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[codex] migrate funowl integration to py-horned-owl (#868)
* migrate funowl integration to py-horned-owl * fix lint issues in owl migration files * skip ubergraph live tests on remote timeouts * expand horned owl graph support and docs * add missing graph projection owl fixture
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‎docs/datamodels/funowl/index.rst‎

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FunOwl
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=======
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FunOwl is a :term:`Datamodel` for expressing :term:`OWL`.
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``funowl`` is the historical name used in OAK for the OWL datamodel-facing
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adapter and documentation surface.
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FunOwl provides an OWL :term:`Axiom`-oriented datamodel, contrasting from a more :term:`Graph`-oriented data model
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The implementation is now backed by
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`py-horned-owl <https://github.com/ontology-tools/py-horned-owl>`_, which
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provides the OWL axiom-oriented object model used by :class:`OwlInterface`.
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See `FunOWL docs <https://github.com/hsolbrig/funowl>`_.
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This contrasts with OAK's more :term:`Graph`-oriented interfaces.

‎docs/faq/general.rst‎

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There are a variety of ways of consuming OWL in OAK
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- The recommended way is to use :ref:`sql_implementation`, which works off of RDF/OWL compiled to sqlite3
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- You can also use :ref:`funowl_implementation`, but this requires the ontology is in :term:`Functional Syntax`
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- You can also use :ref:`funowl_implementation`; the selector name is historical,
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but the adapter is now backed by ``py-horned-owl`` and is the default for local
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``.owl``, ``.ofn``, ``.omn``, and ``.owx`` paths
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- You can use a local or remote OWL ontologies serialized as RDF via the :ref:`sparql_implementation`
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- Using a tool like :ref:`ROBOT` to convert an OWL ontology to a serialization like :term:`OBO Format`
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-----------------------------------
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Yes. See the :ref:`text_annotator_interface`.
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‎docs/intro/tutorial06.rst‎

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Part 6: Working With OWL
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=====================
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========================
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OAK comes bundled with the `funowl <https://github.com/hsolbrig/funowl/>`_ library
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OAK exposes an experimental ``funowl`` adapter for local OWL files.
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The selector name is historical; the adapter is now backed by
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`py-horned-owl <https://github.com/ontology-tools/py-horned-owl>`_.
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Plain local ``.owl``, ``.ofn``, ``.omn``, and ``.owx`` paths default to this
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adapter; explicit schemes such as ``sqlite:foo.owl`` still override that
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default.
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OWL Datamodel
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OwlInterface
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------------
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TODO
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``OwlInterface`` is the low-level OAK view for working with OWL axioms and OWL-
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specific structures directly.
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Loading a local OWL file
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^^^^^^^^^^^^^^^^^^^^^^^^
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For local files, plain ``.owl``, ``.ofn``, ``.omn``, and ``.owx`` paths now
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default to the horned-owl-backed OWL adapter:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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print(type(oi).__name__)
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If you want a different backend, be explicit in the selector:
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.. code-block:: python
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sqlite_oi = get_adapter("sqlite:path/to/my-ontology.owl")
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sparql_oi = get_adapter("sparql:path/to/my-ontology.owl")
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Inspecting asserted OWL axioms
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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You can iterate over raw axioms, or use helpers for common axiom types:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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for axiom in oi.subclass_axioms(subclass="GO:0005634"):
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print(type(axiom).__name__, axiom)
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labels = list(
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oi.annotation_assertion_axioms(
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subject="GO:0005634",
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property="rdfs:label",
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)
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)
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eq_axioms = list(oi.equivalence_axioms(about="GO:0031965"))
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If you need the underlying horned-owl ontology object, use:
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.. code-block:: python
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ontology = oi.owl_ontology()
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print(type(ontology).__name__)
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Projected graph operations
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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The horned-owl adapter also projects a graph view from supported OWL patterns,
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so graph-oriented APIs can often be used alongside axiom APIs:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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direct = list(oi.relationships(subjects=["GO:0005634"]))
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entailed = list(
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oi.relationships(
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subjects=["GO:0005634"],
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include_entailed=True,
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)
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)
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ancestors = list(oi.ancestors("GO:0005634", predicates=["rdfs:subClassOf"]))
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Logical definitions are exposed in OBO Graph form:
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.. code-block:: python
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ldefs = list(oi.logical_definitions(subjects=["GO:0031965"]))
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for ldef in ldefs:
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print(ldef.definedClassId, ldef.genusIds, ldef.restrictions)
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Reasoning status
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^^^^^^^^^^^^^^^^
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``OwlInterface`` does not currently provide a pluggable OWL reasoner. In the
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current horned-owl-backed implementation:
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- ``reasoner_configurations()`` returns an empty list
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- axiom filtering does not accept a ``ReasonerConfiguration``
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- ``include_entailed=True`` on graph methods gives a lightweight projected
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closure over supported OWL patterns, not full OWL reasoning
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For precomputed closure and broader graph-style querying, the recommended
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production path remains the :ref:`sql_implementation`. For external OWL
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reasoners, see the ROBOT plugin below.
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ROBOT Plugin
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------------

‎docs/packages/implementations/funowl.rst‎

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===============
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.. currentmodule:: oaklib.implementations.funowl.funowl_implementation
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The ``funowl`` adapter keeps its historical selector and class name for backward
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compatibility, but it is now implemented on top of
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`py-horned-owl <https://github.com/ontology-tools/py-horned-owl>`_ rather than
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the old ``funowl`` package. Plain local ``.owl``, ``.ofn``, ``.omn``, and
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``.owx`` paths resolve here by default unless you choose an explicit scheme such
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as ``sqlite:`` or ``sparql:``.
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.. autoclass:: FunOwlImplementation

‎docs/packages/interfaces/owl.rst‎

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-------------
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.. currentmodule:: oaklib.interfaces.owl_interface
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``OwlInterface`` exposes OWL axioms and OWL-specific helpers directly, without
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forcing everything through a graph abstraction.
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Quick examples
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^^^^^^^^^^^^^^
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Load a local OWL ontology using the default selector logic:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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Inspect common OWL axiom types:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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subclass_axioms = list(oi.subclass_axioms(subclass="GO:0005634"))
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label_axioms = list(
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oi.annotation_assertion_axioms(
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subject="GO:0005634",
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property="rdfs:label",
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)
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)
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eq_axioms = list(oi.equivalence_axioms(about="GO:0031965"))
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Project graph-style relationships from OWL axioms:
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.. code-block:: python
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from oaklib import get_adapter
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oi = get_adapter("path/to/my-ontology.owl")
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direct = list(oi.relationships(subjects=["GO:0005634"]))
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entailed = list(
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oi.relationships(
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subjects=["GO:0005634"],
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include_entailed=True,
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)
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)
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Reasoning
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^^^^^^^^^
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``OwlInterface`` does not currently expose a general OWL reasoner. The
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horned-owl-backed implementation can still provide a lightweight projected
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closure for graph APIs when ``include_entailed=True`` is used, but that should
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not be interpreted as complete OWL reasoning.
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.. autoclass:: OwlInterface
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:members:

‎docs/packages/selectors.rst‎

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- :code:`tests/input/go-nucleus.obo` - local :term:`OBO Format` file loaded with pronto
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- :code:`tests/input/go-nucleus.json` - local :term:`OBO Graphs` json format file loaded with pronto
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- :code:`tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with rdflib at the moment, may change)
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- :code:`tests/input/go-nucleus.owl` - local OWL file loaded with the horned-owl-backed :ref:`funowl_implementation`
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- :code:`tests/input/go-nucleus.ofn` - local :term:`Functional Syntax` OWL file loaded with the horned-owl-backed :ref:`funowl_implementation`
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- :code:`tests/input/go-nucleus.omn` - local Manchester OWL file loaded with the horned-owl-backed :ref:`funowl_implementation`
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- :code:`tests/input/go-nucleus.owx` - local OWL/XML file loaded with the horned-owl-backed :ref:`funowl_implementation`
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- :code:`tests/input/go-nucleus.owl.ttl` - local OWL :term:`Turtle` file (loaded with rdflib at the moment, may change)
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- :code:`tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation
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- :code:`http://purl.obolibrary.org/obo/pato.obo` - NOT IMPLEMENTED; download locally for now
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- :code:`pronto:tests/input/go-nucleus.obo` - local :term:`OBO Format` file loaded with pronto
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- :code:`pronto:tests/input/go-nucleus.json` - local :term:`OBO Graphs` json format file loaded with pronto
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- :code:`pronto:tests/input/go-nucleus.owl` - local OWL rdf/xml format file (loaded with pronto at the moment may change)
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- :code:`funowl:tests/input/go-nucleus.owl` - local OWL file loaded with the horned-owl-backed OWL object model
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- :code:`funowl:tests/input/go-nucleus.ofn` - local :term:`Functional Syntax` OWL file loaded with the horned-owl-backed OWL object model
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- :code:`pronto:tests/input/go-nucleus.db` - local sqlite3 db loaded with SqlImplementation
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- :code:`prontolib:pato.obo` - remote :term:`OBO Format` file loaded from OBO Library with pronto
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- :code:`prontolib:pato.owl` - remote owl format file loaded from OBO Library with pronto
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Implementation: :ref:`funowl_implementation`
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NOT IMPLEMENTED YET
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This selector name is retained for backward compatibility. The implementation is
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now backed by ``py-horned-owl`` while continuing to accept ``funowl:...``
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selectors. Plain local paths ending in ``.owl``, ``.ofn``, ``.omn``, or
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``.owx`` also resolve to this implementation by default; use an explicit scheme
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such as ``sqlite:`` or ``sparql:`` to force a different backend.
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Functions
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----

‎pyproject.toml‎

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"appdirs>=1.4.4",
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"semsql>=0.3.1",
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"kgcl-schema>=0.6.9,<1",
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"funowl>=0.2.0",
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"py-horned-owl>=1.1.0",
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"kgcl-rdflib==0.5.0",
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"llm>=0.14,<1",
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"pystow>=0.7.28",
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[tool.ruff.lint.mccabe]
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# Unlike Flake8, default to a complexity level of 10.
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max-complexity = 10
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max-complexity = 10

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