Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
Personalized cancer treatment prediction work funded through KCSH Pathway to Impact 2025. Sub-WBSes FCC/1/5932-10-02, FCC/1/5932-11-01, FCC/1/5932-12-10.
KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
Generative-AI methods applied to BCB-themed health and wellness within the KAUST Center of Excellence for Generative AI. Sub-WBS FCC/1/5940-07-02.
Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
Faithful, complete, and explainable machine-learning methods on biomedical ontologies. Grant URF/1/5041-01-01 activated Apr 2023.
Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
Disease modelling using biomimetic peptide scaffolds and patient-derived leukemic cells for precision medicine applications.
A public Saudi pangenome as reference for genomics in the Middle East
Builds an open Saudi pangenome reference to support genomics applications in the Middle East, including rare-disease variant interpretation.
Enabling desert revegetation by AI-tailored soil microbiome fortification
AI-driven design of soil microbiomes for desert plant restoration; functional metagenomics analysis of arid-zone soil microbiomes.
Enabling mangrove restoration by AI-tailored microbiome fortification
Microbiome-based intervention for mangrove ecosystem restoration in coastal Saudi Arabia.
Metagenomics analysis of surface samples for bioprospecting in support of oil and gas upstream applications.
Evolutionary potential of corals to adapt to climate warming
Genomics and computational analysis of coral adaptation to ocean warming in the Red Sea.
Computational methods for functional metagenomics: from protein functions to multi-scale interactions
Multi-scale systems methods for characterising microbial community functions via protein function prediction; downstream produced DeepGOPlus and successor models.
IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
Neuro-symbolic methods integrating biomedical networks and ontologies for quantitative analysis of disease phenotypes and variants.
Development of Algorithms for Biotechnology and Biomedical Applications
Algorithm development for biotechnology and biomedical applications at the CBRC; umbrella fund for several smaller projects.
CompleX: Variant Prioritization in Complex Disease
Semantic methods for prioritising causative variants in complex (polygenic / oligogenic) disease using phenotype ontologies and gene network embeddings.
Health informatics and precision-medicine pipelines tailored to Saudi-population genetic and phenotypic data.
Whole genome sequencing of rare disease patients
Pilot rare-disease whole-genome sequencing and analysis, in collaboration with KAUST Health.
Sequencing and computational analysis of MRSA samples
Microbial genomics and bioinformatics of methicillin-resistant Staphylococcus aureus (MRSA) isolates in Saudi Arabia.
Improvement of genetic variant prioritization technology
Engineering improvements to the semantic variant-prioritization pipeline (PhenomeNet, DeepPVP).
Bio2Vec: Smart analytics infrastructure for the life sciences
Smart analytics infrastructure on biological knowledge graphs; extends Bio2RDF, develops semantic analytics methods that became OPA2Vec / OWL2Vec.
The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
Population genomics of whale sharks; comparative genomics and habitat-use analysis.
Data integration and ontologies for microbial cell factories
Ontology-based data integration for synthetic biology and metabolic engineering. Hoehndorf led the data-integration work package.
KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
Robert leads the Infectious Disease area within the Bioinformatics & Computational Biology (BCB) research theme of the KAUST Center of Excellence for Smart Health.
KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
KCSH "Pathway to Impact 2025" scheme (distinct from CoE theme funds); $50k x 2 periods. Verified email 2026-05-29.
5932-12 CoEP2I Hoehndorf Pathway-to-Impact award (thread:000000000005eeba); WBS corrected to -12-10 (was wrongly -10-02) per budget email 2026-05-29
KAUST Center of Excellence for Generative AI (CoE)
$50,000/year for FY24/25 and FY25/26 (Biomedical/BCB theme). Verified email 2026-05-29.
WBS for CoE GenAI project 5940-07 (thread:000000000005cdc8); grant ID corrected to -07-01 per Robert 2026-05-29
KAUST Competitive Research Grant (CRG11)
$282,000 overall KAUST award; $49,809 subcontract to Cambridge (P. Schofield, Co-PI); net $232,191 to BORG. Verified email 2026-05-29.
CRG11 activation thread (URF/1/5041; "$141,000 each year, $282,000 overall"; sole PI), verified email 2026-05-29
thread:000000000005cc4c (KSHI #4938 3D Leukemia Disease Models)
no activation email found; may have been absorbed into REI/1/5235 (NTGC desert)
follow up with Hirt's BA or check for separate WBS
thread:0000000000046ff6 (Aug 2021 'Robert Hoehndorf CCF allocation' URF/1/1976-34-01); later FCC/1/1976-46-01 + -49-01 (Dec 2023 thread:000000000005857d) [grantID corrected URF->FCC 2026-05-29: all paper acknowledgements use FCC/1/1976-34-01, consistent with -08]
thread:000000000002acd4 (3790 CRG7 Activation)
KAUST OSR Director's Award, Digital Health Initiative
thread:000000000002a307 (OSR Director's Award 4133 activation Apr 2019)
King Abdulaziz City for Science and Technology
thread:00000000000284aa (3689-KACST-Grant activation kickoff)
thread:00000000000258f8 (Sultan Ahmed, Summary CCF Funding Jan 2018)
KAUST Center of Excellence for Smart Health (KCSH)
Area lead (Infectious Disease), BCB theme
$100,000/year for FY24/25 and FY25/26, split across two KCSH pocket IDs (one is FCC/1/5932-10-02, shown at $50k in the 2024/25 BCB budget email; the second pocket covers the remaining $50k/year). Confirmed by Robert 2026-05-29.
KCSH BCB theme budget 2024/25 (thread:0000000000060a33): '$50,000 - Robert Hoehndorf - FCC/1/5932-10-02', BCB theme Lead PI Xin Gao
King Fahd University of Petroleum and Minerals (Assistant Professor)
Semantic Prioritization of Novel Causative Variants
Jubail University College (Assistant Professor)
Multi-modal learning on biological knowledge graphs
Prediction of protein functions and phenotypes
King Abdulaziz University (Assistant Professor)
Ontology design patterns for integrating phenotype ontologies
Prioritizing Causative Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies
Data Driven Mining of Causal Disease Relations to Enhance Disease Centric Predictions
Sano Centre Krakow (Postdoctoral researcher)
Computational Methods for Functional Characterization of Microbial Communities
Reference Bias and Variant Interpretation in Human Disease Genomics
Neuro-symbolic methods for embedding ontologies, and applications in life sciences
Evaluating the Application of Allele Frequency in the Saudi Population Variant Detection
Unsupervised Method for Disease Named Entity Recognition
Automatic annotation of protein functions through text mining
Ontology design patterns for aging mouse ontologies
Ontology-based identification of cancer driver genes
Simulation and visualization of human genomes
Context-aware protein function prediction in bacterial genomes
Protein functional domain identification methodology
3D conformation-based protein function prediction
Predicting effects of non-coding genomic variants
Predicting Protein Functions From Interactions Using Neural Networks and Ontologies
De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge
Rare variant collapsing analysis on UK Biobank
Description Logic EL++ Embeddings with Intersectional Closure
Embedding Ontologies using Category Theory Semantics
Towards Quality and General Knowledge Representation Learning
An Inductive, Supervised Gene-Disease Associations Method
Establishment and Evaluation of a Computational Workflow for the Design and Optimization of Nanobodies
Differential Effects of p38 MAPK Inhibition on Chemoresistance in Patients with Colorectal Cancer
Automated Theorem Proving with Large Language Models in Lean: An Exploration of Specialized In-Context Learning and General-Purpose Hierarchical Architectures
Machine Learning Methods for Survival Analysis: From Outcome-Conditioned Data Synthesis to Decoupled Ranking and Calibration
Genome-Scale Protein Function Adjustment using Constraint Optimization
KAUST MSc Bioengineering (defended 3 May 2026)
King Juan Carlos University (Research Scientist)
MSc Molecular Biology (in progress, expected 2026)
KAUST (Biological & Environmental Sciences)
Former KAUST CBRC director (retired; CBRC now dissolved)
Python 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.
Reference implementation of geometric embeddings for the EL++ description logic, the predecessor of GeometrE and BoxSquaredEL. Preserves subsumption reasoning by mapping classes to convex regions.
Category-theoretic, lattice-preserving embedding of ALC description-logic ontologies that retains the consequence-closure semantics of the original theory.
Deductive EL embeddings: enrich training data with the deductive closure of an ontology before learning, so embeddings recover entailment rather than only asserted axioms.
Combines ontology axioms with associated annotation properties (labels, synonyms, definitions) into a single corpus, then trains Word2Vec to produce semantically rich vectors for ontology classes.
Representation learning for ontologies and their annotations by treating logical axioms as natural-language sentences; predecessor of OPA2Vec.
Encodes description-logic axioms as a directed graph and learns embeddings via random walks; widely used for downstream gene-disease and protein-function prediction.
Original feature-learning method over RDF graphs and OWL ontologies via biased random walks; the seed implementation for many later embedding methods including OWL2Vec*.
Box-shaped geometric embeddings for EL++ that strengthen the topological guarantees of EL Embeddings.
Generates interpretable symbolic rules from learned representations over biomedical knowledge bases.
CNN-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.
Original sequence-based, ontology-aware deep classifier for predicting Gene Ontology functional annotations; basis of the entire DeepGO family of tools.
Next-generation DeepGO model with transformer protein embeddings and improved hierarchical multi-label prediction.
Zero-shot extension of DeepGO using model-theoretic ELEmbeddings to predict GO classes that have never been observed during training.
DeepGO trained specifically for metagenomic communities; predicts functional roles of proteins recovered from environmental samples and links them to biogeochemical processes.
Positive-unlabeled ranking of protein functions with ontology-based priors; directly addresses the partial-annotation problem in CAFA benchmarks.
Predicts loss-of-function organism-level phenotypes (HPO/MPO) directly from a gene's annotated functions, using a hierarchical neural classifier over phenotype ontologies.
LLM-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.
Predicts gene–phenotype associations from predicted Gene Ontology functions; bridges GO function prediction and HPO/MPO phenotype prediction.
Bacterial protein-function prediction that exploits operon and genome-neighbourhood structure in addition to sequence and homology.
Ontology 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.
Generates entailment-aware graph projections of OWL ontologies suitable for downstream graph machine learning while preserving the axioms' deductive structure.
Identifies, diagnoses, and semi-automatically repairs hidden contradictions and unsatisfiable classes introduced by partial imports (MIREOT) into biomedical ontologies.
Ontology-driven enrichment analysis that supports arbitrary OWL ontologies and full subsumption-aware aggregation, not only GO.
Adds embedding-similarity functions to a SPARQL endpoint so that vector-space queries (k-nearest neighbours, cosine similarity) can be mixed with classical graph patterns.
Phenotype-driven variant prioritization for whole-exome and whole-genome sequencing data; widely used implementation of the phenotype-aware variant ranking approach.
Prioritizes structural and copy-number variants by combining patient phenotype with gene-function similarity learned from biomedical ontologies.
Embedding-based phenotype-aware variant predictor that ranks candidate causative variants using joint sequence- and phenotype-derived representations.
Symptom-based tool for automatic ranking of variants using evidence from the biomedical literature and population genomes; combines text mining with phenotype matching.
Inductive prediction of disease–gene associations from phenotype ontologies; generalises to unseen diseases via ontology-aware embeddings.
AI-powered clinical decision-support tool that ingests annotated VCFs and synthesises diagnostic interpretations for rare-disease patients without requiring deep bioinformatics expertise.
Ontology-based prediction of cancer driver genes by integrating phenotype, pathway and function knowledge with somatic-variant features.
Predicts virus–host protein-protein interactions from sequence and infectious-disease phenotypes; trained jointly across coronaviruses, influenza, and other RNA viruses.
Semantic disease-gene embeddings; integrates phenotype, function and pathway ontologies into a unified vector space for downstream prediction.
Drug repurposing method that learns joint embeddings of drugs, targets and diseases from biomedical knowledge graphs and the scientific literature.
Graph neural network for cancer survival analysis that integrates multi-omics (mutation, expression, methylation, CNV) with a curated cancer knowledge graph.
Curated database of pathogens and the disease phenotypes they cause, distributed as an OWL ontology and an interactive web application.
Iterative refinement framework for nanobody/CDR design that explicitly models the antigen–CDR interdependence; companion code to the NanoDesigner paper.
Companion code and worked examples for the Briefings in Bioinformatics tutorial review; the most-starred repository in the group.
Educational/dissemination output (Machine Learning with Ontologies tutorial materials); not the deliverable of a single grant.
Hands-on tutorial that walks new users through OWL, automated reasoning, and ontology-aware data analysis; basis for the AI in Biomedicine summer school.
Educational/dissemination output (ontology engineering tutorial); not the deliverable of a single grant.
Step-by-step worked notebooks that demonstrate every embedding family in mOWL on protein-function, gene-disease, and ontology-completion tasks.
Educational/dissemination output (mOWL tutorial materials); not the deliverable of a single grant.
OBO Foundry ontology of units of measurement; aligned with QUDT and used across biomedical data standards.
Community ontology contribution; not the deliverable of a single grant.
Cross-species phenotype ontology and similarity network combining HPO, MPO, ZP and others; the substrate behind PhenomeNET-VP and DeepPheno.
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
This paper introduces FLOPO, an ontology for integrating morphological traits and phenotypes of vascular plants, which is a clear example of applied ontology and phenotype informatics.
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
This paper evaluates ontology design patterns for combining ontologies, which is a key aspect of applied ontology and ontology engineering.
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Bras\'\ilia, Brazil, August 28 - September 1, 2023
Uses ontology components for NER training; an Applied Ontology paper at ICBO.
Ontology-based prediction of cancer driver genes
This paper uses ontologies for predicting cancer driver genes, which falls under applied ontology and biomedical informatics.
Improving the classification of cardinality phenotypes using collections
Applied ontology design pattern for cardinality in phenotypes.
Combining lexical and context features for automatic ontology extension
This paper focuses on automatic ontology extension using lexical and context features, which is a method in ontology engineering and biomedical informatics.
DDIEM: drug database for inborn errors of metabolism
This paper describes a drug database for inborn errors of metabolism, directly relevant to drug mechanisms and rare disease support.
DeepGOPlus: improved protein function prediction from sequence
This paper introduces DeepGOPlus for protein function prediction, a core area of my work, and uses deep learning with ontologies.
Phenotype-driven discovery of digenic variants in personal genome sequences
This paper focuses on phenotype-driven discovery of digenic variants in personal genome sequences, directly supporting rare disease diagnostics and involving genomics and phenotype informatics.
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
This paper emphasizes the role of formal axioms in biomedical ontologies for data analysis, aligning with applied ontology and ontology engineering.
Klarigi: Characteristic explanations for semantic biomedical data
Tool for explaining semantic biomedical data; infrastructure/engineering, not applied ontology proper.
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
This paper applies Large Language Models to phenotype-based gene prioritization for rare disease diagnosis.
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
BMC Medical Informatics and Decision Making
This paper addresses finding and repairing contradictions in biomedical ontologies to improve semantic interoperability, fitting both ontology engineering and applied ontology.
Handbook on Neurosymbolic AI and Knowledge Graphs
The title directly indicates a focus on Neuro-Symbolic AI in Life Sciences, which is a primary topic.
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
Large-scale knowledge integration into ML for molecular property prediction; this is neuro-symbolic.
Ontology Embedding: A Survey of Methods, Applications and Resources
IEEE Transactions on Knowledge and Data Engineering
A survey of ontology-embedding methods — the core neuro-symbolic contribution. Not Applied Ontology.
Ontology based mining of pathogen--disease associations from literature
This paper focuses on text mining for pathogen-disease associations using ontologies, aligning with biomedical informatics and applied ontology.
PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
This paper describes a biomedical knowledge base linking pathogens to disease phenotypes, supporting infectious disease research and rare disease diagnostics.
Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022
Uniform SPARQL access over data + ontologies + ML; ontology engineering with an applied-ontology slant.
Integrating phenotype ontologies with PhenomeNET
Proceedings of Ontology Matching Workshop 2016
The paper describes integrating phenotype ontologies with PhenomeNET, a system used for rare disease diagnostic support and phenotype analysis.
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
This paper describes Starvar, a tool for symptom-based variant prioritization in rare diseases, integrating evidence from literature and genomes.
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
This paper uses ontology-based text mining to identify gene-phenotype associations for candidate gene prediction, which is a biomedical informatics task supporting rare disease diagnosis.
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018.
This paper integrates SPARQL queries with knowledge graph embeddings, combining symbolic query languages with vector representations, which is a neuro-symbolic AI approach for semantic interoperability.
Improved characterisation of clinical text through ontology-based vocabulary expansion
This paper improves clinical text characterization using ontology-based vocabulary expansion, aligning with biomedical informatics and phenotype informatics.
Semantic similarity and machine learning with ontologies
This paper focuses on semantic similarity measures, their application with machine learning, and the use of ontology embeddings.
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
This paper describes a prediction system for virus-host interactions, which falls under drug mechanisms and systems biology, and general biomedical informatics.
Predicting protein functions using positive-unlabeled ranking with ontology-based priors
Protein function prediction is the application; using ontology axioms as PU priors makes it neuro-symbolic.
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
This paper discusses improving semantic interoperability in life science data, which is a key aspect of ontology engineering and biomedical informatics.
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
This paper focuses on predicting gene loss-of-function phenotypes using an ontology-aware classifier, directly supporting rare disease diagnostics and phenotype informatics.
A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
Biodiversity Information Science and Standards
This paper applies machine learning for similarity search on knowledge graphs, using semantic similarity and implicitly ontology embeddings.
The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
This paper analyzes transcriptomic and metabolomic responses in a bioengineering context, fitting bioengineering and genomics.
Aber-OWL: a framework for ontology-based data access in biology
This paper introduces AberOWL, a framework for ontology-based data access, which is a core component of ontology engineering and biomedical informatics infrastructure.
Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
This paper focuses on genomic diversity and antimicrobial resistance using whole-genome sequencing, directly aligning with genomics and biomedical informatics.
What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
This paper discusses sequencing approaches for consanguineous populations, relevant to genomics and rare disease diagnosis.
Contribution of model organism phenotypes to the computational identification of human disease genes
This paper uses model organism phenotypes to identify human disease genes, which is central to rare disease diagnostic support and phenotype informatics, often relying on semantic similarity.
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
Drug-target / drug-indication prediction by combining KG + text. Drug mechanisms with neuro-symbolic methods.
Neuro-symbolic representation learning on biological knowledge graphs
This paper directly addresses neuro-symbolic representation learning on biological knowledge graphs, a core area of neuro-symbolic AI and ontology engineering.
LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
LEP-AD predicts drug-target binding by combining protein language-model embeddings with attention over drugs — a drug-mechanisms application of representation learning.
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
This paper focuses on prioritizing structural variants for rare disease diagnosis using deep learning and integrating genotype and phenotype data.
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
Variant prioritization for rare disease, leveraging neuro-symbolic methods. Dual-topic.
CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
This paper describes a challenge focused on phenotype and variant predictions for neurodevelopmental disorders, directly supporting rare disease diagnostics.
GFVO: the Genomic Feature and Variation Ontology
This paper introduces a new ontology for genomic features and variation, fitting applied ontology and genomics.
Best behaviour? Ontologies and the formal description of animal behaviour
This paper discusses the formal description of animal behavior using ontologies, aligning with applied ontology and phenotype informatics.
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
This paper introduces FALDO, a semantic standard for biological feature annotation, which is a clear example of applied ontology and semantic interoperability.
Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
This paper focuses on whole-genome transcriptomic profiling, which is a genomics method, and its application to physiological responses, linking to bioengineering.
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
This paper describes predicting metabolic pathway involvement, which is a form of protein function prediction, using data mining techniques.
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
This paper is a report from the CAFA challenge, directly assessing and improving protein function prediction methods.
An open source knowledge graph ecosystem for the life sciences
An ecosystem paper about KGs for the life sciences. Engineering infrastructure, not applied ontology.
Predicting candidate genes from phenotypes, functions and anatomical site of expression
This paper focuses on predicting candidate genes from phenotypic and functional data, which is crucial for rare disease diagnosis.
Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
This paper investigates the molecular and cellular mechanisms of PYK2 coacervates, which relates to understanding drug mechanisms and systems biology.
Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
This paper describes the analysis of a specific phenotype in mouse models, aligning with phenotype informatics and biomedical informatics.
Data science and symbolic AI: Synergies, challenges and opportunities
This paper explicitly discusses the intersection of data science and symbolic AI, which is the core of neuro-symbolic AI.
Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
This paper focuses on analyzing mammalian gene function through large-scale phenotypic screens, which is a key aspect of phenotype informatics and biomedical informatics.
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
This paper introduces DeepGO, a system for protein function prediction that uses deep learning and is aware of ontology structure.
DeepPVP: phenotype-based prioritization of causative variants using deep learning
This paper describes DeepPVP, a deep learning approach for prioritizing causative variants based on patient phenotypes, relevant for rare disease diagnostics.
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
This paper describes DES-TOMATO, a knowledge exploration system for tomato species, which involves applied ontology and semantic interoperability.
DermO; an ontology for the description of dermatologic disease
This paper focuses on the development of DermO, an ontology for dermatologic diseases, which falls under applied ontology and phenotype informatics.
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
This paper introduces FoodOn, a harmonized food ontology designed for global food traceability and data integration, indicating both applied ontology and semantic interoperability.
Age-related differences in gene expression and pathway activation following heatstroke
This paper analyzes gene expression and pathway activation in response to heatstroke, which is a biomedical informatics application with bioengineering relevance.
Ranking Adverse Drug Reactions With Crowdsourcing
This paper focuses on ranking adverse drug reactions using crowdsourcing, which is relevant to drug mechanisms and biomedical informatics.
VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
This paper describes VarLand, a pipeline for mapping missense variants at the proteome scale, which is a genomics and biomedical informatics topic.
Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
This paper investigates the genomic landscape of hepatocellular carcinoma in Saudi patients using whole-genome sequencing, falling under genomics and biomedical informatics.
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
Updating the CIDO domain ontology; canonical Applied Ontology.
Notions of similarity for systems biology models
This paper reviews notions of similarity for systems biology models, directly addressing semantic similarity and its application in an ontological context.
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
Drug-target prediction over interaction networks + ontology priors; drug mechanisms with neuro-symbolic methods.
A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
This paper reviews standards and evolution of histopathology nomenclature, which involves applied ontology and efforts towards semantic interoperability.
Similarity-based search of model organism, disease and drug effect phenotypes
This paper focuses on similarity-based search of phenotypes across different domains, directly addressing semantic similarity and its application in rare disease and drug mechanisms.
The role of ontologies in biological and biomedical research: a functional perspective
This paper discusses the general role of ontologies in biological and biomedical research from a functional perspective, making it a core applied ontology and biomedical informatics paper.
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
This paper analyzes the human diseasome using phenotype similarity, which is a key aspect of rare disease diagnostic support and semantic similarity.
Usage of cell nomenclature in biomedical literature
This paper focuses on the usage of cell nomenclature in biomedical literature, which involves text mining and mapping to ontologies for semantic interoperability.
Evaluating the effect of annotation size on measures of semantic similarity
This paper evaluates the impact of annotation size on semantic similarity measures, a core topic in semantic similarity research.
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
This paper introduces DeepGOWeb for protein function prediction using Gene Ontology and Semantic Web technologies.
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
Protein function prediction with zero-shot from ontology axioms; PFP + neuro-symbolic.
A reference quality, fully annotated diploid genome from a Saudi individual
Pure genome-resource paper. Not Applied Ontology.
Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
This paper focuses on the development of phased genome assemblies and pangenome graphs for specific human populations, which is a core genomics topic.
Nail abnormalities identified in an ageing study of 30 inbred mouse strains
This paper describes the identification and characterization of phenotypes (nail abnormalities) in mouse models, aligning with phenotype informatics.
Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
This paper investigates the genomic landscape of retinoblastoma for risk stratification and precision medicine, combining genomics with diagnostic support.
DELE: Deductive EL++ Embeddings for Knowledge Base Completion
DELE learns ontology embeddings for EL++ with explicit use of the deductive closure to construct negatives — a neuro-symbolic ontology-embedding contribution.
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
This paper describes in silico screening for microbial chassis strains, which falls under metagenomics and microbial function, particularly bioprospecting.
An ontology approach to comparative phenomics in plants
This paper applies an ontology-based approach to comparative phenomics in plants, directly aligning with applied ontology and phenotype informatics.
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
This paper introduces OligoPVP for phenotype-driven prioritization of oligogenic disease variants, a key aspect of rare disease diagnostic support and genomics.
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
This paper introduces Onto2Vec for generating vector-based representations (embeddings) of biological entities and their ontology annotations, which is a neuro-symbolic AI method.
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
This paper describes OPA2Vec, which combines formal and informal ontology content to improve similarity-based prediction, using ontology embeddings (neuro-symbolic AI) and semantic similarity.
In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
This paper involves in silico exploration of microbial genomes for natural product biosynthetic gene clusters, fitting into metagenomics and microbial function.
The anatomy of phenotype ontologies: principles, properties and applications
This paper discusses the principles and applications of phenotype ontologies, directly fitting applied ontology and phenotype informatics.
Semantic prioritization of novel causative genomic variants
This paper focuses on semantic prioritization of genomic variants using phenotype information, which is central to rare disease diagnostic support and semantic similarity.
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
This paper describes a computational tool for designing complex molecules, which aligns with bioengineering and drug mechanisms.
Ontology-based validation and identification of regulatory phenotypes
This paper uses ontologies for validating and identifying regulatory phenotypes, directly aligning with applied ontology and phenotype informatics.
DESM: portal for microbial knowledge exploration systems
This paper describes a portal for microbial knowledge exploration, linking to metagenomics and microbial function, and involving knowledge systems.
Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning
Ontology Engineering: 12th International Experiences and Directions Workshop on OWL, OWLED 2015, co-located with ISWC 2015, Bethlehem, PA, USA, October 9-10, 2015, Revised Selected Papers
This paper discusses experiences with AberOWL, an ontology repository with OWL EL reasoning, directly related to ontology engineering and semantic interoperability.
Multi-faceted semantic clustering with text-derived phenotypes
This paper focuses on semantic clustering using text-derived phenotypes, which falls under biomedical informatics and phenotype informatics.
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
This paper investigates the effects of negation and uncertainty on patient profile similarity from clinical text, fitting biomedical informatics and semantic similarity.
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles
Direct semantic-similarity evaluation paper. Move out of Applied Ontology.
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
This paper introduces semantic disease gene embeddings for prioritization, which is a neuro-symbolic AI approach applied to rare disease diagnostic support.
Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
This paper focuses on recognizing biological traits and taxa from images, which aligns with phenotype informatics and uses biomedical informatics methods.
Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
The paper critically assesses methods for variant prioritization in rare disease diagnosis, directly fitting the rare disease diagnostic support topic and involving genomic data.
DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
This paper introduces DeepGOMeta for functional insights into microbial communities using deep learning for protein function prediction, directly aligning with both metagenomics and protein function prediction.
Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
The paper uses literature mining to identify causal relationships between diseases to improve polygenic risk scores, which is a biomedical informatics approach with implications for disease risk.
Causal knowledge graph analysis identifies adverse drug effects
About discovering adverse drug effects via causal KG analysis. Not ontology engineering.
EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
This paper describes the identification of a specific genetic variant linked to a rare disease, which falls under rare disease diagnostic support and involves genomic analysis.
Semantic units: organizing knowledge graphs into semantically meaningful units of representation
Genuinely Applied Ontology: organising KGs into semantically meaningful units.
BioHackathon 2015: Semantics of data for life sciences and reproducible research
This paper discusses the semantics of data for life sciences and reproducible research, emphasizing interoperability, which aligns with ontology engineering and biomedical informatics.
mOWL: Python library for machine learning with biomedical ontologies
mOWL is the library underpinning ontology embedding work; neuro-symbolic, not applied ontology.
LLM Agent Based Protein Function Prediction
LLM-agent-based protein function prediction at PSB 2026. The contribution is the agent.
INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
This paper introduces the Semanticscience Integrated Ontology (SIO) for biomedical research, which is a clear example of applied ontology and aims for knowledge discovery and interoperability.
Statistical tests for associations between two directed acyclic graphs.
Applying the functional abnormality ontology pattern to anatomical functions.
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
Relations as patterns: bridging the gap between OBO and OWL.
Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies
A top-level ontology of functions and its application in the Open Biomedical Ontologies.
Interoperability between phenotype and anatomy ontologies
This paper focuses on achieving interoperability between phenotype and anatomy ontologies, which is a core aspect of applied ontology, ontology engineering, and phenotype informatics.
A common layer of interoperability for biomedical ontologies based on OWL EL
This paper describes a common interoperability layer for biomedical ontologies based on OWL EL, directly fitting ontology engineering and applied ontology.
The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
This paper introduces the RNA Ontology (RNAO) for integrating RNA sequence and structure data, which is a specific application of ontology development in biomedical informatics.
PhenomeNET: a whole-phenome approach to disease gene discovery
This paper introduces PhenomeNET for disease gene discovery using a whole-phenome approach, directly aligning with rare disease diagnostic support and phenotype informatics, and implicitly using semantic similarity.
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
This paper addresses interoperability between biomedical ontologies through relation expansion and automated reasoning, which is central to ontology engineering and applied ontology.
Integrating systems biology models and biomedical ontologies
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
This paper describes the RICORDO approach for semantic interoperability of biomedical data and models, which is a key aspect of ontology engineering and biomedical informatics.
PIDO: The Primary Immunodeficiency Disease Ontology
Primary Immunodeficiency Disease Ontology
This paper introduces the Primary Immunodeficiency Disease Ontology (PIDO), which is an application of ontology development for a specific disease domain, supporting rare disease diagnosis.
Ontology design patterns to disambiguate relations between genes and gene products in GENIA
This paper focuses on ontology design patterns to disambiguate relations in GENIA, which is an applied ontology and an aspect of ontology engineering, with implications for biomedical text mining.
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
This paper focuses on representing and analyzing phenotype knowledge in human diseases and animal models, which aligns with applied ontology, phenotype informatics, and rare disease diagnostic support.
OBML - Ontologies in Biomedicine and Life Sciences
This paper discusses ontologies in biomedicine and life sciences, fitting applied ontology and biomedical informatics.
Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
This paper links PharmGKB to phenotype studies and animal models for drug repurposing, directly addressing drug mechanisms, rare disease support, and applied ontology.
Mouse genetic and phenotypic resources for human genetics
This paper discusses mouse genetic and phenotypic resources for human genetics, which is relevant to rare disease diagnostic support and phenotype informatics.
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
This paper explores Gene Ontology annotations using OWL, aligning with applied ontology, protein function prediction, and ontology engineering.
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
This paper focuses on semantic integration of physiology phenotypes using the Cellular Phenotype Ontology, fitting applied ontology, phenotype informatics, and ontology engineering.
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
This paper describes an infrastructure for ontology-based information systems in biomedicine, which is a core aspect of ontology engineering and biomedical informatics.
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
This paper focuses on identifying aberrant pathways through integrated analysis in pharmacogenomics, directly relating to drug mechanisms and biomedical informatics.
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
This paper quantitatively compares mapping methods between HPO and MPO, which is a form of semantic similarity and phenotype informatics within applied ontology.
Towards improving phenotype representation in OWL
This paper aims to improve phenotype representation in OWL, directly aligning with applied ontology and phenotype informatics.
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
This paper focuses on ontology-based cross-species integration and analysis of yeast phenotypes, fitting applied ontology, phenotype informatics, and ontology engineering.
Evaluation of research in biomedical ontologies
This paper evaluates research in biomedical ontologies, which is a meta-level topic for applied ontology and biomedical informatics.
The Units Ontology: a tool for integrating units of measurement in science
This paper introduces the Units Ontology for integrating units of measurement, which is a clear example of applied ontology and ontology engineering.
Text-mining solutions for biomedical research: enabling integrative biology
This paper discusses text-mining solutions for biomedical research, directly falling under biomedical informatics.
Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
This paper describes the Neurobehavior Ontology for annotating and integrating behavior and behavioral phenotypes, aligning with applied ontology, phenotype informatics, and ontology engineering.
An integrative, translational approach to understanding rare and orphan genetically based diseases
This paper focuses on integrating data for rare disease understanding, aligning with rare disease diagnostic support and semantic interoperability.
Representing physiological processes and their participants with PhysioMaps
The paper describes the development of PhysioMaps for representing physiological processes, which is a clear application of ontology engineering.
Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
This paper focuses on analyzing experimental phenotype data to reveal gene functions, which falls under phenotype informatics and general biomedical informatics.
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
This paper evaluates gene/protein tagging solutions and lexical resources, which is a core task in biomedical natural language processing and informatics.
Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
The paper evaluates lexical entities of biological interest, combining aspects of biomedical NLP and the use of ontologies.
Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
This paper discusses formal knowledge representation in systems biology, which is a direct application of ontology and relevant to understanding biological mechanisms.
Mouse model phenotypes provide information about human drug targets
This paper uses mouse model phenotypes to identify human drug targets, directly linking to drug mechanisms and potential applications in rare diseases.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Thematic series on biomedical ontologies in JBMS: challenges and new directions
This paper discusses challenges and new directions in biomedical ontologies, making it a general topic in applied ontology.
Analyzing gene expression data in mice with the Neuro Behavior Ontology
This paper applies the Neuro Behavior Ontology to analyze gene expression data in mice, combining ontology application with biomedical data analysis.
Enriched biodiversity data as a resource and service
This paper focuses on enriching biodiversity data as a resource, which involves semantic integration and knowledge representation.
Interactively Exploring Graph Coloring Algorithms in a Bilingual Web Platform with Gamification
Proceedings of EdMedia: World Conference on Educational Media and Technology 2017
Educational graph-coloring web platform; not core research of the group — intentionally untagged.
SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
SIDEKICK integrates drug-related semantic resources (effects, indications, contraindications) for downstream learning and reasoning.
From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings
Proceedings of the 17th International Workshop on Neural-Symbolic Learning and Reasoning, La Certosa di Pontignano, Siena, Italy, July 3-5, 2023
Evaluating graph-based ontology embeddings; neuro-symbolic methodology.
Evaluating Different Methods for Semantic Reasoning Over Ontologies
Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, Athens, Greece, November 6-10, 2023
Evaluation of semantic reasoners; ontology-engineering infrastructure.
Updating the CEMO ontology for future epidemiological challenges
14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023
Domain-ontology update for epidemiology; Applied Ontology.
Large-Scale Reasoning over Functions in Biomedical Ontologies
This paper focuses on large-scale reasoning over functions in biomedical ontologies, which is a core aspect of applied ontology and ontology engineering.
To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)
International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)
This paper investigates the impact of MIREOT in EFO, directly addressing ontology engineering practices and applied ontology.
Ontology based mining of pathogen-disease associations from literature
This paper uses ontology-based methods to mine pathogen-disease associations from literature, combining biomedical text mining with applied ontology.
This paper directly evaluates the effect of annotation size on semantic similarity measures, making it a clear fit for the semantic similarity topic.
EL Embeddings: Geometric construction of models for the Description Logic EL++
This paper focuses on the geometric construction of models for the Description Logic EL++, which is a core topic in neuro-symbolic AI for ontology embeddings.
Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
Geometric embeddings for EL++ are the core neuro-symbolic line. Not Applied Ontology.
Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
This paper focuses on knowledge graph embedding for entity alignment, which falls under neuro-symbolic AI methods for integrating symbolic knowledge with learning.
Ontology-Based Concept Recognition by Using Word Embeddings
This paper uses word embeddings for ontology-based concept recognition, combining symbolic knowledge with statistical learning, and is applied in a biomedical context.
Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
Proceedings of International Conference on Biomedical Ontologies (ICBO)
This paper describes the use of AberOWL for fast and scalable reasoning over BioPortal ontologies, directly addressing ontology engineering and semantic interoperability.
AberOWL: an ontology portal with OWL EL reasoning
This paper introduces AberOWL as an ontology portal with OWL EL reasoning, which is a key component of ontology engineering and semantic interoperability infrastructure.
Robust Knowledge Graph Embedding via Denoising
Robust KG embedding under triple noise — a neuro-symbolic representation-learning contribution.
SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016.
This paper focuses on bridging the semantic gap between RDF and OWL using SPARQL, which is central to semantic interoperability and ontology engineering.
Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence
KG completion methodology; neuro-symbolic, not applied ontology.
Neural Multi-hop Logical Query Answering with Concept-Level Answers
This paper describes neural methods for multi-hop logical query answering, integrating neural networks with symbolic reasoning over knowledge graphs, a core neuro-symbolic AI topic.
Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
Lattice-preserving ALC ontology embeddings; clearly neuro-symbolic.
Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
Geometric embeddings for multi-hop reasoning that explicitly model transitive relations — neuro-symbolic graph reasoning.
Applying ontology design patterns to the implementation of relations in GENIA
Proceedings of the Fourth Symposium on Semantic Mining in Biomedicine (SMBM 2010)
The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes
Proceedings of the 2nd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
Relational patterns in OWL and their application to OBO
Proceedings of the 13th Annual Bio-Ontologies Meeting
The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions
Proceedings of the The 3rd International Symposium on Languages in Biology and Medicine
Developing Consistent and Modular Software Models with Ontologies
Contributions to the formal ontology of functions and dispositions: an application of non-monotonic reasoning
Proceedings of the 12th Annual Bio-Ontologies Meeting
Towards Ontological Interpretations for Improved Text Mining
Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland
From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology
Proceedings of the 11th Annual Bio-Ontologies Meeting
The design of a wiki-based curation system for the Ontology of Functions
Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting
BOWiki - a collaborative annotation and ontology curation framework
Proceedings of Workshop on Social and Collaborative Construction of Structured Knowledge
Higgs bosons, mars missions, and unicorn delusions: How to deal with terms of dubious reference in scientific ontologies
Proceedings of the Second International Conference on Biomedical Ontology
This paper discusses how to deal with terms of dubious reference in scientific ontologies, which is a foundational problem in applied ontology.
Investigation of the fundamental strategy for interoperability of description of biological measurements
This paper investigates strategies for interoperability of biological measurements, which is a core aspect of applied ontology and semantic interoperability.
Exploring Gene Ontology Annotations with OWL
Proceedings of the 13th Bio-Ontology Meeting
This paper explores Gene Ontology annotations using OWL, which is an application of ontology for understanding protein function.
Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
This paper focuses on ontology-based cross-species integration and analysis of phenotypes, which is a key area in applied ontology and phenotype informatics.
This paper focuses on comparing methods for mapping between phenotype ontologies, which falls under phenotype informatics and semantic similarity.
Towards Improving Phenotype Representation in OWL
The paper discusses improving phenotype representation in OWL, which is a core aspect of applied ontology and phenotype informatics.
Formal Ontology in Information Systems, Proceedings of the Sixth International Conference, FOIS 2010
Argumentation to Represent and Reason over Biological Systems
Proceedings of the 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012)
This paper focuses on using argumentation for representing and reasoning over biological systems, which is a method in applied ontology.
A translational medicine approach to orphan diseases
Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012)
The paper describes a translational medicine approach to orphan diseases, aligning with rare disease diagnostic support and biomedical informatics.
Integration of knowledge for personalized medicine: a pharmacogenomics case-study
This paper discusses integrating knowledge for personalized medicine in pharmacogenomics, which relates to drug mechanisms and semantic interoperability.
JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020)
As proceedings of ontology workshops, this entry broadly covers applied ontology and ontology engineering.
Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
This paper describes the development of organoids from Saudi patients for colorectal cancer, which is a bioengineering and biomedical informatics application.
Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
This paper focuses on peptide-based matrices for organoid development and therapeutic applications, fitting bioengineering and drug mechanisms.
Data Mining Techniques for the Life Sciences
This paper discusses data mining with ontologies in life sciences, which is a key aspect of biomedical informatics and applied ontology.
Computational prediction of protein functional annotations
The paper's title explicitly states 'Computational prediction of protein functional annotations', directly aligning with protein function prediction.
The informatics of developmental phenotypes
Kaufman’s Atlas of Mouse Development Supplement
This paper focuses on the informatics of developmental phenotypes, which is a core area of phenotype informatics and biomedical informatics.
Annotating genomes with DeepGO protein function prediction tools
This paper describes annotating genomes using DeepGO tools for protein function prediction, directly linking to protein function prediction and genomics.
Kaufmann's Atlas of Mouse Development Supplement
Theory and Applications of Ontology: Computer Applications
Neuro-symbolic methods in Bioinformatics
We work on methods that integrate symbolic knowledge with statistical learning. This includes mapping entities in formal ontologies into vector spaces while preserving their semantic relations. We develop embedding frameworks for Description Logics (e.g., EL++ and ALC) that provide mathematical guarantees for logical soundness and approximate the interpretation of formalized theories.
Ontology engineering and semantic interoperability
We develop architectures for processing massive, heterogeneous data using Semantic Web standards. This work includes the AberOWL infrastructure for ontology-based data access and methods for establishing interoperability across distributed databases through linked knowledge graphs.
We use ontologies to standardize and analyze complex phenotypes across domains. Earlier work focused on foundational ontologies, including the General Formal Ontology (GFO) and its biological extension GFO-Bio, as well as the development of a formal ontology of functions to curate functional knowledge in the life sciences.
Large-scale ontologies like the Gene Ontology (GO) provide essential background knowledge for understanding protein activity. We develop the DeepGO family of systems, which utilize formalized axioms to constrain deep learning models for protein function prediction. These systems are used to derive functional insights from sequence and interaction data.
The diagnosis of rare diseases requires the integration of patient-specific data with large-scale background knowledge, such as the Human Phenotype Ontology (HPO). We develop systems like PhenomeNET and PVP that use automated reasoning and machine learning to prioritize disease-causing genomic variants based on their phenotypic consequences.
We apply ontologies and knowledge graphs to model drug-target interactions, drug indications, and adverse drug reactions. This work links molecular data to systems biology through causal knowledge graphs, enabling the identification of mechanistic relationships and potential drug repurposing targets.
We contribute to the development of genomic resources and the analysis of population-specific genomic data. This includes reference genome assemblies, pangenome graphs for the Saudi and wider Middle Eastern population, variant-calling and structural-variant pipelines, and the analysis of antimicrobial resistance from whole-genome sequencing.
We work on biomedical informatics infrastructure that turns research-grade data into usable inputs for clinicians and researchers. This includes biomedical knowledge-base construction (PathoPhenoDB, PhenomeNET, PhenomeBrowser), text-mining of biomedical literature, integration of clinical phenotype encodings, and analytics over electronic health records.
We develop and benchmark semantic similarity measures over biomedical ontologies, including measures that operate on the OWL axiomatic structure of an ontology rather than only on its lexical or taxonomic skeleton. These measures underpin phenotype-based disease gene prioritization, ontology-aware protein function transfer, and biodiversity knowledge graph search.
Metagenomics and microbial community function
We develop methods that lift single-protein function prediction up to the level of microbial communities, combining ontology-aware deep learning with multi-scale systems approaches. Applications include desert-soil and mangrove-microbiome design, bioprospecting from Saudi-Arabian extremophile habitats, and metagenomics-driven functional characterisation of patient and environmental microbiomes.
We develop the informatics infrastructure for phenotype data across species and clinical settings: phenotype ontologies (HPO, MP, ZP, FLOPO, plant traits), cross-species phenotype crosswalks, tools that capture and standardise phenotype descriptions, and computational pipelines that link phenotype data to underlying genes, variants, and diseases.
We contribute computational and omics analysis to collaborative bioengineering projects. Examples include analysing transcriptomic and metabolomic responses of cells cultured in biomimetic peptide scaffolds, patient-derived disease-model analysis for precision medicine, and the integration of multi-omics data with engineered biological systems.
Northeastern University, Shenyang, China
Computer science and society / Information
King Abdullah University of Science and Technology