# Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

arXiv: https://arxiv.org/abs/1802.00864 · HTML: https://mlsanity.com/paper/1802.00864/

## Key facts

- Cited by 19 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 31 Jan 2018.

## Built on by (most cited first, 19 of 19)

- [OntoProtein: Protein Pretraining With Gene Ontology Embedding](https://mlsanity.com/paper/2201.11147/) (2022)
- [Contextual Semantic Embeddings for Ontology Subsumption Prediction](https://mlsanity.com/paper/2202.09791/) (2022)
- [Faithiful Embeddings for EL++ Knowledge Bases](https://mlsanity.com/paper/2201.09919/) (2022)
- [Ontology Embedding: A Survey of Methods, Applications and Resources](https://mlsanity.com/paper/2406.10964/) (2024)
- [Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologies](https://mlsanity.com/paper/2105.04944/) (2021)
- [Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases](https://mlsanity.com/paper/2103.04283/) (2021)
- [Ontology Completion with Natural Language Inference and Concept Embeddings: An Analysis](https://mlsanity.com/paper/2403.17216/) (2024)
- [FALCON: Scalable Reasoning over Inconsistent ALC Ontologies](https://mlsanity.com/paper/2208.07628/) (2022)
- [Embedding Ontologies via Incorporating Extensional and Intensional Knowledge](https://mlsanity.com/paper/2402.01677/) (2024)
- [A Self-matching Training Method with Annotation Embedding Models for Ontology Subsumption Prediction](https://mlsanity.com/paper/2402.16278/) (2024)
- [Network representation learning systematic review: ancestors and current development state](https://mlsanity.com/paper/2109.07583/) (2021)
- [Why Settle for Just One? Extending EL++ Ontology Embeddings with Many-to-Many Relationships](https://mlsanity.com/paper/2110.10555/) (2021)
- [Link Analysis meets Ontologies: Are Embeddings the Answer?](https://mlsanity.com/paper/2111.11710/) (2021)
- [Differentiable Fuzzy ALC: A Neural-Symbolic Representation Language for Symbol Grounding](https://mlsanity.com/paper/2211.12006/) (2022)
- [Neuro-Symbolic RDF and Description Logic Reasoners: The State-Of-The-Art and Challenges](https://mlsanity.com/paper/2308.04814/) (2023)
- [T-TExTS (Teaching Text Expansion for Teacher Scaffolding): Enhancing Text Selection in High School Literature through Knowledge Graph-Based Recommendation](https://mlsanity.com/paper/2506.12075/) (2025)
- [Lattice-preserving ALC ontology embeddings with saturation](https://mlsanity.com/paper/2305.07163/) (2023)
- [Extending Ontologies: From Dense Embeddings to Hybrid Quantum-Fuzzy Systems](https://mlsanity.com/paper/2606.08658/) (2026)
- [GO-Based Clustering for Learning Cluster-Level Causal Gene Regulatory Networks](https://mlsanity.com/paper/2610.06042/) (2026)

## Abstract (arXiv)

We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.