Bio2Vec: Smart analytics infrastructure for the life sciences

Mon, May 18 2026

Overview

Smart analytics infrastructure on biological knowledge graphs; extends Bio2RDF, develops semantic analytics methods that became OPA2Vec / OWL2Vec.

Period: 2018–2020

KAUST Competitive Research Grant — Grant ID: URF/1/3454-01-01 (PI) — USD 113,250

Robert Hoehndorf — PI (KAUST (Professor of Computer Science))
Xin Gao — CoI (KAUST (CBRC))
Michel Dumontier — CoI (Maastricht University)
Jens Lehmann — CoI (Amazon (formerly TU Dresden))
Mona Alshahrani — PhD (alumnus) (Jubail University College (Assistant Professor))
Maxat Kulmanov — PhD (alumnus) (KAUST (Research Scientist))
Sumyyah Toonsi — MSc (alumnus)

Bio2Vec — Smart-analytics infrastructure for the life sciences; semantic analytics on biological knowledge graphs (Bio2RDF-based). https://github.com/bio-ontology-research-group/bio2vec
DeepGOPlus — Deep learning model for Gene Ontology-based protein function prediction; CNN ensemble over protein sequences and homology. https://github.com/bio-ontology-research-group/deepgoplus
OPA2Vec — Ontology Property Alignment to Vector representations; integrates ontology axioms with metadata text for embeddings. https://github.com/bio-ontology-research-group/opa2vec
OWL2Vec — OWL ontology embedding method using random-walk + word2vec over OWL axioms. https://github.com/bio-ontology-research-group/walking-rdf-and-owl

(2020) Semantic similarity and machine learning with biomedical ontologies
(2019) Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
(2019) DeepGOPlus: Improved protein function prediction from sequence
(2019) Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
(2019) PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
(2019) Ontology based text mining of gene--phenotype associations: application to candidate gene prediction
(2018) Ontology-based prediction of cancer driver genes
(2018) Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
(2018) Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
(2016) DeepPVP: Phenotype-based prioritization of causative variants using deep learning
(2016) Self-normalizing learning on biomedical ontologies
(2015) Ontology-based prediction of cancer driver genes
(2012) Combining lexical and context features for automatic ontology extension
(2012) DDIEM: Drug Database for Inborn Errors of Metabolism
(2012) DeepPVP: phenotype-based prioritization of causative variants using deep learning
… and 5 more.

Topics: Applied Ontology, Neuro-symbolic AI, Semantic similarity