Project (21)
- A public Saudi pangenome as reference for genomics in the Middle East
- Bio2Vec: Smart analytics infrastructure for the life sciences
- CompleX: Variant Prioritization in Complex Disease
- Computational methods for functional metagenomics: from protein functions to multi-scale interactions
- Data integration and ontologies for microbial cell factories
- Development of Algorithms for Biotechnology and Biomedical Applications
- Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
- Enabling desert revegetation by AI-tailored soil microbiome fortification
- Enabling mangrove restoration by AI-tailored microbiome fortification
- Evolutionary potential of corals to adapt to climate warming
- IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
- Improvement of genetic variant prioritization technology
- Improving health of Saudi population
- KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
- KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
- Metagenomics-based surface prospecting
- Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
- Sequencing and computational analysis of MRSA samples
- The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
- Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
- Whole genome sequencing of rare disease patients
Grant (21)
- A public Saudi pangenome as reference for genomics in the Middle East
- Bio2Vec: Smart analytics infrastructure for the life sciences
- CompleX: Variant Prioritization in Complex Disease
- Computational methods for functional metagenomics: from protein functions to multi-scale interactions
- Data integration and ontologies for microbial cell factories
- Development of Algorithms for Biotechnology and Biomedical Applications
- Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
- Enabling desert revegetation by AI-tailored soil microbiome fortification
- Enabling mangrove restoration by AI-tailored microbiome fortification
- Evolutionary potential of corals to adapt to climate warming
- IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
- Improvement of genetic variant prioritization technology
- Improving health of Saudi population
- KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
- KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
- Metagenomics-based surface prospecting
- Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
- Sequencing and computational analysis of MRSA samples
- The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
- Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
- Whole genome sequencing of rare disease patients
Person (47)
- Abeer Almutairi
- Aleksei Matveev
- Amal Alhelal
- Arne Nägel
- Asaad Mohammedsaleh
- Ashraf Kibraya
- Azza Althagafi
- Charlotte Hauser
- Daulet Toibazar
- Fernando Zhapa-Camacho
- Gabriel Wittum
- Georgios V Gkoutos
- Hatoon Al Ali
- Heribert Hirt
- Imane Boudellioua
- Jens Lehmann
- Kexin Niu
- Mahdi Bu Ali
- Malak Althagafi
- Manuel Aranda
- Maria G Gomez Castillo
- Maxat Kulmanov
- Md Nurul Muttakin
- Melissa Rios Zertuche
- Michael Berumen
- Michel Dumontier
- Miguel Angel Rodriguez Garcia
- Mohammad Ashhad
- Mohammed Al Fageeh
- Mona Alshahrani
- Paul N Schofield
- Robert Hoehndorf
- Rund Tawfiq
- Safana Bakheet
- Sakhaa Alsaedi
- Sara Althubaiti
- Sarah Alghamdi
- Sawsan Al Boeisa
- Shahad Qatan
- Sumyyah Toonsi
- Takashi Gojobori
- Tengwei Song
- Vladimir Bajic
- Xi Peng
- Xin Gao
- Yang Liu
- Zhenwei Tang
Software (43)
- AberOWL
- DELE
- DL2Vec
- DeepGO
- DeepGO2
- DeepGOMeta
- DeepGOPlus
- DeepGOZero
- DeepMOCCA
- DeepPheno
- DeepSVP
- DeepViral
- EL Embeddings
- EL2Box
- EmbedPVP
- GO-Agent
- GenomeLinter
- Genomic Context
- INDIGENA
- Interpretable Learning
- Machine Learning with Ontologies
- Multi-Drug Embedding
- NanoDesigner
- OPA2Vec
- Onto2Graph
- Onto2Vec
- OntoFunc
- Ontology Tutorial
- PU-GO
- PathoPhenoDB
- PhenoGoCon
- PhenomeNET-VP
- PhenomeNet
- STARVar
- SmuDGE
- UNMIREOT
- Units of Measurement Ontology (UO)
- Walking RDF and OWL
- catE
- mOWL
- mOWL Tutorial
- predCAN
- vec2SPARQL
Research topic (12)
- Applied Ontology
- Bioengineering
- Biomedical informatics
- Drug mechanisms and systems biology
- Genomics
- Metagenomics and microbial community function
- Neuro-symbolic methods in Bioinformatics
- Ontology engineering and semantic interoperability
- Phenotype informatics
- Protein function prediction
- Rare disease diagnostic support
- Semantic similarity
Course (28)
- Algorithms in Bioinformatics
- Algorithms in Bioinformatics
- Algorithms in Bioinformatics
- Application of AI in Bioinformatics
- Applied Ontology
- Applied Ontology
- Computer Science Graduate Seminar
- Computer science and society / Information
- Data Analytics
- Data Analytics
- Foundations of Bioengineering
- Foundations of Bioengineering
- Foundations of Bioengineering
- Introduction to Artificial Intelligence
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Knowledge Representation and Reasoning
- Machine learning
- Neurosymbolic AI
- Neurosymbolic AI
- Object-Oriented Programming
- Object-Oriented Programming
- Ontology in medical information systems
- Professional and Personal Development
Publication (203)
- A Formal Ontology of Sequences
- A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
- A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
- A common layer of interoperability for biomedical ontologies based on OWL EL
- A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
- A proposal for a gene functions wiki
- A reference quality, fully annotated diploid genome from a Saudi individual
- A top-level ontology of functions and its application in the Open Biomedical Ontologies.
- A translational medicine approach to orphan diseases
- Aber-OWL: a framework for ontology-based data access in biology
- AberOWL: an ontology portal with OWL EL reasoning
- Age-related differences in gene expression and pathway activation following heatstroke
- An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
- An integrative, translational approach to understanding rare and orphan genetically based diseases
- An ontology approach to comparative phenomics in plants
- An open source knowledge graph ecosystem for the life sciences
- Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
- Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
- Analyzing gene expression data in mice with the Neuro Behavior Ontology
- Annotating genomes with DeepGO protein function prediction tools
- Applying ontology design patterns to the implementation of relations in GENIA
- Applying the functional abnormality ontology pattern to anatomical functions.
- Argumentation to Represent and Reason over Biological Systems
- BOWiki - a collaborative annotation and ontology curation framework
- BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology
- BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
- Best behaviour? Ontologies and the formal description of animal behaviour
- BioHackathon 2015: Semantics of data for life sciences and reproducible research
- BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
- BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
- CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
- Causal knowledge graph analysis identifies adverse drug effects
- Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
- Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
- Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
- Combining lexical and context features for automatic ontology extension
- Computational prediction of protein functional annotations
- Contribution of model organism phenotypes to the computational identification of human disease genes
- Contributions to the formal ontology of functions and dispositions: an application of non-monotonic reasoning
- Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
- DDIEM: drug database for inborn errors of metabolism
- DELE: Deductive EL++ Embeddings for Knowledge Base Completion
- DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
- DESM: portal for microbial knowledge exploration systems
- DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
- Data science and symbolic AI: Synergies, challenges and opportunities
- Datamining with Ontologies
- DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
- DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
- DeepGOPlus: improved protein function prediction from sequence
- DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
- DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
- DeepPVP: phenotype-based prioritization of causative variants using deep learning
- DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
- DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
- DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
- DermO; an ontology for the description of dermatologic disease
- Developing Consistent and Modular Software Models with Ontologies
- EL Embeddings: Geometric construction of models for the Description Logic EL++
- EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
- Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
- Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
- Enriched biodiversity data as a resource and service
- Evaluating Different Methods for Semantic Reasoning Over Ontologies
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
- Evaluating semantic similarity methods for comparison of text-derived phenotype profiles
- Evaluating the effect of annotation size on measures of semantic similarity
- Evaluating the effect of annotation size on measures of semantic similarity
- Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
- Evaluation of research in biomedical ontologies
- Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning
- Exploring Gene Ontology Annotations with OWL
- Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
- FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
- FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
- Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
- From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings
- From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
- Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
- GFO-Bio: A biomedical core ontology
- GFVO: the Genomic Feature and Variation Ontology
- Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
- Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
- Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
- Higgs bosons, mars missions, and unicorn delusions: How to deal with terms of dubious reference in scientific ontologies
- Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
- INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
- Improved characterisation of clinical text through ontology-based vocabulary expansion
- Improving the classification of cardinality phenotypes using collections
- In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
- In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
- Integrating phenotype ontologies with PhenomeNET
- Integrating systems biology models and biomedical ontologies
- Integration of knowledge for personalized medicine: a pharmacogenomics case-study
- Interactively Exploring Graph Coloring Algorithms in a Bilingual Web Platform with Gamification
- Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
- Interoperability between phenotype and anatomy ontologies
- Investigation of the fundamental strategy for interoperability of description of biological measurements
- JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020)
- Kaufmann's Atlas of Mouse Development Supplement
- Klarigi: Characteristic explanations for semantic biomedical data
- LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
- LLM Agent Based Protein Function Prediction
- Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
- Large-Scale Reasoning over Functions in Biomedical Ontologies
- Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
- Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
- Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
- Mouse genetic and phenotypic resources for human genetics
- Mouse model phenotypes provide information about human drug targets
- Multi-faceted semantic clustering with text-derived phenotypes
- Nail abnormalities identified in an ageing study of 30 inbred mouse strains
- Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
- Neural Multi-hop Logical Query Answering with Concept-Level Answers
- Neuro-Symbolic AI in Life Sciences
- Neuro-symbolic representation learning on biological knowledge graphs
- New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
- Notions of similarity for systems biology models
- OBML - Ontologies in Biomedicine and Life Sciences
- OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
- OWLDEF: Integrating OBO and OWL
- OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
- Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
- Ontologies in Biology
- Ontology Embedding: A Survey of Methods, Applications and Resources
- Ontology based mining of pathogen--disease associations from literature
- Ontology based mining of pathogen-disease associations from literature
- Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
- Ontology design patterns to disambiguate relations between genes and gene products in GENIA
- Ontology-Based Concept Recognition by Using Word Embeddings
- Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
- Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
- Ontology-based prediction of cancer driver genes
- Ontology-based validation and identification of regulatory phenotypes
- PIDO: The Primary Immunodeficiency Disease Ontology
- PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
- Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
- PhenomeNET: a whole-phenome approach to disease gene discovery
- Phenotype-driven discovery of digenic variants in personal genome sequences
- Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
- Predicting candidate genes from phenotypes, functions and anatomical site of expression
- Predicting protein functions using positive-unlabeled ranking with ontology-based priors
- Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
- Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
- Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
- Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
- Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
- Ranking Adverse Drug Reactions With Crowdsourcing
- Realism for scientific ontologies
- Relational patterns in OWL and their application to OBO
- 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
- Representing physiological processes and their participants with PhysioMaps
- Robust Knowledge Graph Embedding via Denoising
- SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
- SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL
- Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
- Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
- Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
- Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
- Semantic prioritization of novel causative genomic variants
- Semantic similarity and machine learning with ontologies
- Semantic units: organizing knowledge graphs into semantically meaningful units of representation
- Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
- Similarity-based search of model organism, disease and drug effect phenotypes
- Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
- Statistical tests for associations between two directed acyclic graphs.
- Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
- Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
- Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
- Text-mining solutions for biomedical research: enabling integrative biology
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
- The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
- The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes
- The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
- The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
- The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
- The Units Ontology: a tool for integrating units of measurement in science
- The anatomy of phenotype ontologies: principles, properties and applications
- The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
- The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions
- The design of a wiki-based curation system for the Ontology of Functions
- The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
- The informatics of developmental phenotypes
- The ontology of biological sequences.
- The role of ontologies in biological and biomedical research: a functional perspective
- Thematic series on biomedical ontologies in JBMS: challenges and new directions
- To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)
- Towards Improving Phenotype Representation in OWL
- Towards Ontological Interpretations for Improved Text Mining
- Towards improving phenotype representation in OWL
- Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
- Updating the CEMO ontology for future epidemiological challenges
- Usage of cell nomenclature in biomedical literature
- Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
- Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
- VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
- Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
- What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
- Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
- mOWL: Python library for machine learning with biomedical ontologies