Deeponto

Added

- [X] **Add** external references to `OAEI-Bio-ML` and `HierarchyTransformers`.

Changed

- [X] **Refine** `deeponto.onto.taxonomy` and add more options.

Changed

- [X] **Move** `openprompt` to extra dependencies as its supported version of `sentencepiece` has known conflicts with many packages.
- [X] **Add** `nltk` and `tqdm` as a dependency.

Added

<!-- - [ ] **Add** ICON as a completion service at `deeponto.complete`. -->
- [X] **Add** empty annotation index warning for BERTMap, related to issue 18.
- [X] **Add** `check_consistency()` at `deeponto.onto.Ontology`.
- [X] **Add** a warning message for empty vocab at `deeponto.onto.OntologyVerbaliser`.

Changed

- [X] **Remove** dependency version restrictions.
- [X] **Change** `.instances_of()` to `get_instances()` at `deeponto.onto.OntologyReasoner`.
- [X] **Change** `deeponto.subs` to `deeponto.complete`.
- [X] **Move** `deeponto.probe.ontolama` into `deeponto.complete`.

Added

- [X] **Add** object property domain/range verbalisation at `deeponto.onto.OntologyVerbaliser`.
- [X] **Add** new reasoner type `"struct"` ([Structural Reasoner](https://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html)) at `deeponto.onto.OntologyReasoner`.
- [X] **Add** `load_reasoner()` method at `deeponto.onto.OntologyReasoner` for convenience of changing the reasoner type and remove `reload_reasoner()` method as it is a special case of `load_reasoner()`.
- [x] **Add** `rdflib` into the dependencies for building graph-related features.
- [X] **Add** `deeponto.onto.taxonomy` for building the taxonomy over ontologies and potentially other structured data.

Changed
- [X] **Change** printing to appropriate logging (gradually).
- [X] **Change** `read_table_mappings()` method at `deeponto.align.mapping` from using `dataframe.iterrows()` to `dataframe.itertuples()` which is much more efficient.
- [X] **Change** the default lowcasing argument of `deeponto.utils.process_annotation_literal()` to `False`.
- [X] **Change** the default logging level of `slf4j` to `warn` to prevent tons of printing at ELK (issue (13)[https://github.com/KRR-Oxford/DeepOnto/issues/13]).

Added

- [x] **Add** the OAEI evaluation code for the main track global matching, local ranking, and the special sub-track bio-llm at `deeponto.align.oaei`.
- [x] **Add** `reasoner_type` argument at `deeponto.onto.OntologyReasoner`, now supporting `hermit` (default) and `elk`.
- [x] **Add** `get_all_axioms()` method at `deeponto.onto.Ontology`.
- [x] **Add** `get_iri()` method at `deeponto.onto.Ontology`.

- [x] **Add** new features into `deeponto.onto.OntologyVerbaliser` including:

- `verbalise_object_property_subsumption()` for object property subsumption axioms.
- property chain verbalisation at `verbalise_class_expression()`.
- `verbalise_class_subsumption()` for class subsumption axioms;
- `verbalise_class_equivalence()` for class equivalence axioms;
- `verbalise_class_assertion()` for class assertion axioms;
- `verbalise_relation_assertion()` for relation assertion axioms;
- `auto-correction` option for fixing entity names.
- `keep_iri` option for keeping entity IRIs.
- `add_quantifier_word` option for adding quantifier words as in the Manchester syntax.

- [x] **Add** `get_assertion_axioms()` method at `deeponto.onto.Ontology`.
- [x] **Add** `get_axiom_type()` method at `deeponto.onto.Ontology`.
- [x] **Add** `owl_individuals` attribute at `deeponto.onto.Ontology`.

Changed

- [x] **Change** `get_owl_objects()` method to be anonymous as it is only used for creating pre-processed entity index at `deeponto.onto.Ontology`.
- [x] **Change** `get_owl_object_from_iri()` method to `get_owl_object()` at `deeponto.onto.Ontology`.
- [x] <del>Change the log level of the ELK reasoner to `ERROR`</del>.

Fixed

- [x] **Fix** the file path problem of loading ontologies for Windows systems.
- [x] **Fix** the version of ELK to the latest by manually adding in the dependencies. See download link at <https://github.com/liveontologies/elk-reasoner/wiki/GettingElk>.

Added

- [x] **Add** `set_seed()` method at `deeponto.utils`.

Changed

- [x] **Change** the layout of all utility methods by making them stand-alone instead of static methods.
- [x] **Change** the `.verbalise_class_expression()` method by adding an option to keep entity IRIs without verbalising them using `.vocabs` at `deeponto.onto.OntologyVerbaliser`.
- [x] **Change** default `apply_lowercasing` value to `False` for both `.get_annotations()` and `.build_annotation_index()` methods at `deeponto.onto.Ontology`.
- [x] **Change** the method `.get_owl_object_annotations()` to `.get_annotations()` at `deeponto.onto.Ontology`.
- [x] **Change** the LogMap debugger memory options for BERTMap's mapping repair.
- [x] **Change** the default jar command timeout to 1 hour.

Fixed

- [x] **Fix** duplicate logging in running BERTMap due to progapagation.