OntoAligner 1.6.0
OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment.
License: Apache-2.0
Requires Python: <3.14.0,>=3.10

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<h3 align="center">OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment</h3>

**OntoAligner** is a Python library designed to simplify ontology alignment and matching for researchers, practitioners, and developers. With a modular architecture and robust features, OntoAligner provides powerful tools to bridge ontologies effectively.


## 🧪 Installation

You can install **OntoAligner** from PyPI using `pip`:

```bash
pip install ontoaligner
```

Alternatively, to get the latest version directly from the source, use the following commands:

```bash
git clone git@github.com:sciknoworg/OntoAligner.git
pip install ./ontoaligner
```

Next, verify the installation:

```python
import ontoaligner

print(ontoaligner.__version__)
```

## 📚 Documentation

Comprehensive documentation for OntoAligner, including detailed guides and examples, is available at **[ontoaligner.readthedocs.io](https://ontoaligner.readthedocs.io/)**. Below are some key tutorials with links to both the documentation and the corresponding example codes.



| Example                        | Tutorial                                                                                                |                                            Script                                             |
|:-------------------------------|:--------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------:|
| Lightweight                    | [📚 Fuzzy Matching](https://ontoaligner.readthedocs.io/aligner/lightweight.html)                        |   [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/fuzzy_matching.py)   |
| Retrieval                      | [📚 Retrieval Aligner](https://ontoaligner.readthedocs.io/aligner/retriever.html)                       | [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/retriever_matching.py) |
| Large Language Models          | [📚 LLM Aligner](https://ontoaligner.readthedocs.io/aligner/llm.html)                                   |    [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/llm_matching.py)    |
| Retrieval Augmented Generation | [📚 RAG Aligner](https://ontoaligner.readthedocs.io/aligner/rag.html)                                   |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/rag_matching.py)|
| FewShot                        | [📚 FewShot-RAG Aligner](https://ontoaligner.readthedocs.io/aligner/rag.html#fewshot-rag)               |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/rag_matching.py)
| In-Context Vectors Learning    | [📚 In-Context Vectors RAG](https://ontoaligner.readthedocs.io/aligner/rag.html#in-context-vectors-rag) |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/icv_rag_matching.py)
| Knowledge Graph Embedding      | [📚 KGE Aligner](https://ontoaligner.readthedocs.io/aligner/kge.html)                                   |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/kge.py)
| Property Alignment             | [📚 PropMatch Aligner](https://ontoaligner.readthedocs.io/aligner/propmatch.html)                       |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/main/examples/property_alignment)
| eCommerce  | [📚 Product Alignment in eCommerce](https://ontoaligner.readthedocs.io/usecases/ecommerce.html)                  |       [📝 Code](https://github.com/sciknoworg/OntoAligner/blob/dev/examples/ecommerce_product_alignment.py)

## 🚀 Quick Tour

Below is an example of using Retrieval-Augmented Generation (RAG) step-by-step approach for ontology matching:

```python
from ontoaligner.ontology import MaterialInformationMatOntoOMDataset
from ontoaligner.utils import metrics, xmlify
from ontoaligner.aligner import MistralLLMBERTRetrieverRAG
from ontoaligner.encoder import ConceptParentRAGEncoder
from ontoaligner.postprocess import rag_hybrid_postprocessor

# Step 1: Initialize the dataset object for MaterialInformation MatOnto dataset
task = MaterialInformationMatOntoOMDataset()
print("Test Task:", task)

# Step 2: Load source and target ontologies along with reference matchings
dataset = task.collect(
    source_ontology_path="assets/MI-MatOnto/mi_ontology.xml",
    target_ontology_path="assets/MI-MatOnto/matonto_ontology.xml",
    reference_matching_path="assets/MI-MatOnto/matchings.xml"
)

# Step 3: Encode the source and target ontologies
encoder_model = ConceptParentRAGEncoder()
encoded_ontology = encoder_model(source=dataset['source'], target=dataset['target'])

# Step 4: Define configuration for retriever and LLM
retriever_config = {"device": 'cuda', "top_k": 5}
llm_config = {"device": "cuda", "max_length": 300, "max_new_tokens": 10, "batch_size": 15}

# Step 5: Initialize Generate predictions using RAG-based ontology matcher
model = MistralLLMBERTRetrieverRAG(retriever_config=retriever_config, llm_config=llm_config)
model.load(llm_path = "mistralai/Mistral-7B-v0.3", ir_path="all-MiniLM-L6-v2")
predicts = model.generate(input_data=encoded_ontology)

# Step 6: Apply hybrid postprocessing
hybrid_matchings, hybrid_configs = rag_hybrid_postprocessor(predicts=predicts,
                                                            ir_score_threshold=0.1,
                                                            llm_confidence_th=0.8)

evaluation = metrics.evaluation_report(predicts=hybrid_matchings, references=dataset['reference'])
print("Hybrid Matching Evaluation Report:", evaluation)

# Step 7: Convert matchings to XML format and save the XML representation
xml_str = xmlify.xml_alignment_generator(matchings=hybrid_matchings)
open("matchings.xml", "w", encoding="utf-8").write(xml_str)
```

Ontology alignment pipeline using RAG method:

```python
import ontoaligner

pipeline = ontoaligner.OntoAlignerPipeline(
    task_class=ontoaligner.ontology.MouseHumanOMDataset,
    source_ontology_path="assets/MI-MatOnto/mi_ontology.xml",
    target_ontology_path="assets/MI-MatOnto/matonto_ontology.xml",
    reference_matching_path="assets/MI-MatOnto/matchings.xml"
)

matchings, evaluation = pipeline(
    method="rag",
    encoder_model=ontoaligner.encoder.ConceptRAGEncoder(),
    model_class=ontoaligner.aligner.MistralLLMBERTRetrieverRAG,
    postprocessor=ontoaligner.postprocess.rag_hybrid_postprocessor,
    llm_path='mistralai/Mistral-7B-v0.3',
    retriever_path='all-MiniLM-L6-v2',
    llm_threshold=0.5,
    ir_rag_threshold=0.7,
    top_k=5,
    max_length=512,
    max_new_tokens=10,
    device='cuda',
    batch_size=32,
    return_matching=True,
    evaluate=True
)

print("Matching Evaluation Report:", evaluation)
```
## 👥 Contact & Contributions

We welcome contributions to enhance OntoAligner and make it even better! Please review our contribution guidelines in [CONTRIBUTING.md](CONTRIBUTING.md) before getting started. You are also welcome to assist with the ongoing maintenance by referring to [MAINTENANCE.md](MAINTENANCE.md). Your support is greatly appreciated.


If you encounter any issues or have questions, please submit them in the [GitHub issues tracker](https://github.com/sciknoworg/OntoAligner/issues).


## 📚 Citing this Work

If you use OntoAligner in your work or research, please cite the following preprint:

- OntoAligner Library:
    > Babaei Giglou, H., D’Souza, J., Karras, O., Auer, S. (2025). OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment. In: Curry, E., et al. The Semantic Web. ESWC 2025. Lecture Notes in Computer Science, vol 15719. Springer, Cham. https://doi.org/10.1007/978-3-031-94578-6_10

    📌 BibTeX
    ```bibtex
    @InProceedings{10.1007/978-3-031-94578-6_10,
        author="Babaei Giglou, Hamed and D'Souza, Jennifer and Karras, Oliver and Auer, S{\"o}ren",
        editor="Curry, Edward and Acosta, Maribel and Poveda-Villal{\'o}n, Maria and van Erp, Marieke and Ojo, Adegboyega and Hose, Katja and Shimizu, Cogan and Lisena, Pasquale",
        title="OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment",
        booktitle="The Semantic Web",
        year="2025",
        publisher="Springer Nature Switzerland",
        address="Cham",
        pages="174--191"
    }
    ```

- LLMs4OM (for RAG module)
    >   Babaei Giglou, H., D’Souza, J., Engel, F., Auer, S. (2025). LLMs4OM: Matching Ontologies with Large Language Models. In: Meroño Peñuela, A., et al. The Semantic Web: ESWC 2024 Satellite Events. ESWC 2024. Lecture Notes in Computer Science, vol 15344. Springer, Cham. https://doi.org/10.1007/978-3-031-78952-6_3

    📌 BibTeX
    ```bibtex
    @InProceedings{10.1007/978-3-031-78952-6_3,
      author="Babaei Giglou, Hamed and D'Souza, Jennifer and Engel, Felix and Auer, S{\"o}ren",
      editor="Mero{\~{n}}o Pe{\~{n}}uela, Albert and Corcho, Oscar and Groth, Paul and Simperl, Elena and Tamma, Valentina and Nuzzolese, Andrea Giovanni and Poveda-Villal{\'o}n, Maria and Sabou, Marta and Presutti, Valentina and Celino, Irene and Revenko, Artem and Raad, Joe and Sartini, Bruno and Lisena, Pasquale",
      title="LLMs4OM: Matching Ontologies with Large Language Models",
      booktitle="The Semantic Web: ESWC 2024 Satellite Events",
      year="2025",
      publisher="Springer Nature Switzerland",
      address="Cham",
      pages="25--35",
      isbn="978-3-031-78952-6"
      }
    ```

## 📃 License

This software is licensed under [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0).

[//]: # (This work is licensed under a MIT License)
[//]: # (is archived in Zenodo under the DOI [![DOI]&#40;https://zenodo.org/badge/DOI/10.5281/zenodo.14533133.svg&#41;]&#40;https://doi.org/10.5281/zenodo.14533133&#41; and )