althonos/pronto: v2.3.1

doi:10.5281/zenodo.4041809

Published September 21, 2020 | Version v2.3.1

Software Open

althonos/pronto: v2.3.1

Martin Larralde¹

1. EMBL, @zellerlab

Others:

pronto

A Python frontend to ontologies.

🗺️ Overview

Pronto is a Python library to parse, browse, create, and export ontologies, supporting several ontology languages and formats. It implement the specifications of the Open Biomedical Ontologies 1.4 in the form of an safe high-level interface. If you’re only interested in parsing OBO or OBO Graphs document, you may wish to consider fastobo instead.

🏳️ Supported Languages

Open Biomedical Ontologies 1.4. Because this format is fairly new, not all OBO ontologies can be parsed at the moment. See the OBO Foundry roadmap listing the compliant ontologies, and don’t hesitate to contact their developers to push adoption forward.
OBO Graphs in JSON format. The format is not yet stabilized to the results may change from file to file.
Ontology Web Language 2 in RDF/XML format. OWL2 ontologies are reverse translated to OBO using the mapping defined in the OBO 1.4 Semantics.

🔧 Installing

Installing with pip is the easiest:

# pip install pronto          # if you have the admin rights
$ pip install pronto --user   # install it in a user-site directory

There is also a conda recipe in the bioconda channel:

$ conda install -c bioconda pronto

Finally, a development version can be installed from GitHub using setuptools, provided you have the right dependencies installed already:

$ git clone https://github.com/althonos/pronto
$ cd pronto
# python setup.py install

💡 Examples

If you’re only reading ontologies, you’ll only use the Ontology class, which is the main entry point.

>>> from pronto import Ontology

It can be instantiated from a path to an ontology in one of the supported formats, even if the file is compressed:

>>> go = Ontology("tests/data/go.obo.gz")

Loading a file from a persistent URL is also supported, although you may also want to use the Ontology.from_obo_library method if you’re using persistent URLs a lot:

>>> cl = Ontology("http://purl.obolibrary.org/obo/cl.obo")
>>> stato = Ontology.from_obo_library("stato.owl")

🏷️ Get a term by accession

Ontology objects can be used as mappings to access any entity they contain from their identifier in compact form:

>>> cl['CL:0002116']
Term('CL:0002116', name='B220-low CD38-positive unswitched memory B cell')

🔎 Get a term by alternate ID

Retrieval of an entity by any alternate ID it was declared from is possible using the same syntax:

>>> hp = pronto.Ontology.from_obo_library("hp.obo")
>>> 'HP:0001198' in hp['HP:0009882'].alternate_ids
True
>>> hp['HP:0001198']
Term('HP:0009882', name='Short distal phalanx of finger')

🖊️ Create a new term from scratch

We can load an ontology, and edit it locally. Here, we add a new protein class to the Protein Ontology.

>>> pr = Ontology.from_obo_library("pr.obo")
>>> brh = ms.create_term("PR:XXXXXXXX")
>>> brh.name = "Bacteriorhodopsin"
>>> brh.superclasses().add(pr["PR:000001094"])  # is a rhodopsin-like G-protein
>>> brh.disjoint_from.add(pr["PR:000036194"])   # disjoint from eukaryotic proteins

✏️ Convert an OWL ontology to OBO format

The Ontology.dump method can be used to serialize an ontology to any of the supported formats (currently OBO and OBO JSON):

>>> edam = Ontology("http://edamontology.org/EDAM.owl")
>>> with open("edam.obo", "wb") as f:
...     edam.dump(f, format="obo")

🌿 Find ontology terms without subclasses

The terms method of Ontology instances can be used to iterate over all the terms in the ontology (including the ones that are imported). We can then use the is_leaf method of Term objects to check is the term is a leaf in the class inclusion graph.

>>> ms = Ontology("ms.obo")
>>> for term in ms.terms():
...     if term.is_leaf():
...         print(term.id)
MS:0000000
MS:1000001
...

📖 API Reference

A complete API reference can be found in the online documentation, or directly from the command line using pydoc:

$ pydoc pronto.Ontology

📜 License

This library is provided under the open-source MIT license. Please cite this library if you are using it in a scientific context using the following DOI: 10.5281/zenodo.595572

📒 Changelog

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

2.3.1 - 2020-09-21
- Fixed:
  - pronto.entity package not being included in source distribution.
2.3.0 - 2020-09-21
- Added:
  - Retrieval of entities via their alternate IDs on the source Ontology.
  - Direct edition of entity relationships via the Relationships view.
  - __all__ attribute to all modules of the data model.
  - RelationshipSet container like TermSet with shortcut attributes and proxying of actual Relationship instances.
  - Relationship.subproperties and Relationship.superproperties methods to add, remove, clear and iterate over the subproperties and superproperties of a Relationship instance.
  - Ontology.synonym_types method to count (via SizedIterator) and iterate over the synonym types of an ontology and all of its imports.
  - Ontology.get_synonym_type method to retrieve a single synonym type by ID from an ontology or one of its imports.
  - Changed
  - Management of sub-properties / super-properties is now consistent with the management of subclasses / superclasses.
  - consider, disjoint_from, disjoint_over, equivalent_to, replaced_by transitive_over and union_of properties of Relationship now return a RelationshipSet.
- Fixed:
  - Outdated documentation in Term.subclasses describing the performances of the previous algorithm.
  - Possible AttributeError with the setter of the Entity.synonyms property.
  - Issue with synonym types declared in imported ontologies not being usable with synonyms of the actual ontology.
  - Various type annotations not updated since version 2.2.2.

2.2.4 - 2020-09-11
- Changed:
  - Make Entity.annotations return a mutable set and add a setter.
- Fixed:
  - Term.relationship erroneously updating the Ontology._lineage cache.
  - Unneeded code in pronto.serializers._fastobo handling is_a clauses.
2.2.3 - 2020-07-31
- Changed:
  - Replaced frozendict with immutabledict (#90).
  - Bumped fastobo dependency to v0.9.0 to support inline comments.
  - Parsers will now process their imports in parallel using a thread pool. ### Fixed
  - Argument type checking in view layer is now disabled during the parsing phase to reduce overhead.
2.2.2 - 2020-07-18
- Added:
  - Extraction of basic relationships from RDF/XML documents.
- Fixed:
  - Erroneous type annotations on Term.subclasses and Term.superclasses.
  - Bug with Term.equivalent_to setter crashing with a NameError.
  - Bug with Entity.synonyms setter not extracting synonym data.
2.2.1 - 2020-06-17
- Fixed:
  - Extraction of subclasses/superclasses hierarchy from nested imports.
  - Serialization of OBO frames not being done in order.
  - Parsing issue with anti_symmetric clauses in OBO typedefs.
  - Xrefs not being extracted when declared as axioms in RDF/XML documents.
  - ResourceWarning when creating Ontology from file-handles not mapping to a filesystem location.
2.2.0 - 2020-06-17
- Added:
  - threads parameter to Ontology constructor to control the number of threads used by parsers supporting multithreading (OBO and OBO JSON at the moment).
  - Deprecation warnings for suspected uses of the is_a pseudo-relationship since subclasses/superclasses is now to be handled by the owner Ontology.
  - Support for subclass/superclass edition directly from the objects returned by Term.subclasses() and Term.superclasses(). (#84)
- Changed:
  - Updated fastobo to v0.8, which reduce memory footprint of identifiers, and improves the parser speed.
  - Improved OBO parser performance using threading plus zero-copy validation of identifiers on Xref instantiation.
  - Improved performance in debug mode by having the typechecker only extract the wrapped function signature once.
- Fixed:
  - OBO parser crashing on files containing idspace clauses in their headers.
  - Reference management issue with binary operations of TermSet.
- Removed:
  - nanoset depency, which was not useful anymore in Python 3.8 and caused issues with multithreading when processing OBO frames in parallel.
2.1.0 - 2020-03-23
- Added:
  - Synonym.xrefs now has a setter. (#70)
  - pickle support for Ontology. (#66)
  - RdfXmlParser support for owl:inverseOf and rdfs:subPropertyOf.
- Changed:
  - Synonym.xrefs now returns a mutable set that can be used to add Xref to the synonym directly.
- Fixed:
  - SynonymType.type setter does not consider all synonym types as undeclared anymore. (#71)
  - RdfXmlParser crashing on synonym types definition without a label like in Uberon. (#67)
  - FastoboSerializer crashing when encountering a relationship with at least one replaced_by clause.
2.0.1 - 2020-02-19
- Fixed
  - Internal handling of ontology data forcing an Ontology to outlive all of the Terms created from it.
  - Term.id property missing a return type annotation.
  - Term.equivalent_to not returning a TermSet but a set of strings.
- Changed
  - Refactored implementation of SubclassesIterator and
    SuperclassesIterator to make both use the interal subclassing cache.
  - Make Term.is_leaf use internal subclassing cache to make it run in constant time.
2.0.0 - 2020-02-14
- Added:
  - TermSet.subclasses and TermSet.superclasses methods to query all
    the subclasses / superclasses of all Term.
  - TermSet class to the top-level pronto module.
  - Dynamic management of subclassing cache for the Ontology class.
  - Setters for Term.consider, Term.union_of and Term.intersection_of.
- Removed:
  - cache keyword argument for the Ontology.
- Fixed:
  - SuperclassesIterator.to_set being named to_self because of a typo.
  - Several bugs affecting the fastobo-backed serializer.
1.2.0 - 2020-02-10
- Added:
  - Parameter with_self to disable reflexivity of Term.subclasses and Term.superclasses iterators.
  - TermSet class which stores a set of terms efficiently while providing some useful shortcuts to access the underlying data.
- Changed:
  - Moved code of Term.subclasses and Term.superclasses to a dedicated iterator class in the pronto.logic submodule.
  - Dropped contexter requirement.
- Fixed:
  - Fix a typo in Synonym.type setter leading to a potential bug when the given type is None.
  - Fix miscellaneous bugs found with mypy.
  - fastobo serializer crashing on namespace clauses because of a type issue.
  - fastobo parsers using data version clauses as format version clauses.
1.1.5 - 2020-01-25
- Changed:
  - Bumped fastobo to v0.7.0, switching parser implementation to use multi-threading in order to speedup the parser process.
1.1.4 - 2020-01-21
- Added:
  - Explicit support for Python 3.8.
  - Support for Windows-style line endings (#53)
1.1.3 - 2019-11-10
- Fixed:
  - Handling of some clauses in FastoboParser.
  - OboSerializer occasionaly missing lines between term and typedef frames.
- Added:
  - Missing docstrings to some Entity properties.
1.1.2 - 2019-10-30
- Fixed:
  - RdfXMLParser crashing on entities with rdf:label elements without literal content.
1.1.1 - 2019-10-29
- Fixed:
  - pronto.serializers module not being embedded in Wheel distribution.
1.1.0 - 2019-10-24
- Added:
  - 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.
- Changed:
  - 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.
- Fixed:
  - 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
- Fixed:
  - 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.
- Changed:
  - Bumped fastobo requirement to v0.6.0.
1.0.0-alpha.3 - 2019-10-10
- Added:
  - 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.
- Fixed:
  - Metadata not storing optional description of ID spaces if any.
  - Wrong type hints in RelationshipData.equivalent_to_chain.
- Changed:
  - 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
- Added
  - Support for extraction of relationships from OWL/XML files to OwlXMLParser.
- Fixed:
  - Type hints of RelationshipData.synonyms attribute.
1.0.0-alpha.1 - 2019-10-02
- Changed:
  - 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.
- Added:
  - 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.
- Removed:
  - OBO and JSON serialization support (for now).
  - Term.rchildren and Term.rparents and stop making direction assumptions on relationships.

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