Predicting missing annotations in Gene Ontology with Knowledge Graph Embeddings and True Path Rule
Gene Ontology (GO) and its Annotations (GOA) provide a controlled and evolving vocabulary for gene products and gene functions widely used in molecular biology. GO \& GOA are updated and maintained both automatically from biological publications and manually by curators. These knowledge bases however are often incomplete for two reasons: 1) Research in biological domain itself is still ongoing; 2) The amount of experimental evidence might not be yet sufficient to validate annotations. In this paper, we address the gap in evidence between gene products and their annotations by making link predictions using Knowledge Graph Embedding (KGE) methods. Through the application of the True Path Rule (TPR) in the training stage of KGE, we were able to improve the performance of traditional KGE methods. We report two experimental scenarios with GO and GO Chicken Annotation datasets to show the contribution of embedding TPR to prediction accuracy.
Code (1)
Tasks
Graph EmbeddingKnowledge Graph EmbeddingKnowledge Graph EmbeddingsSimilar Papers 제목 키워드 기반
Ontology-enhanced Prompt-tuning for Few-shot Learning
Few-shot Learning (FSL) is aimed to make predictions based on a limited number of samples. Structured data such as knowledge graphs and ontology libraries has been leveraged to benefit the few-shot setting in various tas…
Event ExtractionFew-Shot LearningKnowledge Graph CompletionKnowledge Graphs+1GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data
By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the…
Preliminary results on Ontology-based Open Data Publishing
Despite the current interest in Open Data publishing, a formal and comprehensive methodology supporting an organization in deciding which data to publish and carrying out precise procedures for publishing high-quality da…
ManagementPattern-based Visualization of Knowledge Graphs
We present a novel approach to knowledge graph visualization based on ontology design patterns. This approach relies on OPLa (Ontology Pattern Language) annotations and on a catalogue of visual frames, which are associat…
Knowledge GraphsLattice-preserving $\mathcal{ALC}$ ontology embeddings with saturation
Generating vector representations (embeddings) of OWL ontologies is a growing task due to its applications in predicting missing facts and knowledge-enhanced learning in fields such as bioinformatics. The underlying sema…
DescriptiveKnowledge Base CompletionOntology Embedding