Ontolearn

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0.8.0

We are happy to share with you our newest release [v0.8.0](https://pypi.org/project/ontolearn/0.8.0/).

Please upgrade as usual:

pip install -U ontolearn


This new release features some refactoring done to ontolearn, among others, highlighting the removal of `ModelAdapter`, code adjustments due to _owlapy's_ newest versions and refactoring done for Enexa project. Other major changes include integration of NCES in ontolearn-web service as well as fixes DL-learner binding and some changes to our triple store related classes. Work to improve the triple store experience is still in progress.

Louis-Mozart and sapkotaruz11 have made their first contributions to the project. Your contribution is well appreciated.

You can check the notes below about PRs and specific commits of interest:

What's Changed
* repr() is being used at OWLLiteral with string value to adress by Demirrr in https://github.com/dice-group/Ontolearn/pull/431
* Saving data of TDL by Demirrr in https://github.com/dice-group/Ontolearn/pull/434
* Retrieval eval incomplete by Louis-Mozart in https://github.com/dice-group/Ontolearn/pull/436
* update docs Concept_Learning by sapkotaruz11 in https://github.com/dice-group/Ontolearn/pull/437
* Python version bandage and logo + favicon added to docs by alkidbaci in https://github.com/dice-group/Ontolearn/pull/438
* Added to parser by Louis-Mozart in https://github.com/dice-group/Ontolearn/pull/440
* Removing model adapter by alkidbaci in https://github.com/dice-group/Ontolearn/pull/441
* owlapy version increased by Demirrr in https://github.com/dice-group/Ontolearn/pull/442
* Fixing KeyError in max card. by Demirrr in https://github.com/dice-group/Ontolearn/pull/443
* updated to owlapy 1.3.0 by alkidbaci in https://github.com/dice-group/Ontolearn/pull/444
* TripleStoreReasoner.equivalent_classes() only works on named concepts by Demirrr in https://github.com/dice-group/Ontolearn/pull/452
* Refactoring for Enexa by Demirrr in https://github.com/dice-group/Ontolearn/pull/455
* Retrieval eval incomplete by Louis-Mozart in https://github.com/dice-group/Ontolearn/pull/449
* Update 06_concept_learners.md by LckyLke in https://github.com/dice-group/Ontolearn/pull/461
* Integrate NCES in ontolearn-web service and fix dllearner binding script in examples by Jean-KOUAGOU in https://github.com/dice-group/Ontolearn/pull/450
* Incremented to owlapy 1.3.1 and some refactoring on triple_store.py by alkidbaci in https://github.com/dice-group/Ontolearn/pull/462
* New release by alkidbaci in https://github.com/dice-group/Ontolearn/pull/463
* Ontolearn 0.8.0 by alkidbaci in https://github.com/dice-group/Ontolearn/pull/464

New Contributors
* Louis-Mozart made their first contribution in https://github.com/dice-group/Ontolearn/pull/436
* sapkotaruz11 made their first contribution in https://github.com/dice-group/Ontolearn/pull/437

**Full Changelog**: https://github.com/dice-group/Ontolearn/compare/0.7.3...0.8.0

0.7.3

Install/upgrade:


pip install -U ontolearn


**Full Changelog**: https://github.com/dice-group/Ontolearn/compare/0.7.2...0.7.3

What's Changed
* ALCQIO retrieval with neural nets by Demirrr in https://github.com/dice-group/Ontolearn/pull/425
* Triples based on literals can be now parsed: by Demirrr in https://github.com/dice-group/Ontolearn/pull/427
* TDL refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/428
* OWLLiteral with string added by Demirrr in https://github.com/dice-group/Ontolearn/pull/429
* Bug fixing and new release changes by alkidbaci in https://github.com/dice-group/Ontolearn/pull/430


**Full Changelog**: https://github.com/dice-group/Ontolearn/compare/0.7.2...0.7.3

0.7.2

Happy to share with you our new release: ontolearn 0.7.2

shell
pip install -U ontolearn


Important API changes:
Modules inside `ontolearn/base` directory **removed** from ontolearn and classes belonging to those modules are now **moved** to [_owlapy_](https://github.com/dice-group/owlapy).

Respective PRs:
- ontolearn: https://github.com/dice-group/Ontolearn/pull/403
- owlapy: https://github.com/dice-group/owlapy/pull/42

Documentation guides for the classes are also moved to owlapy's documentation which you can find [here](https://dice-group.github.io/owlapy/).




What's Changed
* Triplestore improvements and some tests refactoring by alkidbaci in https://github.com/dice-group/Ontolearn/pull/399
* Ontolearn-webservice API changes & Nominals in DRILL by Demirrr in https://github.com/dice-group/Ontolearn/pull/402
* Refactoring (related to owlapy 1.1.0) by alkidbaci in https://github.com/dice-group/Ontolearn/pull/403
* Default cardinality restriction by Demirrr in https://github.com/dice-group/Ontolearn/pull/406
* Refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/407
* Verbosity unified and 10Fold CV over Family repeated by Demirrr in https://github.com/dice-group/Ontolearn/pull/409
* refactoring and cv eval with 60 seconds by Demirrr in https://github.com/dice-group/Ontolearn/pull/410
* tDL refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/412
* Neural triplestore by LckyLke in https://github.com/dice-group/Ontolearn/pull/413
* Version fix by Demirrr in https://github.com/dice-group/Ontolearn/pull/416
* Added licensing terms to source files by alkidbaci in https://github.com/dice-group/Ontolearn/pull/417
* Documentation update and some general changes by alkidbaci in https://github.com/dice-group/Ontolearn/pull/418
* Code coverage nces and clip by Jean-KOUAGOU in https://github.com/dice-group/Ontolearn/pull/419
* Luke neural reasoner by Demirrr in https://github.com/dice-group/Ontolearn/pull/420
* Code coverage update by alkidbaci in https://github.com/dice-group/Ontolearn/pull/421
* Added logo to readme by alkidbaci in https://github.com/dice-group/Ontolearn/pull/422

New Contributors
* LckyLke made their first contribution in https://github.com/dice-group/Ontolearn/pull/413

**Full Changelog**: https://github.com/dice-group/Ontolearn/compare/0.7.1...0.7.2

0.7.1

pip install -U ontolearn

Important Updates: `ontolearn-webservice`

`ontolearn-webservice --path_knowledge_base KGs/Mutagenesis/mutagenesis.owl`


`ontolearn-webservice --endpoint_triple_store http://0.0.0.0:9080/sparql`

What's Changed
* Refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/354
* Examples Clean Up by alkidbaci in https://github.com/dice-group/Ontolearn/pull/353
* Last commit of refactoring DRILL by Demirrr in https://github.com/dice-group/Ontolearn/pull/356
* Nominals fix by Demirrr in https://github.com/dice-group/Ontolearn/pull/358
* LLM based verbalizer included by Demirrr in https://github.com/dice-group/Ontolearn/pull/360
* Prompt is revised to lead an LLM to generate shorter texts. by Demirrr in https://github.com/dice-group/Ontolearn/pull/361
* TripleStore via rdflib.graph by Demirrr in https://github.com/dice-group/Ontolearn/pull/364
* Tdl triplestore by Demirrr in https://github.com/dice-group/Ontolearn/pull/365
* Tdl triplestore by Demirrr in https://github.com/dice-group/Ontolearn/pull/367
* OWL Class expression learning with tDL, over a DBpedia Endpoint by Demirrr in https://github.com/dice-group/Ontolearn/pull/368
* python dependencies are removed in the github action for docs by Demirrr in https://github.com/dice-group/Ontolearn/pull/369
* Unifying best_hypotheses function and updating the tests by Demirrr in https://github.com/dice-group/Ontolearn/pull/370
* Update README.md by Demirrr in https://github.com/dice-group/Ontolearn/pull/371
* Release refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/373
* Drill Enexa Server by Demirrr in https://github.com/dice-group/Ontolearn/pull/375
* Fixing few open issues by Demirrr in https://github.com/dice-group/Ontolearn/pull/378
* Adaptation to owlapy1.0.1 by alkidbaci in https://github.com/dice-group/Ontolearn/pull/379
* Fix:Drill: No embeddings provided implies Quality based reward used by Demirrr in https://github.com/dice-group/Ontolearn/pull/380
* Evaluation setup for NCES and CLIP by alkidbaci in https://github.com/dice-group/Ontolearn/pull/382
* ontolearn-webservice with drill examples over local kg tested by Demirrr in https://github.com/dice-group/Ontolearn/pull/384
* tDL, DRILL, Triplestore Fuseki refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/386
* Fix data properties drill tdl by Demirrr in https://github.com/dice-group/Ontolearn/pull/388
* Refactoring by alkidbaci in https://github.com/dice-group/Ontolearn/pull/390
* Tentris drill tdl refactoring by Demirrr in https://github.com/dice-group/Ontolearn/pull/391
* License update by alkidbaci in https://github.com/dice-group/Ontolearn/pull/392
* Making ontolearn-webservice more responsive by Demirrr in https://github.com/dice-group/Ontolearn/pull/393
* webservice fix is done by Demirrr in https://github.com/dice-group/Ontolearn/pull/394
* Readme updated by <details> and <\details> by Demirrr in https://github.com/dice-group/Ontolearn/pull/395


**Full Changelog**: https://github.com/dice-group/Ontolearn/compare/0.7.0...0.7.1

0.7.0

Release Notes:

Drill is now available in Ontolearn:

You can import it as follows:
python
from ontolearn.learners import Drill


Examples:
1. [examples/concept_learning_evaluation.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_evaluation.py)
2. [examples/concept_learning_cv_evaluation.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_cv_evaluation.py)

---------------------------------------------------

Tree-based DL Learner (tDL) is now available in Ontolearn:

You can import it as follows:
python
from ontolearn.learners import TDL

Examples:
1. [examples/concept_learning_evaluation.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_evaluation.py)
2. [examples/concept_learning_cv_evaluation.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_cv_evaluation.py)
3. [examples/concept_learning_with_tdl_and_triplestore_kb.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_with_tdl_and_triplestore_kb.py)

---------------------------------------------------


CLIP is now available in Ontolearn:

You can import it as follows:
python
from ontolearn.concept_learner import CLIP


Examples:
1. [examples/concept_learning_cv_evaluation.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_cv_evaluation.py)


---------------------------------------------------

Changes to KnowledgeBase class:

- You can make type retrieval methods to return the type of OWLNamedIndividual for individuals which do not explicitly specify that type. You can do that by setting the argument `include_implicit_individuals` of class `KnowledgeBase` to `True`. By default it is `False`.
- Ontology and reasoner can be accessed directly:
- From `kb.ontology()` &rarr; To `kb.ontology`
- From `kb.reasoner()` &rarr; To `kb.reasoner`
- Added methods for triple retrieval:
- `abox` &rarr; returns all related Abox axioms of a given individual, list of individuals or None (all Abox axioms).
- `tbox` &rarr; method returns all related Tbox axioms of a given concept, data property, object property, a list of them or None (all Tbox axioms)
- `triples` &rarr; returns all triples of the ontology.

Return type in 3 formats defined by the `mode` argument which accepts the following strings:
1) `'native'` -> triples are represented as tuples of owlapy objects.
2) `'iri'` -> triples are represented as tuples of IRIs as strings.
3) `'axiom'` -> triples are represented as owlapy axioms.

- New property methods to retrieve classes/properties:
- `concepts`
- `object_properties`
- `object_properties`

- Removed triplestore logic (as well as from OWLOntology_Owlready2 and OWLReasoner_Owlready2). It is now moved to `ontolearn.triple_store` (described below).

Check everything [here](https://ontolearn-docs-dice-group.netlify.app/autoapi/ontolearn/knowledge_base/)

---------------------------------------------------

Triple Store Knowledge Base:

Added `TripleStoreOntology`, `TripleStoreReasoner` and `TripleStoreKnowledgeBase`.
`TripleStoreKnowledgeBase` can be initialized using just an SPARQL endpoint and it can be used instead of the `KnowledgeBase`
to execute a concept learner. All dataset queries are made using SPARQL and are directed to the provided endpoint.

To import:

python
from ontolearn.triple_store import TripleStoreOntology, TripleStoreReasoner, TripleStoreKnowledgeBase


For more, you can visit the guide in our documentation [here](https://ontolearn-docs-dice-group.netlify.app/usage/06_concept_learners#use-triplestore-knowledge-base) , check the [API docs](https://ontolearn-docs-dice-group.netlify.app/autoapi/ontolearn/triple_store/) and see the examples listed below.

Examples:
1. [examples/concept_learning_via_triplestore_example.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_via_triplestore_example.py)
2. [examples/concept_learning_with_tdl_and_triplestore_kb.py](https://github.com/dice-group/Ontolearn/blob/develop/examples/concept_learning_with_tdl_and_triplestore_kb.py)

---------------------------------------------------


Documentation and more:

- At [README.md](https://github.com/dice-group/Ontolearn/blob/master/README.md) you can find the _Benchmark Results_ which displays the performance of all our learners.

- Documentation has been updated to the latest changes. You can always access the up-to-date documentation [here](https://ontolearn-docs-dice-group.netlify.app/usage/01_introduction).

- [Ontosample](https://ontolearn-docs-dice-group.netlify.app/autoapi/ontosample/) is now integrated into Ontolearn. We have also added a [guide](https://ontolearn-docs-dice-group.netlify.app/usage/04_knowledge_base#sampling-the-knowledge-base) on how to use it as well as an [example](https://github.com/dice-group/Ontolearn/blob/develop/examples/sampling_example.py).

_Note: `ontosample` is not part of the default dependencies. To get it you should either install it directly or use:_ `pip install ontolearn[full]`.

---------------------------------------------------

Changes on dependencies:
- We have added some new dependencies and increased the minimum required version for some of them.
- Some dependencies are made optional. You can now install all of them or just the minimum required ones.
- `pip install ontolearn[min]` &rarr; the default one when you execute `pip install ontolearn`
- `pip install ontolearn[full]` &rarr; to install the extra dependenices.
You can check them [here](https://github.com/dice-group/Ontolearn/blob/master/setup.py).


---------------------------------------------------

Bug Fixes and others:

- Fixed a bug where using the same EvoLearner model to fit more than one learning problem would cause quality drop.
- Added learning problem generator as Python module
- Other minor changes that in case you are interested, you can check the [PRs comments](https://github.com/dice-group/Ontolearn/pulls?q=is%3Apr+is%3Aclosed).

---------------------------------------------------


As always you can upgrade with pip:


pip install -U ontolearn


_Brought to you by Ontolearn Team._

0.6.1

We're happy to announce the 0.6.1 release.

You can upgrade with pip as usual:

`pip install -U ontolearn`

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