首页|A Cross-Domain Ontology Semantic Representa-tion Based on NCBI-BlueBERT Embedding
A Cross-Domain Ontology Semantic Representa-tion Based on NCBI-BlueBERT Embedding
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A common but critical task in biological ontologies data analysis is to compare the difference between ontologies.There have been numerous ontology-based semantic-similarity measures proposed in specific ontology domain,but it still remains a challenge for cross-domain ontologies comparison.An ontology contains the scientific natural language description for the correspond-ing biological aspect.Therefore,we develop a new meth-od based on natural language processing(NLP)represent-ation model bidirectional encoder representations from transformers(BERT)for cross-domain semantic repres-entation of biological ontologies.This article uses the BERT model to represent the word-level of the ontolo-gies as a set of vectors,facilitating the semantic analysis or comparing the biomedical entities named in an onto-logy or associated with ontology terms.We evaluated the ability of our method in two experiments:calculating sim-ilarities of pair-wise disease ontology and human pheno-type ontology terms and predicting the pair-wise of pro-teins interaction.The experimental results demonstrated the comparative performance.This gives promise to the development of NLP methods in biological data analysis.
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