OAEI Bio-ML

This repository provides dataset pointer and evaluation scripts for the Bio-ML Track of the OAEI.

Example code of OM evaluation is available at bertmap_scripts/bertmap_eval.ipynb.

Links

• OAEI Page: https://krr-oxford.github.io/OAEI-Bio-ML/
• Detailed Documentation: https://krr-oxford.github.io/DeepOnto/bio-ml/
• Resource Paper: https://arxiv.org/abs/2205.03447
• Dataset Download:
  • OAEI 2024: https://doi.org/10.5281/zenodo.13119437
  • OAEI 2023: https://doi.org/10.5281/zenodo.8193375
  • OAEI 2022: https://doi.org/10.5281/zenodo.6946466

Results will be published on the OAEI webpage.

Relevant Publications

• [1] Yuan He‚ Jiaoyan Chen‚ Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian and Ian Horrocks. Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. The 21st International Semantic Web Conference (ISWC-2022, Best Resource Paper Candidate). /arxiv/ /iswc/
• [2] Yuan He, Jiaoyan Chen, Hang Dong, and Ian Horrocks. Exploring Large Language Models for Ontology Alignment. The 22nd International Semantic Web Conference (ISWC-2023 Posters & Demos). /arxiv/ /iswc/
• [3] Yuan He, Jiaoyan Chen, Hang Dong, Ian Horrocks, Carlo Allocca, Taehun Kim, and Brahmananda Sapkota. DeepOnto: A Python Package for Ontology Engineering with Deep Learning. Semantic Web (2024). /arxiv/ /swj/