Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
A public Saudi pangenome as reference for genomics in the Middle East
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
Computational methods for functional metagenomics: from protein functions to multi-scale interactions
IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
Development of Algorithms for Biotechnology and Biomedical Applications
CompleX: Variant Prioritization in Complex Disease
Whole genome sequencing of rare disease patients
Sequencing and computational analysis of MRSA samples
Improvement of genetic variant prioritization technology
Bio2Vec: Smart analytics infrastructure for the life sciences
The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
Data integration and ontologies for microbial cell factories
KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
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
Ontology-based prediction of cancer driver genes
Improving the classification of cardinality phenotypes using collections
Combining lexical and context features for automatic ontology extension
DDIEM: drug database for inborn errors of metabolism
DeepGOPlus: improved protein function prediction from sequence
Phenotype-driven discovery of digenic variants in personal genome sequences
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
Klarigi: Characteristic explanations for semantic biomedical data
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
BMC Medical Informatics and Decision Making
Handbook on Neurosymbolic AI and Knowledge Graphs
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
Ontology Embedding: A Survey of Methods, Applications and Resources
IEEE Transactions on Knowledge and Data Engineering
Ontology based mining of pathogen--disease associations from literature
PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
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
Integrating phenotype ontologies with PhenomeNET
Proceedings of Ontology Matching Workshop 2016
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
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.
Improved characterisation of clinical text through ontology-based vocabulary expansion
Semantic similarity and machine learning with ontologies
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
Predicting protein functions using positive-unlabeled ranking with ontology-based priors
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
Biodiversity Information Science and Standards
The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
Aber-OWL: a framework for ontology-based data access in biology
Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
Contribution of model organism phenotypes to the computational identification of human disease genes
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
Neuro-symbolic representation learning on biological knowledge graphs
LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
GFVO: the Genomic Feature and Variation Ontology
Best behaviour? Ontologies and the formal description of animal behaviour
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
An open source knowledge graph ecosystem for the life sciences
Predicting candidate genes from phenotypes, functions and anatomical site of expression
Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
Data science and symbolic AI: Synergies, challenges and opportunities
Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
DeepPVP: phenotype-based prioritization of causative variants using deep learning
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
DermO; an ontology for the description of dermatologic disease
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
Age-related differences in gene expression and pathway activation following heatstroke
Ranking Adverse Drug Reactions With Crowdsourcing
VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
Notions of similarity for systems biology models
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
Similarity-based search of model organism, disease and drug effect phenotypes
The role of ontologies in biological and biomedical research: a functional perspective
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
Usage of cell nomenclature in biomedical literature
Evaluating the effect of annotation size on measures of semantic similarity
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
A reference quality, fully annotated diploid genome from a Saudi individual
Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
Nail abnormalities identified in an ageing study of 30 inbred mouse strains
Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
DELE: Deductive EL++ Embeddings for Knowledge Base Completion
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
An ontology approach to comparative phenomics in plants
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
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
The anatomy of phenotype ontologies: principles, properties and applications
Semantic prioritization of novel causative genomic variants
Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
Ontology-based validation and identification of regulatory phenotypes
DESM: portal for microbial knowledge exploration 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
Multi-faceted semantic clustering with text-derived phenotypes
Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
Evaluating semantic similarity methods for comparison of text-derived phenotype profiles
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
Causal knowledge graph analysis identifies adverse drug effects
EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
Semantic units: organizing knowledge graphs into semantically meaningful units of representation
BioHackathon 2015: Semantics of data for life sciences and reproducible research
mOWL: Python library for machine learning with biomedical ontologies
LLM Agent Based Protein Function Prediction
INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
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
A common layer of interoperability for biomedical ontologies based on OWL EL
The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
PhenomeNET: a whole-phenome approach to disease gene discovery
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
Integrating systems biology models and biomedical ontologies
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
PIDO: The Primary Immunodeficiency Disease Ontology
Ontology design patterns to disambiguate relations between genes and gene products in GENIA
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
OBML - Ontologies in Biomedicine and Life Sciences
Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
Mouse genetic and phenotypic resources for human genetics
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
Towards improving phenotype representation in OWL
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
Evaluation of research in biomedical ontologies
The Units Ontology: a tool for integrating units of measurement in science
Text-mining solutions for biomedical research: enabling integrative biology
Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
An integrative, translational approach to understanding rare and orphan genetically based diseases
Representing physiological processes and their participants with PhysioMaps
Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
Mouse model phenotypes provide information about human drug targets
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
Analyzing gene expression data in mice with the Neuro Behavior Ontology
Enriched biodiversity data as a resource and service
Interactively Exploring Graph Coloring Algorithms in a Bilingual Web Platform with Gamification
Proceedings of EdMedia: World Conference on Educational Media and Technology 2017
SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
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 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
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
Large-Scale Reasoning over Functions in Biomedical Ontologies
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)
Ontology based mining of pathogen-disease associations from literature
EL Embeddings: Geometric construction of models for the Description Logic EL++
Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
Ontology-Based Concept Recognition by Using Word Embeddings
Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
Proceedings of International Conference on Biomedical Ontologies (ICBO)
AberOWL: an ontology portal with OWL EL reasoning
Robust Knowledge Graph Embedding via Denoising
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.
Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence
Neural Multi-hop Logical Query Answering with Concept-Level Answers
Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
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
Investigation of the fundamental strategy for interoperability of description of biological measurements
Exploring Gene Ontology Annotations with OWL
Proceedings of the 13th Bio-Ontology Meeting
Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
Towards Improving Phenotype Representation in OWL
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)
A translational medicine approach to orphan diseases
Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012)
Integration of knowledge for personalized medicine: a pharmacogenomics case-study
JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020)
Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
Data Mining Techniques for the Life Sciences
Computational prediction of protein functional annotations
The informatics of developmental phenotypes
Kaufman’s Atlas of Mouse Development Supplement
Annotating genomes with DeepGO protein function prediction tools
Kaufmann's Atlas of Mouse Development Supplement
Theory and Applications of Ontology: Computer Applications
Neuro-symbolic methods in Bioinformatics
Ontology engineering and semantic interoperability
Metagenomics and microbial community function
Computer science and society / Information
King Abdullah University of Science and Technology
King Abdulaziz City for Science and Technology