1.0.0 - 2019-10-11


  • Issues with typedef serialization in FastoboSerializer.

  • Ontology.create_term and Ontology.create_relationship not raising ValueError when given an identifier already in the knowledge graph.

  • Signature of BaseSerializer.dump to remove encoding argument.

  • Missing __slots__ in Entity in non-typechecking runtime.


  • Bumped fastobo requirement to v0.6.0.

1.0.0-alpha.3 - 2019-10-10


  • Extraction of oboInOwl:consider annotation in RdfXMLParser.

  • Extraction of oboInOwl:savedBy annotation in RdfXMLParser.

  • Extraction of subsetdef and synonymtypedef as annotation properties in RdfXMLParser.

  • Support for doap:Version instead of owl:VersionIri for specification of ontology data version.

  • Proper comparison of PropertyValue classes, based on the lexicographic order of their serialization.

  • Ontology.dump and Ontology.dumps methods to serialize an ontology in obo or obojson format.


  • Metadata not storing optional description of ID spaces if any.

  • Wrong type hints in RelationshipData.equivalent_to_chain.


  • Added type checking to some more property setters.

  • Avoid using networkx in Term.subclasses.

  • fastobo-derived parsers will not create a new entity if one exists in the graph of dependencies already.

  • Exposed pronto.warnings and the complete warnings hierarchy.

1.0.0-alpha.2 - 2019-10-03


  • Support for extraction of relationships from OWL/XML files to OwlXMLParser.


  • Type hints of RelationshipData.synonyms attribute.

1.0.0-alpha.1 - 2019-10-02


  • Dropped support for Python earlier than 3.6.

  • Brand new data model that follow the OBO 1.4 object model.

  • Partial OWL XML parser implementation using the OBO 1.4 semantics.

  • New OBO parser implementation based on fastobo.

  • Imports are properly separated from the top-level ontology.

  • Ontology.__getitem__ can also access entities from imports.

  • Term, Relationship, Xref, SynonymType compare only based on their ID.

  • Subset, Definition compare only based on their textual value.


  • Support for OBO JSON parser based on fastobo.

  • Provisional mypy type hints.

  • Type checking for most properties in __debug__ mode.

  • Proper repr implementation that should roundtrip most of the time.

  • Detection of file format and encoding based on buffer content.


  • OBO and JSON serialization support (for now).

  • Term.rchildren and Term.rparents and stop making direction assumptions on relationships.