Software Research OverviewOpen-source tools, libraries, services, and ontologies maintained by the Bio-Ontology Research Group. Source is on github.com/bio-ontology-research-group. Ontology Embedding & Machine Learning Libraries and methods that turn ontologies into vector representations or otherwise combine logical structure with statistical learning. mOWLPython library for machine learning with biomedical ontologies. Unifies projection-, axiom- and geometric-embedding methods (EL Embeddings, ELBE, BoxSquaredEL, OWL2Vec*, DL2Vec, OPA2Vec) behind one API, with first-class OWLAPI access and PyTorch integration.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information · Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11) GitHub · Homepage · 91 Walking RDF and OWLOriginal feature-learning method over RDF graphs and OWL ontologies via biased random walks; the seed implementation for many later embedding methods including OWL2Vec*.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 47 OPA2VecCombines ontology axioms with associated annotation properties (labels, synonyms, definitions) into a single corpus, then trains Word2Vec to produce semantically rich vectors for ontology classes.From: Bio2Vec: Smart analytics infrastructure for the life sciences · CompleX: Variant Prioritization in Complex Disease GitHub · 37 EL EmbeddingsReference implementation of geometric embeddings for the EL++ description logic, the predecessor of GeometrE and BoxSquaredEL. Preserves subsumption reasoning by mapping classes to convex regions.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information GitHub · 28 Onto2VecRepresentation learning for ontologies and their annotations by treating logical axioms as natural-language sentences; predecessor of OPA2Vec.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 21 DL2VecEncodes description-logic axioms as a directed graph and learns embeddings via random walks; widely used for downstream gene-disease and protein-function prediction.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 20 Interpretable LearningGenerates interpretable symbolic rules from learned representations over biomedical knowledge bases.From: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11) GitHub · 5 catECategory-theoretic, lattice-preserving embedding of ALC description-logic ontologies that retains the consequence-closure semantics of the original theory.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information GitHub · 3 DELEDeductive EL embeddings: enrich training data with the deductive closure of an ontology before learning, so embeddings recover entailment rather than only asserted axioms.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information GitHub · 2 EL2BoxBox-shaped geometric embeddings for EL++ that strengthen the topological guarantees of EL Embeddings.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information GitHub · 2 Protein Function Prediction Deep-learning and neuro-symbolic models for predicting Gene Ontology functional annotations of proteins. DeepGOPlusCNN-ensemble protein-function predictor that augments sequence-based scoring with k-nearest-neighbour homology and GO axioms; one of the strongest CAFA-evaluated open models.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions · Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · Homepage · 103 DeepGOOriginal sequence-based, ontology-aware deep classifier for predicting Gene Ontology functional annotations; basis of the entire DeepGO family of tools.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions · Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 87 DeepGO2Next-generation DeepGO model with transformer protein embeddings and improved hierarchical multi-label prediction.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 57 DeepGOZeroZero-shot extension of DeepGO using model-theoretic ELEmbeddings to predict GO classes that have never been observed during training.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 34 DeepGOMetaDeepGO trained specifically for metagenomic communities; predicts functional roles of proteins recovered from environmental samples and links them to biogeochemical processes.From: Enabling desert revegetation by AI-tailored soil microbiome fortification · Enabling mangrove restoration by AI-tailored microbiome fortification GitHub · 8 GO-AgentLLM-agent framework that decomposes protein-function prediction into tool-calling sub-tasks (sequence search, structure lookup, domain reasoning) and stitches the evidence into a final GO annotation.From: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme) GitHub · 7 DeepPhenoPredicts loss-of-function organism-level phenotypes (HPO/MPO) directly from a gene's annotated functions, using a hierarchical neural classifier over phenotype ontologies.From: CompleX: Variant Prioritization in Complex Disease GitHub · 6 PU-GOPositive-unlabeled ranking of protein functions with ontology-based priors; directly addresses the partial-annotation problem in CAFA benchmarks.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 4 PhenoGoConPredicts gene–phenotype associations from predicted Gene Ontology functions; bridges GO function prediction and HPO/MPO phenotype prediction.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 3 Genomic ContextBacterial protein-function prediction that exploits operon and genome-neighbourhood structure in addition to sequence and homology.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 3 Variant and Disease Prioritization Tools that combine phenotype, ontology, and sequence data to rank candidate disease-causing variants and predict gene-disease associations. PhenomeNET-VPPhenotype-driven variant prioritization for whole-exome and whole-genome sequencing data; widely used implementation of the phenotype-aware variant ranking approach.From: CompleX: Variant Prioritization in Complex Disease GitHub · 43 DeepSVPPrioritizes structural and copy-number variants by combining patient phenotype with gene-function similarity learned from biomedical ontologies.From: CompleX: Variant Prioritization in Complex Disease · A public Saudi pangenome as reference for genomics in the Middle East GitHub · 18 DeepViralPredicts virus–host protein-protein interactions from sequence and infectious-disease phenotypes; trained jointly across coronaviruses, influenza, and other RNA viruses.From: CompleX: Variant Prioritization in Complex Disease GitHub · 12 EmbedPVPEmbedding-based phenotype-aware variant predictor that ranks candidate causative variants using joint sequence- and phenotype-derived representations.From: CompleX: Variant Prioritization in Complex Disease GitHub · 8 STARVarSymptom-based tool for automatic ranking of variants using evidence from the biomedical literature and population genomes; combines text mining with phenotype matching.From: CompleX: Variant Prioritization in Complex Disease GitHub · 7 predCANOntology-based prediction of cancer driver genes by integrating phenotype, pathway and function knowledge with somatic-variant features.From: CompleX: Variant Prioritization in Complex Disease GitHub · 5 INDIGENAInductive prediction of disease–gene associations from phenotype ontologies; generalises to unseen diseases via ontology-aware embeddings.From: CompleX: Variant Prioritization in Complex Disease GitHub · 1 GenomeLinterAI-powered clinical decision-support tool that ingests annotated VCFs and synthesises diagnostic interpretations for rare-disease patients without requiring deep bioinformatics expertise. GitHub Ontology Reasoning & Tooling Reasoning-as-a-service infrastructure, ontology repositories, and utilities for working with OWL. vec2SPARQLAdds embedding-similarity functions to a SPARQL endpoint so that vector-space queries (k-nearest neighbours, cosine similarity) can be mixed with classical graph patterns.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 14 Onto2GraphGenerates entailment-aware graph projections of OWL ontologies suitable for downstream graph machine learning while preserving the axioms' deductive structure.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information · Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 12 AberOWLOntology repository delivering OWL EL reasoning as a service: stores hundreds of bio-ontologies, exposes SPARQL with class-expression query expansion, and powers semantic search over PubMed/PMC.From: Data integration and ontologies for microbial cell factories · Phenotype ontologies and translational research (Cambridge / Aberystwyth) GitHub · Homepage · 10 UNMIREOTIdentifies, diagnoses, and semi-automatically repairs hidden contradictions and unsatisfiable classes introduced by partial imports (MIREOT) into biomedical ontologies.From: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information GitHub · 2 OntoFuncOntology-driven enrichment analysis that supports arbitrary OWL ontologies and full subsumption-aware aggregation, not only GO.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub Knowledge Graphs & Drug Discovery Biomedical knowledge graph construction, drug repurposing, drug-drug interactions, and graph-based prediction. Multi-Drug EmbeddingDrug repurposing method that learns joint embeddings of drugs, targets and diseases from biomedical knowledge graphs and the scientific literature.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 36 NanoDesignerIterative refinement framework for nanobody/CDR design that explicitly models the antigen–CDR interdependence; companion code to the NanoDesigner paper.From: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications GitHub · 16 DeepMOCCAGraph neural network for cancer survival analysis that integrates multi-omics (mutation, expression, methylation, CNV) with a curated cancer knowledge graph.From: Bio2Vec: Smart analytics infrastructure for the life sciences GitHub · 14 SmuDGESemantic disease-gene embeddings; integrates phenotype, function and pathway ontologies into a unified vector space for downstream prediction.From: Bio2Vec: Smart analytics infrastructure for the life sciences · CompleX: Variant Prioritization in Complex Disease GitHub · 12 PathoPhenoDBCurated database of pathogens and the disease phenotypes they cause, distributed as an OWL ontology and an interactive web application.From: Computational methods for functional metagenomics: from protein functions to multi-scale interactions GitHub · 8 Teaching & Tutorials Self-contained teaching material accompanying our courses and review articles. Machine Learning with OntologiesCompanion code and worked examples for the Briefings in Bioinformatics tutorial review; the most-starred repository in the group. GitHub · 132 Ontology TutorialHands-on tutorial that walks new users through OWL, automated reasoning, and ontology-aware data analysis; basis for the AI in Biomedicine summer school. GitHub · 73 mOWL TutorialStep-by-step worked notebooks that demonstrate every embedding family in mOWL on protein-function, gene-disease, and ontology-completion tasks. GitHub · 8 Ontologies & Resources Bio-ontologies and curated resources maintained by the group. Units of Measurement Ontology (UO)OBO Foundry ontology of units of measurement; aligned with QUDT and used across biomedical data standards. GitHub · 23 PhenomeNetCross-species phenotype ontology and similarity network combining HPO, MPO, ZP and others; the substrate behind PhenomeNET-VP and DeepPheno.From: CompleX: Variant Prioritization in Complex Disease · Phenotype ontologies and translational research (Cambridge / Aberystwyth) GitHub · 1
