Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
type: Project
start year: 2025
end year: 2026
abstract: 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.
funded by: Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
has member: Robert Hoehndorf
tag: machine learning
tag: knowledge graphs
tag: cancer
tag: complex disease
tag: phenotype reasoning
tag: Saudi-specific
tags by group:
  theme: machine learning
  theme: knowledge graphs
  application: cancer
  application: complex disease
  method: phenotype reasoning
  population: Saudi-specific
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Robert Hoehndorf
role on project: PI
role on project: CoI
type: Person
given name: Robert
family name: Hoehndorf
position: Faculty
current affiliation: KAUST (Professor of Computer Science)
orcid: 0000-0001-8149-5890
on project: Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
on project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
on project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
on project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
on project: A public Saudi pangenome as reference for genomics in the Middle East
on project: Enabling desert revegetation by AI-tailored soil microbiome fortification
on project: Enabling mangrove restoration by AI-tailored microbiome fortification
on project: Metagenomics-based surface prospecting
on project: Evolutionary potential of corals to adapt to climate warming
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
on project: Development of Algorithms for Biotechnology and Biomedical Applications
on project: CompleX: Variant Prioritization in Complex Disease
on project: Improving health of Saudi population
on project: Whole genome sequencing of rare disease patients
on project: Sequencing and computational analysis of MRSA samples
on project: Improvement of genetic variant prioritization technology
on project: Bio2Vec: Smart analytics infrastructure for the life sciences
on project: The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
on project: Data integration and ontologies for microbial cell factories
on project: KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics
topic: Phenotype informatics
topic: Genomics
topic: Drug mechanisms and systems biology
topic: Semantic similarity
topic: Protein function prediction
topic: Metagenomics and microbial community function
topic: Bioengineering

KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
type: Project
start year: 2024
abstract: 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.
funded by: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
has member: Robert Hoehndorf
has member: Mahdi Bu Ali
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Neuro-Symbolic AI in Life Sciences
tag: generative AI
tag: knowledge graphs
tag: neuro-symbolic AI
tag: drug discovery
tag: rare disease
tag: ontology embeddings
tags by group:
  theme: generative AI
  theme: knowledge graphs
  theme: neuro-symbolic AI
  application: drug discovery
  application: rare disease
  method: ontology embeddings
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
end year: 2025

Mahdi Bu Ali
role on project: MSc (alumnus)
type: Person
given name: Mahdi
family name: Bu Ali
position: MSc (alumnus)
thesis title: Automated Theorem Proving with Large Language Models in Lean: An Exploration of Specialized In-Context Learning and General-Purpose Hierarchical Architectures
thesis file: mahdi-thesis/Thesis.pdf
thesis defense date: 2025-05-12
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/mahdi-bu-ali
borg profile nid: 8345
start year: 2024
end year: 2025
on project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
on project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
topic: Semantic similarity
topic: Drug mechanisms and systems biology
topic: Rare disease diagnostic support

Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
type: Project
start year: 2023
end year: 2026
abstract: Faithful, complete, and explainable machine-learning methods on biomedical ontologies. Grant URF/1/5041-01-01 activated Apr 2023.
funded by: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
has member: Robert Hoehndorf
has member: Paul N Schofield
has member: Fernando Zhapa-Camacho
has member: Mahdi Bu Ali
has member: Tengwei Song
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Neuro-Symbolic AI in Life Sciences
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
tag: neuro-symbolic AI
tag: ontologies
tag: knowledge graphs
tag: knowledge representation and reasoning
tag: ontology embeddings
tag: semantic similarity
tags by group:
  theme: neuro-symbolic AI
  theme: ontologies
  theme: knowledge graphs
  theme: knowledge representation and reasoning
  method: ontology embeddings
  method: semantic similarity
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Semantic similarity
start year: 2022
start year: 2024
end year: 2025
start year: 2025
start year: 2026

Paul N Schofield
role on project: CoI
type: Person
position: External collaborator
current affiliation: University of Cambridge
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity
topic: Ontology engineering and semantic interoperability

Fernando Zhapa-Camacho
role on project: PhD (alumnus)
type: Person
given name: Fernando
family name: Zhapa-Camacho
position: PhD (alumnus)
current affiliation: KAUST (Postdoctoral Fellow)
thesis title: Neuro-symbolic methods for embedding ontologies, and applications in life sciences
thesis file: fernando-phd-thesis/Thesis.pdf
thesis defense date: 2026-04-26
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2022
end year: 2026
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
on project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
position: MSc (alumnus)
thesis title: Embedding Ontologies using Category Theory Semantics
thesis file: fernando-thesis/Thesis.pdf
start year: 2021
end year: 2022
position: Postdoc
current affiliation: KAUST
from: KAUST (PhD)
start year: 2026
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Ontology engineering and semantic interoperability
topic: Semantic similarity

Tengwei Song
role on project: Postdoc
type: Person
given name: Tengwei
family name: Song
position: Postdoc
current affiliation: KAUST
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2025
on project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Semantic similarity

Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
type: Project
start year: 2023
end year: 2026
abstract: Disease modelling using biomimetic peptide scaffolds and patient-derived leukemic cells for precision medicine applications.
funded by: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
has member: Robert Hoehndorf
has member: Charlotte Hauser
has member: Yang Liu
has member: Sawsan Al Boeisa
has member: Aleksei Matveev
tag: machine learning
tag: leukemia
tag: cancer
tag: phenotype reasoning
tags by group:
  theme: machine learning
  application: leukemia
  application: cancer
  method: phenotype reasoning
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
start year: 2022
start year: 2024
end year: 2025
start year: 2026

Charlotte Hauser
role on project: PI
type: Person
position: External collaborator
current affiliation: KAUST (Biological & Environmental Sciences)
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Yang Liu
role on project: PhD (alumnus)
role on project: MSc (alumnus)
type: Person
given name: Yang
family name: Liu
position: PhD (alumnus)
thesis title: Reference Bias and Variant Interpretation in Human Disease Genomics
thesis file: yang-thesis/Thesis.pdf
thesis defense date: 2026-04-27
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2022
end year: 2026
on project: A public Saudi pangenome as reference for genomics in the Middle East
on project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
position: MSc (alumnus)
thesis title: Rare variant collapsing analysis on UK Biobank
start year: 2021
end year: 2022
on project: Improving health of Saudi population
topic: Genomics
topic: Rare disease diagnostic support
topic: Neuro-symbolic methods in Bioinformatics
topic: Bioengineering
topic: Biomedical informatics
topic: Protein function prediction
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Sawsan Al Boeisa
role on project: MSc (alumnus)
type: Person
given name: Sawsan
family name: Al Boeisa
position: MSc (alumnus)
thesis title: Differential Effects of p38 MAPK Inhibition on Chemoresistance in Patients with Colorectal Cancer
thesis defense date: 2025-11-17
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/sawsan-al-boeisa
borg profile nid: 8344
start year: 2024
end year: 2025
on project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Aleksei Matveev
role on project: Visiting student
type: Person
given name: Aleksei
family name: Matveev
position: Visiting student
program: MSc Molecular Biology (in progress, expected 2026)
institution at BORG: KAUST (visiting)
advisor: borg-id:person/robert-hoehndorf
from: Kazan Federal University, Russia
borg profile URL: /profiles/aleksei-matveev
borg profile nid: 8346
start year: 2026
end year: 2026
start date: 2026-04-20
end date: 2026-07-15
on project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

A public Saudi pangenome as reference for genomics in the Middle East
type: Project
start year: 2024
end year: 2026
abstract: Builds an open Saudi pangenome reference to support genomics applications in the Middle East, including rare-disease variant interpretation.
funded by: A public Saudi pangenome as reference for genomics in the Middle East
has member: Robert Hoehndorf
has member: Malak Althagafi
has member: Yang Liu
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
tag: machine learning
tag: rare disease
tag: pangenome
tag: variant prioritization
tag: Saudi-specific
tags by group:
  theme: machine learning
  application: rare disease
  method: pangenome
  method: variant prioritization
  population: Saudi-specific
topic: Genomics
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
start year: 2022

Malak Althagafi
role on project: CoI
type: Person
position: External collaborator
current affiliation: Emory University
topic: Genomics
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Enabling desert revegetation by AI-tailored soil microbiome fortification
type: Project
start year: 2023
end year: 2025
abstract: AI-driven design of soil microbiomes for desert plant restoration; functional metagenomics analysis of arid-zone soil microbiomes.
funded by: Enabling desert revegetation by AI-tailored soil microbiome fortification
has member: Heribert Hirt
has member: Robert Hoehndorf
has member: Gabriel Wittum
has member: Arne Nägel
has member: Rund Tawfiq
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
tag: machine learning
tag: plant-microbiome
tag: microbial communities
tag: metagenomics
tag: protein function prediction
tags by group:
  theme: machine learning
  application: plant-microbiome
  application: microbial communities
  method: metagenomics
  method: protein function prediction
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
start year: 2021

Heribert Hirt
role on project: PI
type: Person
position: External collaborator
current affiliation: KAUST (Center for Desert Agriculture)
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
topic: Genomics

Gabriel Wittum
role on project: CoI
type: Person
position: External collaborator
current affiliation: Goethe University Frankfurt / KAUST
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Arne Nägel
role on project: CoI
type: Person
position: External collaborator
current affiliation: Goethe University Frankfurt
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Rund Tawfiq
role on project: PhD (alumnus)
type: Person
given name: Rund
family name: Tawfiq
position: PhD (alumnus)
current affiliation: Sano Centre Krakow (Postdoctoral researcher)
thesis title: Computational Methods for Functional Characterization of Microbial Communities
thesis file: rund-thesis/Thesis.pdf
thesis defense date: 2025-11-17
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2025
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
on project: Enabling desert revegetation by AI-tailored soil microbiome fortification
topic: Protein function prediction
topic: Genomics
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology

Enabling mangrove restoration by AI-tailored microbiome fortification
type: Project
start year: 2023
end year: 2023
abstract: Microbiome-based intervention for mangrove ecosystem restoration in coastal Saudi Arabia.
funded by: Enabling mangrove restoration by AI-tailored microbiome fortification
has member: Heribert Hirt
has member: Robert Hoehndorf
tag: machine learning
tag: plant-microbiome
tag: microbial communities
tag: marine biology
tag: metagenomics
tags by group:
  theme: machine learning
  application: plant-microbiome
  application: microbial communities
  application: marine biology
  method: metagenomics
topic: Genomics
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics

Metagenomics-based surface prospecting
type: Project
start year: 2022
end year: 2024
abstract: Metagenomics analysis of surface samples for bioprospecting in support of oil and gas upstream applications.
funded by: Metagenomics-based surface prospecting
has member: Robert Hoehndorf
has member: Takashi Gojobori
tag: microbial communities
tag: metagenomics
tags by group:
  application: microbial communities
  method: metagenomics
topic: Metagenomics and microbial community function

Takashi Gojobori
role on project: CoI
role on project: PI
type: Person
position: External collaborator
current affiliation: KAUST (formerly CBRC, now dissolved)
topic: Metagenomics and microbial community function
topic: Genomics
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Evolutionary potential of corals to adapt to climate warming
type: Project
start year: 2022
end year: 2025
abstract: Genomics and computational analysis of coral adaptation to ocean warming in the Red Sea.
funded by: Evolutionary potential of corals to adapt to climate warming
has member: Manuel Aranda
has member: Robert Hoehndorf
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Neuro-Symbolic AI in Life Sciences
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
tag: marine biology
tag: protein function prediction
tag: cross-species
tags by group:
  application: marine biology
  method: protein function prediction
  population: cross-species
topic: Genomics
topic: Protein function prediction

Manuel Aranda
role on project: PI
type: Person
position: External collaborator
current affiliation: KAUST (Marine Science)
topic: Genomics
topic: Protein function prediction

Computational methods for functional metagenomics: from protein functions to multi-scale interactions
type: Project
start year: 2022
end year: 2024
abstract: Multi-scale systems methods for characterising microbial community functions via protein function prediction; downstream produced DeepGOPlus and successor models.
funded by: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
has member: Robert Hoehndorf
has member: Takashi Gojobori
has member: Maxat Kulmanov
has member: Rund Tawfiq
has member: Daulet Toibazar
has member: Amal Alhelal
has member: Md Nurul Muttakin
has member: Shahad Qatan
has member: Kexin Niu
has member: Asaad Mohammedsaleh
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Neuro-Symbolic AI in Life Sciences
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
produced pub: Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
tag: deep learning
tag: ontologies
tag: microbial communities
tag: protein function prediction
tag: metagenomics
tags by group:
  theme: deep learning
  theme: ontologies
  application: microbial communities
  method: protein function prediction
  method: metagenomics
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
start year: 2015
end year: 2020
start year: 2021
end year: 2025
end year: 2023
end year: 2022
start year: 2025
end year: 2026
start year: 2020
end year: 2021

Maxat Kulmanov
role on project: PhD (alumnus)
type: Person
given name: Maxat
family name: Kulmanov
position: PhD (alumnus)
current affiliation: KAUST (Research Scientist)
thesis title: Prediction of protein functions and phenotypes
thesis file: maxat-thesis/Thesis.pdf
thesis defense date: 2020-04-06
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2015
end year: 2020
on project: Bio2Vec: Smart analytics infrastructure for the life sciences
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
position: Postdoc
from: KAUST (PhD)
start year: 2020
end year: 2021
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
topic: Applied Ontology
topic: Rare disease diagnostic support
topic: Genomics
topic: Semantic similarity
topic: Phenotype informatics
topic: Ontology engineering and semantic interoperability
topic: Metagenomics and microbial community function
topic: Biomedical informatics
topic: Drug mechanisms and systems biology
topic: Bioengineering

Daulet Toibazar
role on project: MSc (alumnus)
type: Person
given name: Daulet
family name: Toibazar
position: MSc (alumnus)
thesis title: Context-aware protein function prediction in bacterial genomes
thesis defense date: 2024-07-23
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2022
end year: 2024
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Amal Alhelal
role on project: MSc (alumnus)
type: Person
given name: Amal
family name: Alhelal
position: MSc (alumnus)
thesis title: Protein functional domain identification methodology
thesis defense date: 2024-05-07
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/amal-alhelal
borg profile nid: 8340
start year: 2022
end year: 2024
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Md Nurul Muttakin
role on project: MSc (alumnus)
type: Person
given name: Md
family name: Nurul Muttakin
position: MSc (alumnus)
thesis title: 3D conformation-based protein function prediction
thesis file: mdnurul-thesis/Thesis.pdf
thesis defense date: 2023-04-30
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/md-nurul-muttakin
borg profile nid: 8341
start year: 2022
end year: 2023
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Shahad Qatan
role on project: MSc (alumnus)
type: Person
given name: Shahad
family name: Qatan
position: MSc (alumnus)
thesis title: Predicting Protein Functions From Interactions Using Neural Networks and Ontologies
thesis defense date: 2022-11-09
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2022
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Kexin Niu
role on project: MSc (alumnus)
type: Person
given name: Kexin
family name: Niu
position: MSc (alumnus)
thesis title: De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge
thesis file: kexin-thesis/Thesis.pdf
thesis defense date: 2022-07-04
program: Bioscience
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2022
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Protein function prediction
topic: Metagenomics and microbial community function
topic: Genomics
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Asaad Mohammedsaleh
role on project: MSc (alumnus)
type: Person
given name: Asaad
family name: Mohammedsaleh
position: MSc (alumnus)
thesis title: Genome-Scale Protein Function Adjustment using Constraint Optimization
thesis file: asaad-thesis/Thesis.pdf
thesis defense date: 2026-04-29
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2025
end year: 2026
on project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
type: Project
start year: 2021
end year: 2023
abstract: Neuro-symbolic methods integrating biomedical networks and ontologies for quantitative analysis of disease phenotypes and variants.
funded by: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
has member: Robert Hoehndorf
has member: Paul N Schofield
has member: Georgios V Gkoutos
has member: Sarah Alghamdi
has member: Azza Althagafi
has member: Sumyyah Toonsi
has member: Fernando Zhapa-Camacho
has member: Xi Peng
has member: Zhenwei Tang
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Neuro-Symbolic AI in Life Sciences
produced pub: Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
produced pub: Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
tag: neuro-symbolic AI
tag: ontologies
tag: knowledge graphs
tag: complex disease
tag: rare disease
tag: ontology embeddings
tag: variant prioritization
tag: phenotype reasoning
tag: cross-species
tags by group:
  theme: neuro-symbolic AI
  theme: ontologies
  theme: knowledge graphs
  application: complex disease
  application: rare disease
  method: ontology embeddings
  method: variant prioritization
  method: phenotype reasoning
  population: cross-species
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
start year: 2018
start year: 2019
start year: 2020
end year: 2025
start year: 2022
end year: 2026
end year: 2022

Georgios V Gkoutos
role on project: CoI
type: Person
position: External collaborator
current affiliation: University of Birmingham
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Sarah Alghamdi
role on project: PhD (alumnus)
type: Person
given name: Sarah
family name: Alghamdi
position: PhD (alumnus)
current affiliation: King Abdulaziz University (Assistant Professor)
thesis title: Ontology design patterns for integrating phenotype ontologies
thesis file: sarah-phd-thesis/Thesis.pdf
thesis defense date: 2023-07-20
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2018
end year: 2023
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
on project: CompleX: Variant Prioritization in Complex Disease
position: MSc (alumnus)
thesis title: Ontology design patterns for aging mouse ontologies
thesis file: sarah-thesis/Thesis.pdf
start year: 2017
end year: 2018
topic: Applied Ontology
topic: Rare disease diagnostic support
topic: Phenotype informatics
topic: Semantic similarity
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

Azza Althagafi
role on project: PhD (alumnus)
type: Person
given name: Azza
family name: Althagafi
position: PhD (alumnus)
current affiliation: Taif University (Assistant Professor)
thesis title: Prioritizing Causative Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies
thesis file: azza-phd-thesis/Thesis.pdf
thesis defense date: 2023-07-20
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2019
end year: 2023
on project: CompleX: Variant Prioritization in Complex Disease
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
position: MSc (alumnus)
thesis title: Simulation and visualization of human genomes
thesis file: azza-ms-thesis/Thesis.pdf
start year: 2017
end year: 2018
topic: Rare disease diagnostic support
topic: Genomics
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Semantic similarity
topic: Phenotype informatics

Sumyyah Toonsi
role on project: PhD (alumnus)
role on project: MSc (alumnus)
type: Person
given name: Sumyyah
family name: Toonsi
position: PhD (alumnus)
current affiliation: Effat University (Assistant Professor)
thesis title: Data Driven Mining of Causal Disease Relations to Enhance Disease Centric Predictions
thesis file: sumyyah-thesis/Thesis.pdf
thesis defense date: 2025-05-15
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2020
end year: 2025
on project: Development of Algorithms for Biotechnology and Biomedical Applications
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
position: MSc (alumnus)
thesis title: Automatic annotation of protein functions through text mining
start year: 2019
end year: 2019
on project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Rare disease diagnostic support
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Biomedical informatics
topic: Phenotype informatics
topic: Drug mechanisms and systems biology
topic: Semantic similarity

Xi Peng
role on project: MSc (alumnus)
type: Person
given name: Xi
family name: Peng
position: MSc (alumnus)
thesis title: Description Logic EL++ Embeddings with Intersectional Closure
thesis file: peng-thesis/Thesis.pdf
thesis defense date: 2022-03-29
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2022
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
topic: Applied Ontology
topic: Rare disease diagnostic support
topic: Neuro-symbolic methods in Bioinformatics
topic: Genomics

Zhenwei Tang
role on project: MSc (alumnus)
type: Person
given name: Zhenwei
family name: Tang
position: MSc (alumnus)
thesis title: Towards Quality and General Knowledge Representation Learning
thesis defense date: 2022-04-05
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2022
on project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Protein function prediction
topic: Rare disease diagnostic support

Development of Algorithms for Biotechnology and Biomedical Applications
type: Project
start year: 2021
end year: 2023
abstract: Algorithm development for biotechnology and biomedical applications at the CBRC; umbrella fund for several smaller projects.
funded by: Development of Algorithms for Biotechnology and Biomedical Applications
has member: Robert Hoehndorf
has member: Sumyyah Toonsi
produced pub: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
produced pub: Improving the classification of cardinality phenotypes using collections
produced pub: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
produced pub: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
produced pub: Ontology Embedding: A Survey of Methods, Applications and Resources
produced pub: Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
tag: machine learning
tag: deep learning
tags by group:
  theme: machine learning
  theme: deep learning
topic: Neuro-symbolic methods in Bioinformatics
start year: 2020
end year: 2025

CompleX: Variant Prioritization in Complex Disease
type: Project
start year: 2019
end year: 2021
abstract: Semantic methods for prioritising causative variants in complex (polygenic / oligogenic) disease using phenotype ontologies and gene network embeddings.
funded by: CompleX: Variant Prioritization in Complex Disease
has member: Robert Hoehndorf
has member: Paul N Schofield
has member: Georgios V Gkoutos
has member: Imane Boudellioua
has member: Mona Alshahrani
has member: Sarah Alghamdi
has member: Azza Althagafi
has member: Abeer Almutairi
has member: Sara Althubaiti
has member: Hatoon Al Ali
has member: Safana Bakheet
has member: Ashraf Kibraya
produced pub: Ontology-based prediction of cancer driver genes
produced pub: DDIEM: drug database for inborn errors of metabolism
produced pub: DeepGOPlus: improved protein function prediction from sequence
produced pub: Klarigi: Characteristic explanations for semantic biomedical data
produced pub: Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
produced pub: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
produced pub: Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
produced pub: Improved characterisation of clinical text through ontology-based vocabulary expansion
tag: machine learning
tag: ontologies
tag: complex disease
tag: rare disease
tag: variant prioritization
tag: semantic similarity
tag: phenotype reasoning
tags by group:
  theme: machine learning
  theme: ontologies
  application: complex disease
  application: rare disease
  method: variant prioritization
  method: semantic similarity
  method: phenotype reasoning
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity
start year: 2015
end year: 2019
start year: 2018
end year: 2023
start year: 2017
end year: 2018
start year: 2021
start year: 2024
end year: 2025
start year: 2020

Imane Boudellioua
role on project: PhD (alumnus)
type: Person
given name: Imane
family name: Boudellioua
position: PhD (alumnus)
current affiliation: King Fahd University of Petroleum and Minerals (Assistant Professor)
thesis title: Semantic Prioritization of Novel Causative Variants
thesis file: imene-thesis/Thesis.pdf
thesis defense date: 2019-02-05
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2015
end year: 2019
on project: CompleX: Variant Prioritization in Complex Disease
topic: Rare disease diagnostic support
topic: Genomics
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity
topic: Phenotype informatics
topic: Biomedical informatics
topic: Applied Ontology

Mona Alshahrani
role on project: PhD (alumnus)
type: Person
given name: Mona
family name: Alshahrani
position: PhD (alumnus)
current affiliation: Jubail University College (Assistant Professor)
thesis title: Multi-modal learning on biological knowledge graphs
thesis file: mona-thesis/Thesis.pdf
thesis defense date: 2019-11-03
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2015
end year: 2019
on project: Bio2Vec: Smart analytics infrastructure for the life sciences
on project: CompleX: Variant Prioritization in Complex Disease
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
topic: Rare disease diagnostic support
topic: Semantic similarity
topic: Phenotype informatics
topic: Drug mechanisms and systems biology

Abeer Almutairi
role on project: MSc (alumnus)
type: Person
given name: Abeer
family name: Almutairi
position: MSc (alumnus)
thesis title: Unsupervised Method for Disease Named Entity Recognition
thesis defense date: 2019-11-04
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2018
end year: 2019
on project: CompleX: Variant Prioritization in Complex Disease
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Sara Althubaiti
role on project: MSc (alumnus)
type: Person
given name: Sara
family name: Althubaiti
position: MSc (alumnus)
thesis title: Ontology-based identification of cancer driver genes
thesis file: sara-thesis/Thesis.pdf
thesis defense date: 2018-11-05
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2017
end year: 2018
on project: CompleX: Variant Prioritization in Complex Disease
topic: Biomedical informatics
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Rare disease diagnostic support
topic: Semantic similarity

Hatoon Al Ali
role on project: MSc (alumnus)
type: Person
given name: Hatoon
family name: Al Ali
position: MSc (alumnus)
thesis title: Predicting effects of non-coding genomic variants
thesis file: hatoon-thesis/Thesis.pdf
thesis defense date: 2023-05-01
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2021
end year: 2023
on project: CompleX: Variant Prioritization in Complex Disease
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Safana Bakheet
role on project: MSc (alumnus)
type: Person
given name: Safana
family name: Bakheet
position: MSc (alumnus)
thesis title: An Inductive, Supervised Gene-Disease Associations Method
thesis file: safana-thesis/Thesis.pdf
thesis defense date: 2025-05-04
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/safana-bakheet
borg profile nid: 8342
start year: 2024
end year: 2025
on project: CompleX: Variant Prioritization in Complex Disease
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Ashraf Kibraya
role on project: Postdoc
type: Person
given name: Ashraf
family name: Kibraya
position: Postdoc
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2020
end year: 2021
on project: CompleX: Variant Prioritization in Complex Disease
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Improving health of Saudi population
type: Project
start year: 2019
end year: 2021
abstract: Health informatics and precision-medicine pipelines tailored to Saudi-population genetic and phenotypic data.
funded by: Improving health of Saudi population
has member: Robert Hoehndorf
has member: Sakhaa Alsaedi
has member: Yang Liu
produced pub: DDIEM: drug database for inborn errors of metabolism
produced pub: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
tag: machine learning
tag: rare disease
tag: complex disease
tag: variant prioritization
tag: Saudi-specific
tags by group:
  theme: machine learning
  application: rare disease
  application: complex disease
  method: variant prioritization
  population: Saudi-specific
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
end year: 2020
start year: 2021
end year: 2022

Sakhaa Alsaedi
role on project: MSc (alumnus)
type: Person
given name: Sakhaa
family name: Alsaedi
position: MSc (alumnus)
thesis title: Evaluating the Application of Allele Frequency in the Saudi Population Variant Detection
thesis file: sakhaa-thesis/KAUST_Thesis_Sakhaa_2020/Thesis.tex
thesis defense date: 2020-04-07
program: Computer Science
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2019
end year: 2020
on project: Improving health of Saudi population
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Whole genome sequencing of rare disease patients
type: Project
start year: 2019
end year: 2019
abstract: Pilot rare-disease whole-genome sequencing and analysis, in collaboration with KAUST Health.
funded by: Whole genome sequencing of rare disease patients
has member: Robert Hoehndorf
tag: rare disease
tag: variant prioritization
tag: Saudi-specific
tags by group:
  application: rare disease
  method: variant prioritization
  population: Saudi-specific
topic: Rare disease diagnostic support

Sequencing and computational analysis of MRSA samples
type: Project
start year: 2018
end year: 2021
abstract: Microbial genomics and bioinformatics of methicillin-resistant Staphylococcus aureus (MRSA) isolates in Saudi Arabia.
funded by: Sequencing and computational analysis of MRSA samples
has member: Robert Hoehndorf
has member: Mohammed Al Fageeh
has member: Takashi Gojobori
has member: Vladimir Bajic
tag: infectious disease
tag: metagenomics
tag: Saudi-specific
tags by group:
  application: infectious disease
  method: metagenomics
  population: Saudi-specific
topic: Genomics
topic: Metagenomics and microbial community function

Mohammed Al Fageeh
role on project: PI
type: Person
position: External collaborator
current affiliation: KACST
topic: Genomics
topic: Metagenomics and microbial community function

Vladimir Bajic
role on project: CoI
role on project: PI
type: Person
position: External collaborator
current affiliation: Former KAUST CBRC director (retired; CBRC now dissolved)
topic: Metagenomics and microbial community function
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Genomics
topic: Rare disease diagnostic support
topic: Drug mechanisms and systems biology

Improvement of genetic variant prioritization technology
type: Project
start year: 2018
end year: 2019
abstract: Engineering improvements to the semantic variant-prioritization pipeline (PhenomeNet, DeepPVP).
funded by: Improvement of genetic variant prioritization technology
has member: Robert Hoehndorf
has member: Paul N Schofield
has member: Georgios V Gkoutos
has member: Vladimir Bajic
produced pub: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
tag: machine learning
tag: ontologies
tag: rare disease
tag: variant prioritization
tag: phenotype reasoning
tags by group:
  theme: machine learning
  theme: ontologies
  application: rare disease
  method: variant prioritization
  method: phenotype reasoning
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Bio2Vec: Smart analytics infrastructure for the life sciences
type: Project
start year: 2018
end year: 2020
abstract: Smart analytics infrastructure on biological knowledge graphs; extends Bio2RDF, develops semantic analytics methods that became OPA2Vec / OWL2Vec.
funded by: Bio2Vec: Smart analytics infrastructure for the life sciences
has member: Robert Hoehndorf
has member: Xin Gao
has member: Michel Dumontier
has member: Jens Lehmann
has member: Mona Alshahrani
has member: Maxat Kulmanov
has member: Sumyyah Toonsi
produced pub: Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
produced pub: Ontology-based prediction of cancer driver genes
produced pub: Combining lexical and context features for automatic ontology extension
produced pub: DDIEM: drug database for inborn errors of metabolism
produced pub: DeepGOPlus: improved protein function prediction from sequence
produced pub: Phenotype-driven discovery of digenic variants in personal genome sequences
produced pub: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
produced pub: Ontology based mining of pathogen--disease associations from literature
produced pub: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
produced pub: Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
produced pub: Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
tag: knowledge graphs
tag: ontologies
tag: machine learning
tag: ontology embeddings
tag: semantic similarity
tag: cross-species
tags by group:
  theme: knowledge graphs
  theme: ontologies
  theme: machine learning
  method: ontology embeddings
  method: semantic similarity
  population: cross-species
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity
start year: 2015
end year: 2019
start year: 2019

Xin Gao
role on project: CoI
role on project: PI
type: Person
position: External collaborator
current affiliation: KAUST (formerly CBRC, now dissolved)
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

Michel Dumontier
role on project: CoI
type: Person
position: External collaborator
current affiliation: Maastricht University
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

Jens Lehmann
role on project: CoI
type: Person
position: External collaborator
current affiliation: Amazon (formerly TU Dresden)
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
type: Project
start year: 2018
end year: 2020
abstract: Population genomics of whale sharks; comparative genomics and habitat-use analysis.
funded by: The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
has member: Takashi Gojobori
has member: Michael Berumen
has member: Robert Hoehndorf
tag: marine biology
tag: cross-species
tags by group:
  application: marine biology
  population: cross-species
topic: Genomics

Michael Berumen
role on project: CoI
type: Person
position: External collaborator
current affiliation: KAUST (Marine Science)
topic: Genomics

Data integration and ontologies for microbial cell factories
type: Project
start year: 2016
end year: 2018
abstract: Ontology-based data integration for synthetic biology and metabolic engineering. Hoehndorf led the data-integration work package.
funded by: Data integration and ontologies for microbial cell factories
has member: Vladimir Bajic
has member: Robert Hoehndorf
has member: Miguel Angel Rodriguez Garcia
produced pub: Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
produced pub: Ontology-based prediction of cancer driver genes
produced pub: Combining lexical and context features for automatic ontology extension
produced pub: DDIEM: drug database for inborn errors of metabolism
produced pub: DeepGOPlus: improved protein function prediction from sequence
produced pub: Phenotype-driven discovery of digenic variants in personal genome sequences
produced pub: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
produced pub: Ontology based mining of pathogen--disease associations from literature
produced pub: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
produced pub: Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
produced pub: Integrating phenotype ontologies with PhenomeNET
produced pub: Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
produced pub: Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
tag: ontologies
tag: knowledge graphs
tag: microbial communities
tag: drug discovery
tag: ontology embeddings
tags by group:
  theme: ontologies
  theme: knowledge graphs
  application: microbial communities
  application: drug discovery
  method: ontology embeddings
topic: Applied Ontology
topic: Drug mechanisms and systems biology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics

Miguel Angel Rodriguez Garcia
role on project: Postdoc
type: Person
given name: Miguel
family name: Angel Rodriguez Garcia
position: Postdoc
current affiliation: King Juan Carlos University (Research Scientist)
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
from: University of Murcia
start year: 2016
end year: 2018
on project: Data integration and ontologies for microbial cell factories
topic: Rare disease diagnostic support
topic: Phenotype informatics
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Drug mechanisms and systems biology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics

KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
type: Project
start year: 2024
end year: 2026
abstract: Robert leads the Infectious Disease area within the Bioinformatics & Computational Biology (BCB) research theme of the KAUST Center of Excellence for Smart Health.
funded by: KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
has member: Xin Gao
has member: Robert Hoehndorf

Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST KCSH
role of RH: PI
start year: 2025
end year: 2026
amount currency: USD
amount total: 100000
amount to BORG: 100000
amount note: KCSH "Pathway to Impact 2025" scheme (distinct from CoE theme funds); $50k x 2 periods. Verified email 2026-05-29.
grant ID: FCC/1/5932-12-10
internal project ID: 5932
grant ID sources: 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
additional type: https://schema.org/MonetaryGrant
was derived from: 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 for Smart Health, Pathway to Impact Grant Program 2025
type: Organization
name: KAUST Center of Excellence for Generative AI (CoE)
name: KAUST Competitive Research Grant (CRG11)
name: KAUST Smart Health Initiative
name: KAUST Near Term Grand Challenge
name: KAUST Climate and Livability Initiative
name: KAUST Competitive Research Grant
name: KAUST Center Competitive Fund
name: KAUST OSR Director's Award, Digital Health Initiative
name: KAUST Center Partnership Fund
name: KAUST Center Competitive Funding
name: KAUST Center of Excellence for Smart Health (KCSH)
name: King Abdullah University of Science and Technology

KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CoE GenAI
role of RH: PI
start year: 2024
amount currency: USD
amount total: 100000
amount to BORG: 100000
amount note: $50,000/year for FY24/25 and FY25/26 (Biomedical/BCB theme). Verified email 2026-05-29.
grant ID: FCC/1/5940-07-01
internal project ID: 5940
grant ID sources: WBS for CoE GenAI project 5940-07 (thread:000000000005cdc8); grant ID corrected to -07-01 per Robert 2026-05-29
additional type: https://schema.org/MonetaryGrant
was derived from: WBS for CoE GenAI project 5940-07 (thread:000000000005cdc8); grant ID corrected to -07-01 per Robert 2026-05-29

Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: PI
start year: 2023
end year: 2026
amount currency: USD
amount total: 282000
amount to BORG: 232191
amount note: $282,000 overall KAUST award; $49,809 subcontract to Cambridge (P. Schofield, Co-PI); net $232,191 to BORG. Verified email 2026-05-29.
amount source: CRG11 activation thread (URF/1/5041; "$141,000 each year, $282,000 overall"; sole PI), verified email 2026-05-29
grant ID: URF/1/5041-01-01
internal project ID: 5041
grant ID sources: thread:00000000000539ca (5041 CRG11 Apr 2023); Robert PI (confirmed 2026-05-17)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:00000000000539ca (5041 CRG11 Apr 2023); Robert PI (confirmed 2026-05-17)
was derived from: CRG11 activation thread (URF/1/5041; "$141,000 each year, $282,000 overall"; sole PI), verified email 2026-05-29

Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST Smart Health
role of RH: PI (co-PI)
start year: 2023
end year: 2026
amount currency: USD
amount total: 894500
amount to BORG: 200000
grant ID: REI/1/4938-01-01
internal project ID: 4938
grant ID sources: thread:000000000005cc4c (KSHI #4938 3D Leukemia Disease Models)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000005cc4c (KSHI #4938 3D Leukemia Disease Models)

A public Saudi pangenome as reference for genomics in the Middle East
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST Smart Health
role of RH: PI
start year: 2024
end year: 2026
amount currency: USD
amount total: 210000
amount to BORG: 210000
grant ID: REI/1/5659-01-01
internal project ID: 5659
grant ID sources: thread:0000000000056ced (5659 KSHI2023 Activation Sep 2023)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:0000000000056ced (5659 KSHI2023 Activation Sep 2023)

Enabling desert revegetation by AI-tailored soil microbiome fortification
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST NTGC
role of RH: CoI
start year: 2023
end year: 2025
amount currency: USD
amount total: 1000000
amount to BORG: 150000
grant ID: REI/1/5235-01-01
internal project ID: 5235
grant ID sources: thread:000000000005dc92 + thread:0000000000058f3c (ORFS-2022-NTGC-5235.2 Progress Report)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000005dc92 + thread:0000000000058f3c (ORFS-2022-NTGC-5235.2 Progress Report)

Enabling mangrove restoration by AI-tailored microbiome fortification
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CLI
role of RH: CoI
start year: 2023
end year: 2023
amount currency: USD
amount total: 100000
amount to BORG: 25000
grant ID sources: no activation email found; may have been absorbed into REI/1/5235 (NTGC desert)
note: follow up with Hirt's BA or check for separate WBS
additional type: https://schema.org/MonetaryGrant
was derived from: no activation email found; may have been absorbed into REI/1/5235 (NTGC desert)

Metagenomics-based surface prospecting
type: Grant
funder: Saudi Aramco (industry contract)
funder short: Saudi Aramco
role of RH: PI
start year: 2022
end year: 2024
amount currency: USD
grant ID: RGC/3/4267-01-01
internal project ID: 4267
grant ID sources: thread:000000000004ebf2 (4267 Aramco Activation Jun 2022); Aramco CRPO# 6511079970 (thread:000000000005c09f)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000004ebf2 (4267 Aramco Activation Jun 2022); Aramco CRPO# 6511079970 (thread:000000000005c09f)

Saudi Aramco (industry contract)
type: Organization
name: Saudi Aramco

Evolutionary potential of corals to adapt to climate warming
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: CoI
start year: 2022
end year: 2025
amount currency: USD
amount total: 1044509
amount to BORG: 150000
grant ID: URF/1/4697-01-01
internal project ID: 4697
grant ID sources: thread:0000000000050e95 (Aranda Oct 2022)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:0000000000050e95 (Aranda Oct 2022)

Computational methods for functional metagenomics: from protein functions to multi-scale interactions
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: PI
start year: 2022
end year: 2024
amount currency: USD
amount total: 347500
amount to BORG: 247500
grant ID: URF/1/4675-01-01
internal project ID: 4675
grant ID sources: thread:000000000004cb34 (4675 CRG10 Activation)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000004cb34 (4675 CRG10 Activation)

IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: PI
start year: 2021
end year: 2023
amount currency: USD
amount total: 399992
amount to BORG: 239999
grant ID: URF/1/4355-01-01
internal project ID: 4355
grant ID sources: thread:00000000000408b3 (4355 CRG9 Activation)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:00000000000408b3 (4355 CRG9 Activation)

Development of Algorithms for Biotechnology and Biomedical Applications
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CCF
role of RH: PI
start year: 2021
end year: 2023
amount currency: USD
amount total: 360000
amount to BORG: 360000
grant ID: FCC/1/1976-34-01
internal project ID: 1976
grant ID sources: 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]
additional type: https://schema.org/MonetaryGrant
was derived from: 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]

CompleX: Variant Prioritization in Complex Disease
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: PI
start year: 2019
end year: 2021
amount currency: USD
amount total: 399998
amount to BORG: 240000
grant ID: URF/1/3790-01-01
internal project ID: 3790
grant ID sources: thread:000000000002acd4 (3790 CRG7 Activation)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000002acd4 (3790 CRG7 Activation)

Improving health of Saudi population
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CCF
role of RH: PI
start year: 2019
end year: 2021
amount currency: USD
amount total: 324000
amount to BORG: 324000
grant ID: URF/1/1976-31-01
internal project ID: 1976
grant ID sources: thread:0000000000025828 (CBRC CCF CARF Pocket IDs Sep 2020); URF/1/1976-31-01 + URF/1/1976-29-01 in this period
additional type: https://schema.org/MonetaryGrant
was derived from: thread:0000000000025828 (CBRC CCF CARF Pocket IDs Sep 2020); URF/1/1976-31-01 + URF/1/1976-29-01 in this period

Whole genome sequencing of rare disease patients
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST OSR Director's Award
role of RH: PI
start year: 2019
end year: 2019
amount currency: USD
amount total: 138600
amount to BORG: 138600
grant ID: REP/1/4133-01-01
internal project ID: 4133
grant ID sources: thread:000000000002a307 (OSR Director's Award 4133 activation Apr 2019)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000002a307 (OSR Director's Award 4133 activation Apr 2019)

Sequencing and computational analysis of MRSA samples
type: Grant
funder: King Abdulaziz City for Science and Technology
funder short: KACST
role of RH: PI
start year: 2018
end year: 2021
amount currency: USD
amount total: 362159
amount to BORG: 362159
grant ID: RGC/3/3689-01-01
internal project ID: 3689
grant ID sources: thread:00000000000284aa (3689-KACST-Grant activation kickoff)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:00000000000284aa (3689-KACST-Grant activation kickoff)

King Abdulaziz City for Science and Technology
type: Organization

Improvement of genetic variant prioritization technology
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CPF
role of RH: PI
start year: 2018
end year: 2019
amount currency: USD
amount total: 129715
amount to BORG: 9500
grant ID: FCS/1/3657-01-01
internal project ID: 3657
grant ID sources: thread:0000000000027509 (CPF funding Apr 2018) + thread:000000000001f04a
additional type: https://schema.org/MonetaryGrant
was derived from: thread:0000000000027509 (CPF funding Apr 2018) + thread:000000000001f04a

Bio2Vec: Smart analytics infrastructure for the life sciences
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: PI
start year: 2018
end year: 2020
amount currency: USD
amount total: 399986
amount to BORG: 113250
grant ID: URF/1/3454-01-01
internal project ID: 3454
grant ID sources: thread:000000000002771e (3454 CRG6 Activation, Apr 2018)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:000000000002771e (3454 CRG6 Activation, Apr 2018)

The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CRG
role of RH: CoI
start year: 2018
end year: 2020
amount currency: USD
amount total: 389713
amount to BORG: 105838
grant ID: URF/1/3451-01-01
internal project ID: 3451
grant ID sources: thread:00000000000258f8 (Sultan Ahmed)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:00000000000258f8 (Sultan Ahmed)

Data integration and ontologies for microbial cell factories
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST CCF
role of RH: WP-lead
start year: 2016
end year: 2018
amount currency: USD
amount total: 4786036
amount to BORG: 115691
grant ID: FCC/1/1976-08-01
internal project ID: 1976
grant ID sources: thread:00000000000258f8 (Sultan Ahmed, Summary CCF Funding Jan 2018)
additional type: https://schema.org/MonetaryGrant
was derived from: thread:00000000000258f8 (Sultan Ahmed, Summary CCF Funding Jan 2018)

KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
type: Grant
funder: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025
funder short: KAUST KCSH
role of RH: Area lead (Infectious Disease), BCB theme
start year: 2024
end year: 2026
amount currency: USD
amount total: 200000
amount to BORG: 200000
amount note: $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.
grant ID: FCC/1/5932-10-02
internal project ID: 5932
grant ID sources: KCSH BCB theme budget 2024/25 (thread:0000000000060a33): '$50,000 - Robert Hoehndorf - FCC/1/5932-10-02', BCB theme Lead PI Xin Gao
additional type: https://schema.org/MonetaryGrant
was derived from: KCSH BCB theme budget 2024/25 (thread:0000000000060a33): '$50,000 - Robert Hoehndorf - FCC/1/5932-10-02', BCB theme Lead PI Xin Gao

Applied Ontology
weight: 104
weight: 1
weight: 3
weight: 4
weight: 2
weight: 9
type: Topic
short name: Applied Ontology
section: Foundations
abstract: 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.
keyword: formal ontology
keyword: GFO
keyword: GFO-Bio
keyword: ontology of functions
keyword: phenotype ontology
keyword: FLOPO
keyword: ontology design patterns
linked paper: Semantic similarity and machine learning with ontologies
linked paper: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
linked paper: Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
linked paper: Improving the classification of cardinality phenotypes using collections
linked paper: Ontology-based prediction of cancer driver genes
linked paper: GFVO: the Genomic Feature and Variation Ontology
linked paper: Best behaviour? Ontologies and the formal description of animal behaviour
linked paper: FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
linked paper: DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
linked paper: DermO; an ontology for the description of dermatologic disease
linked paper: FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
linked paper: A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
linked paper: Notions of similarity for systems biology models
linked paper: A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
linked paper: The role of ontologies in biological and biomedical research: a functional perspective
linked paper: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
linked paper: Evaluating the effect of annotation size on measures of semantic similarity
linked paper: DELE: Deductive EL++ Embeddings for Knowledge Base Completion
linked paper: An ontology approach to comparative phenomics in plants
linked paper: Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
linked paper: Ontology based mining of pathogen--disease associations from literature
linked paper: The anatomy of phenotype ontologies: principles, properties and applications
linked paper: Ontology-based validation and identification of regulatory phenotypes
linked paper: Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
linked paper: Semantic units: organizing knowledge graphs into semantically meaningful units of representation
linked paper: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
linked paper: Statistical tests for associations between two directed acyclic graphs.
linked paper: Applying the functional abnormality ontology pattern to anatomical functions.
linked paper: The ontology of biological sequences.
linked paper: BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
linked paper: Relations as patterns: bridging the gap between OBO and OWL.
linked paper: GFO-Bio: A biomedical core ontology
linked paper: Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies
linked paper: A top-level ontology of functions and its application in the Open Biomedical Ontologies.
linked paper: Interoperability between phenotype and anatomy ontologies
linked paper: A common layer of interoperability for biomedical ontologies based on OWL EL
linked paper: The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
linked paper: Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
linked paper: Integrating systems biology models and biomedical ontologies
linked paper: PIDO: The Primary Immunodeficiency Disease Ontology
linked paper: Ontology design patterns to disambiguate relations between genes and gene products in GENIA
linked paper: New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
linked paper: OBML - Ontologies in Biomedicine and Life Sciences
linked paper: Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
linked paper: Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
linked paper: Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
linked paper: Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
linked paper: Towards improving phenotype representation in OWL
linked paper: Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
linked paper: Evaluation of research in biomedical ontologies
linked paper: The Units Ontology: a tool for integrating units of measurement in science
linked paper: Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
linked paper: Representing physiological processes and their participants with PhysioMaps
linked paper: Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
linked paper: Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
linked paper: BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
linked paper: Thematic series on biomedical ontologies in JBMS: challenges and new directions
linked paper: Analyzing gene expression data in mice with the Neuro Behavior Ontology
linked paper: Enriched biodiversity data as a resource and service
linked paper: Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
linked paper: Updating the CEMO ontology for future epidemiological challenges
linked paper: Large-Scale Reasoning over Functions in Biomedical Ontologies

Neuro-symbolic methods in Bioinformatics
weight: 64
weight: 2
weight: 5
weight: 1
weight: 3
weight: 4
weight: 14
type: Topic
short name: Neuro-symbolic AI
section: Foundations
abstract: 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.
keyword: ontology embeddings
keyword: description logic
keyword: geometric embeddings
keyword: EL++
keyword: ALC
keyword: neuro-symbolic AI
keyword: knowledge graph embedding
keyword: mOWL
linked paper: Semantic similarity and machine learning with ontologies
linked paper: Predicting protein functions using positive-unlabeled ranking with ontology-based priors
linked paper: DeepGOPlus: improved protein function prediction from sequence
linked paper: DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
linked paper: A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
linked paper: Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
linked paper: Neuro-symbolic representation learning on biological knowledge graphs
linked paper: LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
linked paper: Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
linked paper: Ontology Embedding: A Survey of Methods, Applications and Resources
linked paper: Data science and symbolic AI: Synergies, challenges and opportunities
linked paper: DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
linked paper: DeepPVP: phenotype-based prioritization of causative variants using deep learning
linked paper: DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
linked paper: DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
linked paper: DELE: Deductive EL++ Embeddings for Knowledge Base Completion
linked paper: Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
linked paper: OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
linked paper: Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
linked paper: mOWL: Python library for machine learning with biomedical ontologies
linked paper: SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
linked paper: From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings
linked paper: Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
linked paper: EL Embeddings: Geometric construction of models for the Description Logic EL++
linked paper: Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
linked paper: Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
linked paper: Ontology-Based Concept Recognition by Using Word Embeddings
linked paper: Robust Knowledge Graph Embedding via Denoising
linked paper: Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
linked paper: Neural Multi-hop Logical Query Answering with Concept-Level Answers
linked paper: Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
linked paper: Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
linked paper: Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
linked paper: Neuro-Symbolic AI in Life Sciences
linked project: Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
linked project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
linked project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
linked project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
linked project: A public Saudi pangenome as reference for genomics in the Middle East
linked project: Enabling desert revegetation by AI-tailored soil microbiome fortification
linked project: Enabling mangrove restoration by AI-tailored microbiome fortification
linked project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
linked project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
linked project: Development of Algorithms for Biotechnology and Biomedical Applications
linked project: CompleX: Variant Prioritization in Complex Disease
linked project: Improving health of Saudi population
linked project: Improvement of genetic variant prioritization technology
linked project: Bio2Vec: Smart analytics infrastructure for the life sciences
linked project: Data integration and ontologies for microbial cell factories
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sarah Alghamdi
linked person: Sumyyah Toonsi
linked person: Sara Althubaiti
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Miguel Angel Rodriguez Garcia
linked person: Zhenwei Tang
linked person: Yang Liu

Rare disease diagnostic support
weight: 50
weight: 5
weight: 2
weight: 1
weight: 4
weight: 3
weight: 12
weight: 8
type: Topic
short name: Rare disease
section: Applications
abstract: 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.
keyword: PhenomeNET
keyword: DeepPVP
keyword: PVP
keyword: variant prioritization
keyword: Human Phenotype Ontology
keyword: HPO
keyword: rare disease
keyword: complex disease
keyword: consanguinity
keyword: Saudi population
linked paper: DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
linked paper: DDIEM: drug database for inborn errors of metabolism
linked paper: What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
linked paper: Contribution of model organism phenotypes to the computational identification of human disease genes
linked paper: DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
linked paper: Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
linked paper: CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
linked paper: Predicting candidate genes from phenotypes, functions and anatomical site of expression
linked paper: Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
linked paper: DeepPVP: phenotype-based prioritization of causative variants using deep learning
linked paper: Similarity-based search of model organism, disease and drug effect phenotypes
linked paper: Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
linked paper: Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
linked paper: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
linked paper: Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
linked paper: OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
linked paper: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
linked paper: Semantic prioritization of novel causative genomic variants
linked paper: Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
linked paper: Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
linked paper: Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
linked paper: EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
linked paper: PhenomeNET: a whole-phenome approach to disease gene discovery
linked paper: PIDO: The Primary Immunodeficiency Disease Ontology
linked paper: New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
linked paper: Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
linked paper: Mouse genetic and phenotypic resources for human genetics
linked paper: An integrative, translational approach to understanding rare and orphan genetically based diseases
linked paper: Mouse model phenotypes provide information about human drug targets
linked paper: Integrating phenotype ontologies with PhenomeNET
linked paper: Phenotype-driven discovery of digenic variants in personal genome sequences
linked paper: A translational medicine approach to orphan diseases
linked project: Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
linked project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
linked project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
linked project: A public Saudi pangenome as reference for genomics in the Middle East
linked project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
linked project: CompleX: Variant Prioritization in Complex Disease
linked project: Improving health of Saudi population
linked project: Whole genome sequencing of rare disease patients
linked project: Improvement of genetic variant prioritization technology
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sarah Alghamdi
linked person: Sumyyah Toonsi
linked person: Sara Althubaiti
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Miguel Angel Rodriguez Garcia
linked person: Zhenwei Tang
linked person: Yang Liu
linked person: Xi Peng
linked person: Paul N Schofield
linked person: Charlotte Hauser
linked person: Malak Althagafi
linked person: Georgios V Gkoutos

Ontology engineering and semantic interoperability
weight: 46
weight: 2
weight: 1
weight: 4
type: Topic
short name: Ontology engineering
section: Foundations
abstract: 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.
keyword: AberOWL
keyword: Semantic Web
keyword: OWL
keyword: OWL EL reasoning
keyword: ontology-based data access
keyword: linked data
keyword: interoperability
linked paper: BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
linked paper: Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
linked paper: Aber-OWL: a framework for ontology-based data access in biology
linked paper: Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
linked paper: Neuro-symbolic representation learning on biological knowledge graphs
linked paper: FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
linked paper: An open source knowledge graph ecosystem for the life sciences
linked paper: DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
linked paper: FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
linked paper: A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
linked paper: Usage of cell nomenclature in biomedical literature
linked paper: DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
linked paper: DELE: Deductive EL++ Embeddings for Knowledge Base Completion
linked paper: Combining lexical and context features for automatic ontology extension
linked paper: DESM: portal for microbial knowledge exploration systems
linked paper: Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning
linked paper: Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
linked paper: Klarigi: Characteristic explanations for semantic biomedical data
linked paper: BioHackathon 2015: Semantics of data for life sciences and reproducible research
linked paper: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
linked paper: Interoperability between phenotype and anatomy ontologies
linked paper: A common layer of interoperability for biomedical ontologies based on OWL EL
linked paper: Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
linked paper: The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
linked paper: Ontology design patterns to disambiguate relations between genes and gene products in GENIA
linked paper: Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
linked paper: Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
linked paper: An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
linked paper: Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
linked paper: The Units Ontology: a tool for integrating units of measurement in science
linked paper: Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
linked paper: An integrative, translational approach to understanding rare and orphan genetically based diseases
linked paper: Evaluating Different Methods for Semantic Reasoning Over Ontologies
linked paper: Large-Scale Reasoning over Functions in Biomedical Ontologies
linked paper: To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)
linked paper: Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
linked paper: AberOWL: an ontology portal with OWL EL reasoning
linked paper: Robust Knowledge Graph Embedding via Denoising
linked paper: SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL
linked paper: Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
linked paper: Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
linked paper: Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
linked paper: Investigation of the fundamental strategy for interoperability of description of biological measurements
linked paper: Integration of knowledge for personalized medicine: a pharmacogenomics case-study
linked paper: JOWO 2020: The Joint Ontology Workshops : Proceedings of the Joint Ontology Workshops co-located with the Bolzano Summer of Knowledge (BOSK 2020)
linked project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sarah Alghamdi
linked person: Sara Althubaiti
linked person: Maxat Kulmanov
linked person: Miguel Angel Rodriguez Garcia
linked person: Yang Liu
linked person: Tengwei Song
linked person: Paul N Schofield
linked person: Fernando Zhapa-Camacho
linked person: Mahdi Bu Ali
linked course: Knowledge Representation and Reasoning
linked course: Applied Ontology

Biomedical informatics
weight: 46
weight: 1
weight: 2
weight: 3
weight: 4
type: Topic
short name: Biomedical informatics
section: Applications
abstract: 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.
keyword: biomedical knowledge base
keyword: PathoPhenoDB
keyword: PhenomeBrowser
keyword: text mining
keyword: biomedical NLP
keyword: clinical informatics
keyword: EHR analytics
keyword: phenotype standardisation
linked paper: DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
linked paper: BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
linked paper: Aber-OWL: a framework for ontology-based data access in biology
linked paper: Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
linked paper: Ontology-based prediction of cancer driver genes
linked paper: Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
linked paper: Predicting candidate genes from phenotypes, functions and anatomical site of expression
linked paper: Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
linked paper: Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
linked paper: Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
linked paper: Age-related differences in gene expression and pathway activation following heatstroke
linked paper: Ranking Adverse Drug Reactions With Crowdsourcing
linked paper: VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
linked paper: Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
linked paper: The role of ontologies in biological and biomedical research: a functional perspective
linked paper: Usage of cell nomenclature in biomedical literature
linked paper: Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
linked paper: The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
linked paper: Combining lexical and context features for automatic ontology extension
linked paper: Ontology based mining of pathogen--disease associations from literature
linked paper: PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
linked paper: Multi-faceted semantic clustering with text-derived phenotypes
linked paper: Improved characterisation of clinical text through ontology-based vocabulary expansion
linked paper: Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
linked paper: Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
linked paper: Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
linked paper: BioHackathon 2015: Semantics of data for life sciences and reproducible research
linked paper: The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
linked paper: The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
linked paper: Ontology design patterns to disambiguate relations between genes and gene products in GENIA
linked paper: OBML - Ontologies in Biomedicine and Life Sciences
linked paper: An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
linked paper: Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
linked paper: Evaluation of research in biomedical ontologies
linked paper: Text-mining solutions for biomedical research: enabling integrative biology
linked paper: Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
linked paper: Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
linked paper: Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
linked paper: Analyzing gene expression data in mice with the Neuro Behavior Ontology
linked paper: Enriched biodiversity data as a resource and service
linked paper: Ontology based mining of pathogen-disease associations from literature
linked paper: Ontology-Based Concept Recognition by Using Word Embeddings
linked paper: A translational medicine approach to orphan diseases
linked paper: Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
linked paper: Datamining with Ontologies
linked paper: The informatics of developmental phenotypes
linked person: Robert Hoehndorf
linked person: Sarah Alghamdi
linked person: Sumyyah Toonsi
linked person: Sara Althubaiti
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Yang Liu
linked course: Application of AI in Bioinformatics
linked course: Algorithms in Bioinformatics
linked course: Data Analytics

Phenotype informatics
weight: 31
weight: 1
weight: 3
weight: 4
type: Topic
short name: Phenotype informatics
section: Applications
abstract: 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.
keyword: phenotype ontology
keyword: HPO
keyword: MP
keyword: FLOPO
keyword: phenotype standardisation
keyword: trait recognition
keyword: PhenomeNET
keyword: cross-species phenotypes
linked paper: DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
linked paper: Contribution of model organism phenotypes to the computational identification of human disease genes
linked paper: CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
linked paper: Best behaviour? Ontologies and the formal description of animal behaviour
linked paper: Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
linked paper: Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
linked paper: DermO; an ontology for the description of dermatologic disease
linked paper: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
linked paper: Nail abnormalities identified in an ageing study of 30 inbred mouse strains
linked paper: An ontology approach to comparative phenomics in plants
linked paper: The anatomy of phenotype ontologies: principles, properties and applications
linked paper: Ontology-based validation and identification of regulatory phenotypes
linked paper: Multi-faceted semantic clustering with text-derived phenotypes
linked paper: Improved characterisation of clinical text through ontology-based vocabulary expansion
linked paper: Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
linked paper: Interoperability between phenotype and anatomy ontologies
linked paper: PhenomeNET: a whole-phenome approach to disease gene discovery
linked paper: New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
linked paper: Mouse genetic and phenotypic resources for human genetics
linked paper: Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
linked paper: Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
linked paper: Towards improving phenotype representation in OWL
linked paper: Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
linked paper: Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
linked paper: Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
linked paper: Integrating phenotype ontologies with PhenomeNET
linked paper: Phenotype-driven discovery of digenic variants in personal genome sequences
linked paper: Towards Improving Phenotype Representation in OWL
linked paper: The informatics of developmental phenotypes
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sarah Alghamdi
linked person: Sumyyah Toonsi
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Miguel Angel Rodriguez Garcia

Genomics
weight: 26
weight: 2
weight: 3
weight: 6
weight: 1
weight: 7
type: Topic
short name: Genomics
section: Applications
abstract: 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.
keyword: Saudi pangenome
keyword: reference genome
keyword: pangenome graph
keyword: variant calling
keyword: structural variant
keyword: whole-genome sequencing
keyword: GWAS
keyword: population genomics
linked paper: The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
linked paper: Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
linked paper: What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
linked paper: DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
linked paper: GFVO: the Genomic Feature and Variation Ontology
linked paper: Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
linked paper: VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
linked paper: Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
linked paper: A reference quality, fully annotated diploid genome from a Saudi individual
linked paper: Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
linked paper: Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
linked paper: OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
linked paper: Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
linked paper: EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
linked paper: Phenotype-driven discovery of digenic variants in personal genome sequences
linked paper: Annotating genomes with DeepGO protein function prediction tools
linked project: A public Saudi pangenome as reference for genomics in the Middle East
linked project: Enabling mangrove restoration by AI-tailored microbiome fortification
linked project: Evolutionary potential of corals to adapt to climate warming
linked project: Sequencing and computational analysis of MRSA samples
linked project: The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
linked person: Robert Hoehndorf
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Yang Liu
linked person: Xi Peng
linked person: Rund Tawfiq
linked person: Kexin Niu
linked person: Malak Althagafi
linked person: Heribert Hirt
linked person: Takashi Gojobori
linked person: Manuel Aranda
linked person: Mohammed Al Fageeh
linked person: Vladimir Bajic
linked person: Michael Berumen
linked course: Algorithms in Bioinformatics

Drug mechanisms and systems biology
weight: 21
weight: 1
type: Topic
short name: Drug mechanisms
section: Applications
abstract: 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.
keyword: drug-target interaction
keyword: DTI-Voodoo
keyword: drug repurposing
keyword: PharmGKB
keyword: SBML Harvester
keyword: causal knowledge graph
keyword: adverse drug reaction
keyword: systems biology
linked paper: DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
linked paper: DDIEM: drug database for inborn errors of metabolism
linked paper: Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
linked paper: LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
linked paper: Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
linked paper: Ranking Adverse Drug Reactions With Crowdsourcing
linked paper: DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
linked paper: Similarity-based search of model organism, disease and drug effect phenotypes
linked paper: Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
linked paper: Causal knowledge graph analysis identifies adverse drug effects
linked paper: Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
linked paper: Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
linked paper: Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
linked paper: Mouse model phenotypes provide information about human drug targets
linked paper: SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
linked paper: Integration of knowledge for personalized medicine: a pharmacogenomics case-study
linked paper: Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
linked project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
linked project: Data integration and ontologies for microbial cell factories
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sumyyah Toonsi
linked person: Maxat Kulmanov
linked person: Miguel Angel Rodriguez Garcia
linked person: Vladimir Bajic
linked person: Mahdi Bu Ali

Semantic similarity
weight: 21
weight: 2
weight: 1
weight: 6
type: Topic
short name: Semantic similarity
section: Methods (cross-cutting)
abstract: 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.
keyword: semantic similarity
keyword: ontology similarity
keyword: Resnik
keyword: Lin
keyword: phenotype similarity
keyword: PhenomeNET similarity
keyword: OPA2Vec
linked paper: Semantic similarity and machine learning with ontologies
linked paper: A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
linked paper: Contribution of model organism phenotypes to the computational identification of human disease genes
linked paper: Notions of similarity for systems biology models
linked paper: Similarity-based search of model organism, disease and drug effect phenotypes
linked paper: Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
linked paper: Evaluating the effect of annotation size on measures of semantic similarity
linked paper: OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
linked paper: Semantic prioritization of novel causative genomic variants
linked paper: Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
linked paper: Evaluating semantic similarity methods for comparison of text-derived phenotype profiles
linked paper: PhenomeNET: a whole-phenome approach to disease gene discovery
linked paper: Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
linked project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
linked project: CompleX: Variant Prioritization in Complex Disease
linked project: Bio2Vec: Smart analytics infrastructure for the life sciences
linked person: Robert Hoehndorf
linked person: Mona Alshahrani
linked person: Sarah Alghamdi
linked person: Sumyyah Toonsi
linked person: Sara Althubaiti
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Azza Althagafi
linked person: Tengwei Song
linked person: Paul N Schofield
linked person: Georgios V Gkoutos
linked person: Xin Gao
linked person: Michel Dumontier
linked person: Jens Lehmann
linked person: Fernando Zhapa-Camacho
linked person: Abeer Almutairi
linked person: Hatoon Al Ali
linked person: Safana Bakheet
linked person: Mahdi Bu Ali
linked person: Ashraf Kibraya

Protein function prediction
weight: 19
weight: 2
weight: 4
weight: 1
weight: 3
weight: 12
type: Topic
short name: Protein function
section: Applications
abstract: 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.
keyword: Gene Ontology
keyword: GO
keyword: DeepGO
keyword: DeepGOPlus
keyword: DeepGO-SE
keyword: DeepGOZero
keyword: protein function
keyword: semantic entailment
keyword: metagenomics function
linked paper: Predicting protein functions using positive-unlabeled ranking with ontology-based priors
linked paper: DeepGOPlus: improved protein function prediction from sequence
linked paper: Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
linked paper: The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
linked paper: DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
linked paper: DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
linked paper: DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
linked paper: DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
linked paper: LLM Agent Based Protein Function Prediction
linked paper: Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
linked paper: Exploring Gene Ontology Annotations with OWL
linked paper: Computational prediction of protein functional annotations
linked paper: Annotating genomes with DeepGO protein function prediction tools
linked project: Enabling desert revegetation by AI-tailored soil microbiome fortification
linked project: Evolutionary potential of corals to adapt to climate warming
linked project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
linked person: Robert Hoehndorf
linked person: Maxat Kulmanov
linked person: Imane Boudellioua
linked person: Zhenwei Tang
linked person: Yang Liu
linked person: Rund Tawfiq
linked person: Kexin Niu
linked person: Heribert Hirt
linked person: Gabriel Wittum
linked person: Arne Nägel
linked person: Takashi Gojobori
linked person: Manuel Aranda
linked person: Daulet Toibazar
linked person: Amal Alhelal
linked person: Md Nurul Muttakin
linked person: Shahad Qatan
linked person: Asaad Mohammedsaleh
linked course: Application of AI in Bioinformatics
linked course: Algorithms in Bioinformatics

Metagenomics and microbial community function
weight: 16
weight: 3
weight: 1
weight: 2
type: Topic
short name: Microbial communities
section: Applications
abstract: 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.
keyword: metagenomics
keyword: microbial communities
keyword: DeepGOMeta
keyword: soil microbiome
keyword: marine microbiome
keyword: extremophile
keyword: functional metagenomics
linked paper: In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
linked paper: In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
linked paper: DESM: portal for microbial knowledge exploration systems
linked paper: DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
linked project: Enabling desert revegetation by AI-tailored soil microbiome fortification
linked project: Enabling mangrove restoration by AI-tailored microbiome fortification
linked project: Metagenomics-based surface prospecting
linked project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
linked project: Sequencing and computational analysis of MRSA samples
linked project: Data integration and ontologies for microbial cell factories
linked person: Robert Hoehndorf
linked person: Maxat Kulmanov
linked person: Miguel Angel Rodriguez Garcia
linked person: Rund Tawfiq
linked person: Kexin Niu
linked person: Heribert Hirt
linked person: Gabriel Wittum
linked person: Arne Nägel
linked person: Takashi Gojobori
linked person: Mohammed Al Fageeh
linked person: Vladimir Bajic
linked person: Daulet Toibazar
linked person: Amal Alhelal
linked person: Md Nurul Muttakin
linked person: Shahad Qatan
linked person: Asaad Mohammedsaleh

Bioengineering
weight: 7
weight: 2
weight: 1
type: Topic
short name: Bioengineering
section: Applications
abstract: 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.
keyword: bioengineering
keyword: biomimetic scaffold
keyword: patient-derived disease model
keyword: multi-omics
keyword: tissue engineering
keyword: transcriptomics
keyword: metabolomics
linked paper: The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
linked paper: Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
linked paper: Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
linked paper: Age-related differences in gene expression and pathway activation following heatstroke
linked paper: Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
linked paper: Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
linked paper: Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
linked person: Robert Hoehndorf
linked person: Maxat Kulmanov
linked person: Yang Liu
linked course: Foundations of Bioengineering

PropertyValue
property ID: ORCID
value: https://orcid.org/0000-0001-8149-5890

Maria G Gomez Castillo
type: Person
given name: Maria
family name: G Gomez Castillo
position: MSc (alumnus)
thesis title: Heatstroke multi-omics analysis
thesis file: maria-thesis/Thesis.pdf
thesis defense date: 2024-07-24
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
start year: 2022
end year: 2024

Melissa Rios Zertuche
type: Person
given name: Melissa
family name: Rios Zertuche
position: MSc (alumnus)
thesis title: Establishment and Evaluation of a Computational Workflow for the Design and Optimization of Nanobodies
thesis file: melissa-thesis/Thesis.pdf
thesis defense date: 2024-07-22
program: Bioscience
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/melissa-rios-zertuche
borg profile nid: 8343
start year: 2023
end year: 2024

Mohammad Ashhad
type: Person
given name: Mohammad
family name: Ashhad
position: MSc (alumnus)
thesis title: Machine Learning Methods for Survival Analysis: From Outcome-Conditioned Data Synthesis to Decoupled Ranking and Calibration
thesis file: ashhad-thesis/Thesis.tex
thesis defense date: 2026-05-03
program: Bioengineering
institution at BORG: KAUST
advisor: borg-id:person/robert-hoehndorf
borg profile URL: /profiles/mohammad-ashhad
borg profile nid: 8273
start year: 2025
end year: 2026
position: PhD (current)
program: Computer Science
from: KAUST MSc Bioengineering (defended 3 May 2026)
start year: 2026

mOWL
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/mowl
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)

EL Embeddings
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/el-embeddings
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

catE
type: SoftwareApplication
description: Category-theoretic, lattice-preserving embedding of ALC description-logic ontologies that retains the consequence-closure semantics of the original theory.
code repository: https://github.com/bio-ontology-research-group/catE
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

DELE
type: SoftwareApplication
description: Deductive EL embeddings: enrich training data with the deductive closure of an ontology before learning, so embeddings recover entailment rather than only asserted axioms.
code repository: https://github.com/bio-ontology-research-group/DELE
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

OPA2Vec
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/opa2vec
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease

Onto2Vec
type: SoftwareApplication
description: Representation learning for ontologies and their annotations by treating logical axioms as natural-language sentences; predecessor of OPA2Vec.
code repository: https://github.com/bio-ontology-research-group/onto2vec
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DL2Vec
type: SoftwareApplication
description: Encodes description-logic axioms as a directed graph and learns embeddings via random walks; widely used for downstream gene-disease and protein-function prediction.
code repository: https://github.com/bio-ontology-research-group/DL2Vec
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

Walking RDF and OWL
type: SoftwareApplication
description: Original feature-learning method over RDF graphs and OWL ontologies via biased random walks; the seed implementation for many later embedding methods including OWL2Vec*.
code repository: https://github.com/bio-ontology-research-group/walking-rdf-and-owl
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

EL2Box
type: SoftwareApplication
description: Box-shaped geometric embeddings for EL++ that strengthen the topological guarantees of EL Embeddings.
code repository: https://github.com/bio-ontology-research-group/EL2Box_embedding
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

Interpretable Learning
type: SoftwareApplication
description: Generates interpretable symbolic rules from learned representations over biomedical knowledge bases.
code repository: https://github.com/bio-ontology-research-group/interpretable-learning
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)

DeepGOPlus
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/deepgoplus
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DeepGO
type: SoftwareApplication
description: Original sequence-based, ontology-aware deep classifier for predicting Gene Ontology functional annotations; basis of the entire DeepGO family of tools.
code repository: https://github.com/bio-ontology-research-group/deepgo
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DeepGO2
type: SoftwareApplication
description: Next-generation DeepGO model with transformer protein embeddings and improved hierarchical multi-label prediction.
code repository: https://github.com/bio-ontology-research-group/deepgo2
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepGOZero
type: SoftwareApplication
description: Zero-shot extension of DeepGO using model-theoretic ELEmbeddings to predict GO classes that have never been observed during training.
code repository: https://github.com/bio-ontology-research-group/deepgozero
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepGOMeta
type: SoftwareApplication
description: DeepGO trained specifically for metagenomic communities; predicts functional roles of proteins recovered from environmental samples and links them to biogeochemical processes.
code repository: https://github.com/bio-ontology-research-group/deepgometa
from project: Enabling desert revegetation by AI-tailored soil microbiome fortification
from project: Enabling mangrove restoration by AI-tailored microbiome fortification

PU-GO
type: SoftwareApplication
description: Positive-unlabeled ranking of protein functions with ontology-based priors; directly addresses the partial-annotation problem in CAFA benchmarks.
code repository: https://github.com/bio-ontology-research-group/PU-GO
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepPheno
type: SoftwareApplication
description: Predicts loss-of-function organism-level phenotypes (HPO/MPO) directly from a gene's annotated functions, using a hierarchical neural classifier over phenotype ontologies.
code repository: https://github.com/bio-ontology-research-group/deeppheno
from project: CompleX: Variant Prioritization in Complex Disease

GO-Agent
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/go-agent
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)

PhenoGoCon
type: SoftwareApplication
description: Predicts gene–phenotype associations from predicted Gene Ontology functions; bridges GO function prediction and HPO/MPO phenotype prediction.
code repository: https://github.com/bio-ontology-research-group/phenogocon
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

Genomic Context
type: SoftwareApplication
description: Bacterial protein-function prediction that exploits operon and genome-neighbourhood structure in addition to sequence and homology.
code repository: https://github.com/bio-ontology-research-group/Genomic_context
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

AberOWL
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/AberOWL
from project: Data integration and ontologies for microbial cell factories

Onto2Graph
type: SoftwareApplication
description: Generates entailment-aware graph projections of OWL ontologies suitable for downstream graph machine learning while preserving the axioms' deductive structure.
code repository: https://github.com/bio-ontology-research-group/Onto2Graph
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

UNMIREOT
type: SoftwareApplication
description: Identifies, diagnoses, and semi-automatically repairs hidden contradictions and unsatisfiable classes introduced by partial imports (MIREOT) into biomedical ontologies.
code repository: https://github.com/bio-ontology-research-group/UNMIREOT
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

OntoFunc
type: SoftwareApplication
description: Ontology-driven enrichment analysis that supports arbitrary OWL ontologies and full subsumption-aware aggregation, not only GO.
code repository: https://github.com/bio-ontology-research-group/ontofunc
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

vec2SPARQL
type: SoftwareApplication
description: 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.
code repository: https://github.com/bio-ontology-research-group/vec2sparql
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

PhenomeNET-VP
type: SoftwareApplication
description: Phenotype-driven variant prioritization for whole-exome and whole-genome sequencing data; widely used implementation of the phenotype-aware variant ranking approach.
code repository: https://github.com/bio-ontology-research-group/phenomenet-vp
from project: CompleX: Variant Prioritization in Complex Disease
from project: Sequencing and computational analysis of MRSA samples

DeepSVP
type: SoftwareApplication
description: Prioritizes structural and copy-number variants by combining patient phenotype with gene-function similarity learned from biomedical ontologies.
code repository: https://github.com/bio-ontology-research-group/DeepSVP
from project: CompleX: Variant Prioritization in Complex Disease
from project: A public Saudi pangenome as reference for genomics in the Middle East

EmbedPVP
type: SoftwareApplication
description: Embedding-based phenotype-aware variant predictor that ranks candidate causative variants using joint sequence- and phenotype-derived representations.
code repository: https://github.com/bio-ontology-research-group/EmbedPVP
from project: CompleX: Variant Prioritization in Complex Disease

STARVar
type: SoftwareApplication
description: Symptom-based tool for automatic ranking of variants using evidence from the biomedical literature and population genomes; combines text mining with phenotype matching.
code repository: https://github.com/bio-ontology-research-group/STARVar
from project: CompleX: Variant Prioritization in Complex Disease

INDIGENA
type: SoftwareApplication
description: Inductive prediction of disease–gene associations from phenotype ontologies; generalises to unseen diseases via ontology-aware embeddings.
code repository: https://github.com/bio-ontology-research-group/indigena
from project: CompleX: Variant Prioritization in Complex Disease

GenomeLinter
type: SoftwareApplication
description: AI-powered clinical decision-support tool that ingests annotated VCFs and synthesises diagnostic interpretations for rare-disease patients without requiring deep bioinformatics expertise.
code repository: https://github.com/bio-ontology-research-group/genome-linter
from project: Improvement of genetic variant prioritization technology

predCAN
type: SoftwareApplication
description: Ontology-based prediction of cancer driver genes by integrating phenotype, pathway and function knowledge with somatic-variant features.
code repository: https://github.com/bio-ontology-research-group/predCAN
from project: CompleX: Variant Prioritization in Complex Disease

DeepViral
type: SoftwareApplication
description: Predicts virus–host protein-protein interactions from sequence and infectious-disease phenotypes; trained jointly across coronaviruses, influenza, and other RNA viruses.
code repository: https://github.com/bio-ontology-research-group/DeepViral
from project: CompleX: Variant Prioritization in Complex Disease

SmuDGE
type: SoftwareApplication
description: Semantic disease-gene embeddings; integrates phenotype, function and pathway ontologies into a unified vector space for downstream prediction.
code repository: https://github.com/bio-ontology-research-group/SMUDGE
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease

Multi-Drug Embedding
type: SoftwareApplication
description: Drug repurposing method that learns joint embeddings of drugs, targets and diseases from biomedical knowledge graphs and the scientific literature.
code repository: https://github.com/bio-ontology-research-group/multi-drug-embedding
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DeepMOCCA
type: SoftwareApplication
description: Graph neural network for cancer survival analysis that integrates multi-omics (mutation, expression, methylation, CNV) with a curated cancer knowledge graph.
code repository: https://github.com/bio-ontology-research-group/DeepMOCCA
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

PathoPhenoDB
type: SoftwareApplication
description: Curated database of pathogens and the disease phenotypes they cause, distributed as an OWL ontology and an interactive web application.
code repository: https://github.com/bio-ontology-research-group/pathophenodb
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

NanoDesigner
type: SoftwareApplication
description: Iterative refinement framework for nanobody/CDR design that explicitly models the antigen–CDR interdependence; companion code to the NanoDesigner paper.
code repository: https://github.com/bio-ontology-research-group/NanoDesigner
from project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications

Machine Learning with Ontologies
type: SoftwareApplication
description: Companion code and worked examples for the Briefings in Bioinformatics tutorial review; the most-starred repository in the group.
code repository: https://github.com/bio-ontology-research-group/machine-learning-with-ontologies
note: Educational/dissemination output (Machine Learning with Ontologies tutorial materials); not the deliverable of a single grant.

Ontology Tutorial
type: SoftwareApplication
description: Hands-on tutorial that walks new users through OWL, automated reasoning, and ontology-aware data analysis; basis for the AI in Biomedicine summer school.
code repository: https://github.com/bio-ontology-research-group/ontology-tutorial
note: Educational/dissemination output (ontology engineering tutorial); not the deliverable of a single grant.

mOWL Tutorial
type: SoftwareApplication
description: Step-by-step worked notebooks that demonstrate every embedding family in mOWL on protein-function, gene-disease, and ontology-completion tasks.
code repository: https://github.com/bio-ontology-research-group/mowl-tutorial
note: Educational/dissemination output (mOWL tutorial materials); not the deliverable of a single grant.

Units of Measurement Ontology (UO)
type: SoftwareApplication
description: OBO Foundry ontology of units of measurement; aligned with QUDT and used across biomedical data standards.
code repository: https://github.com/bio-ontology-research-group/unit-ontology
note: Community ontology contribution; not the deliverable of a single grant.

PhenomeNet
type: SoftwareApplication
description: Cross-species phenotype ontology and similarity network combining HPO, MPO, ZP and others; the substrate behind PhenomeNET-VP and DeepPheno.
code repository: https://github.com/bio-ontology-research-group/phenomeblast
from project: CompleX: Variant Prioritization in Complex Disease

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
type: ScholarlyArticle
acknowledges external grant: BB/J004464/1
date published: 2016
venue: Journal of Biomedical Semantics
bib key: Hoehndorf2016
bib type: article
author raw: Hoehndorf, Robert
author raw: Alshahrani, Mona
author raw: Gkoutos, Georgios V.
author raw: Gosline, George
author raw: Groom, Quentin
author raw: Hamann, Thomas
author raw: Kattge, Jens
author raw: de Oliveira, Sylvia Mota
author raw: Schmidt, Marco
author raw: Sierra, Soraya
author raw: Smets, Erik
author raw: Vos, Rutger A.
author raw: Weiland, Claus
author: Robert Hoehndorf
author: Mona Alshahrani
keyword: FLOPO
keyword: flora phenotype ontology
keyword: vascular plants
keyword: morphological traits
keyword: phenotype integration
keyword: ontology development
tag rationale: 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.
topic: Applied Ontology
topic: Phenotype informatics

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2019
venue: Scientific Reports
bib key: aging-ontologies
bib type: article
author raw: Sarah M. Alghamdi
author raw: Beth A. Sundberg
author raw: John P. Sundberg
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Sarah Alghamdi
author: Robert Hoehndorf
keyword: ontology design patterns
keyword: pathology ontology
keyword: anatomy ontology
keyword: ontology evaluation
keyword: OWL
tag rationale: This paper evaluates ontology design patterns for combining ontologies, which is a key aspect of applied ontology and ontology engineering.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
date published: 2023
venue: 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
bib key: DBLP:conf/icbo/ToonsiKH23
bib type: inproceedings
author raw: Sumyyah Toonsi
author raw: Senay Kafkas
author raw: Robert Hoehndorf
author: Sumyyah Toonsi
author: Robert Hoehndorf
keyword: named entity recognition
keyword: distant supervision
keyword: disease NER
keyword: phenotype NER
keyword: ICBO 2023
tag rationale: Uses ontology components for NER training; an Applied Ontology paper at ICBO.
topic: Applied Ontology

Ontology-based prediction of cancer driver genes
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease
acknowledges external grant: MR/M016587/1
date published: 2019
venue: Scientific Reports
bib key: Althubaiti561480
bib type: article
author raw: Althubaiti, Sara
author raw: Karwath, Andreas
author raw: Dallol, Ashraf
author raw: Noor, Adeeb
author raw: Alkhayyat, Shadi Salem
author raw: Alwassia, Rolina
author raw: Mineta, Katsuhiko
author raw: Gojobori, Takashi
author raw: Beggs, Andrew D
author raw: Schofield, Paul N
author raw: Gkoutos, Georgios V
author raw: Hoehndorf, Robert
author: Sara Althubaiti
author: Robert Hoehndorf
keyword: cancer driver genes
keyword: ontology-based prediction
keyword: gene prediction
keyword: semantic similarity
keyword: Human Phenotype Ontology
tag rationale: This paper uses ontologies for predicting cancer driver genes, which falls under applied ontology and biomedical informatics.
topic: Applied Ontology
topic: Biomedical informatics

Improving the classification of cardinality phenotypes using collections
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
date published: 2023
venue: Journal of Biomedical Semantics
bib key: Alghamdi2023
bib type: article
author raw: Sarah M. Alghamdi
author raw: Robert Hoehndorf
author: Sarah Alghamdi
author: Robert Hoehndorf
keyword: phenotype ontology
keyword: cardinality
keyword: ontology design pattern
keyword: HPO
keyword: phenotype representation
tag rationale: Applied ontology design pattern for cardinality in phenotypes.
topic: Applied Ontology

Combining lexical and context features for automatic ontology extension
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2020
venue: Journal of Biomedical Semantics
bib key: ontoextend
bib type: article
author raw: Sara Althubaiti
author raw: Senay Kafkas
author raw: Marwa Abdelhakim
author raw: Robert Hoehndorf
author: Sara Althubaiti
author: Robert Hoehndorf
keyword: automatic ontology extension
keyword: lexical features
keyword: context features
keyword: biomedical ontologies
keyword: text mining
keyword: ontology learning
tag rationale: This paper focuses on automatic ontology extension using lexical and context features, which is a method in ontology engineering and biomedical informatics.
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

DDIEM: drug database for inborn errors of metabolism
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Improving health of Saudi population
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: Data integration and ontologies for microbial cell factories
from project: Improving health of Saudi population
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease
date published: 2020
venue: Orphanet Journal of Rare Diseases
bib key: Abdelhakim2020
bib type: article
author raw: Marwa Abdelhakim
author raw: Eunice McMurray
author raw: Ali Raza Syed
author raw: Senay Kafkas
author raw: Allan Anthony Kamau
author raw: Paul N Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: DDIEM
keyword: drug database
keyword: inborn errors of metabolism
keyword: rare diseases
keyword: drug repurposing
tag rationale: This paper describes a drug database for inborn errors of metabolism, directly relevant to drug mechanisms and rare disease support.
topic: Drug mechanisms and systems biology
topic: Rare disease diagnostic support

DeepGOPlus: improved protein function prediction from sequence
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease
date published: 2020
venue: Bioinformatics
bib key: 10.1093/bioinformatics/btz595
bib type: article
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: protein function prediction
keyword: DeepGOPlus
keyword: sequence-based prediction
keyword: Gene Ontology
keyword: deep learning
tag rationale: This paper introduces DeepGOPlus for protein function prediction, a core area of my work, and uses deep learning with ontologies.
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics

Phenotype-driven discovery of digenic variants in personal genome sequences
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2017
venue: Proceedings of VarI-SIG
bib key: varisig2017
bib type: inproceedings
author raw: Imane Boudellioua
author raw: Maxat Kulmanov
author raw: Paul N Schofield
author raw: Georgios V Gkoutos
author raw: Robert Hoehndorf
author: Imane Boudellioua
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: phenotype-driven discovery
keyword: digenic variants
keyword: personal genome sequences
keyword: rare disease
keyword: variant prioritization
keyword: Human Phenotype Ontology
tag rationale: 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.
topic: Rare disease diagnostic support
topic: Genomics
topic: Phenotype informatics

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Improving health of Saudi population
acknowledges: Improvement of genetic variant prioritization technology
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Improving health of Saudi population
from project: Improvement of genetic variant prioritization technology
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2020
venue: Bioinformatics
bib key: 10754/631015
bib type: article
author raw: Smaili, Fatima Z.
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: formal axioms
keyword: biomedical ontologies
keyword: data analysis
keyword: ontology reasoning
keyword: OWL
tag rationale: This paper emphasizes the role of formal axioms in biomedical ontologies for data analysis, aligning with applied ontology and ontology engineering.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Klarigi: Characteristic explanations for semantic biomedical data
type: ScholarlyArticle
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: CompleX: Variant Prioritization in Complex Disease
acknowledges external grant: MR/S003991/1
date published: 2023
venue: Computers in Biology and Medicine
bib key: Slater2022
bib type: article
author raw: Luke T. Slater
author raw: John A. Williams
author raw: Paul N. Schofield
author raw: Sophie Russell
author raw: Samantha C. Pendleton
author raw: Andreas Karwath
author raw: Hilary Fanning
author raw: Simon Ball
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: explanation
keyword: characteristic explanation
keyword: semantic data
keyword: Klarigi
keyword: ontology analytics
tag rationale: Tool for explaining semantic biomedical data; infrastructure/engineering, not applied ontology proper.
topic: Ontology engineering and semantic interoperability

The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
date published: 2025
venue: Scientific Reports
bib key: Kafkas2025
bib type: article
author raw: Kafkas, Senay
author raw: Abdelhakim, Marwa
author raw: Althagafi, Azza
author raw: Toonsi, Sumyyah
author raw: Alghamdi, Malak
author raw: Schofield, Paul N.
author raw: Hoehndorf, Robert
author: Azza Althagafi
author: Sumyyah Toonsi
author: Robert Hoehndorf
keyword: Large Language Models
keyword: LLMs
keyword: phenotype-based prioritization
keyword: causative genes
keyword: rare disease
keyword: diagnostic support
tag rationale: This paper applies Large Language Models to phenotype-based gene prioritization for rare disease diagnosis.
topic: Rare disease diagnostic support
topic: Biomedical informatics

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
type: ScholarlyArticle
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: CompleX: Variant Prioritization in Complex Disease
date published: 2020
venue: BMC Medical Informatics and Decision Making
bib key: Slater2020
bib type: article
author raw: Luke T. Slater
author raw: Georgios V. Gkoutos
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: semantic interoperability
keyword: biomedical ontologies
keyword: contradiction detection
keyword: ontology repair
keyword: OWL
tag rationale: This paper addresses finding and repairing contradictions in biomedical ontologies to improve semantic interoperability, fitting both ontology engineering and applied ontology.
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Neuro-Symbolic AI in Life Sciences
type: ScholarlyArticle
acknowledges: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
date published: 2025
venue: Handbook on Neurosymbolic AI and Knowledge Graphs
bib key: Hoehndorf2025
bib type: inbook
author raw: Hoehndorf, Robert
author raw: Pesquita, Catia
author raw: Zhapa-Camacho, Fernando
author: Robert Hoehndorf
keyword: neuro-symbolic AI
keyword: life sciences
keyword: knowledge graphs
keyword: symbolic reasoning
keyword: machine learning
tag rationale: The title directly indicates a focus on Neuro-Symbolic AI in Life Sciences, which is a primary topic.
topic: Neuro-symbolic methods in Bioinformatics

Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: Enabling desert revegetation by AI-tailored soil microbiome fortification
acknowledges: A public Saudi pangenome as reference for genomics in the Middle East
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: Enabling desert revegetation by AI-tailored soil microbiome fortification
from project: A public Saudi pangenome as reference for genomics in the Middle East
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
date published: 2024
venue: Neural-Symbolic Learning and Reasoning
bib key: Ghunaim2024
bib type: inbook
author raw: Ghunaim, Yasir
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: molecular property prediction
keyword: knowledge integration
keyword: NeSy
keyword: ontology
keyword: background knowledge
tag rationale: Large-scale knowledge integration into ML for molecular property prediction; this is neuro-symbolic.
topic: Neuro-symbolic methods in Bioinformatics

Ontology Embedding: A Survey of Methods, Applications and Resources
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: Enabling desert revegetation by AI-tailored soil microbiome fortification
acknowledges: A public Saudi pangenome as reference for genomics in the Middle East
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
acknowledges: Evolutionary potential of corals to adapt to climate warming
acknowledges: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: Enabling desert revegetation by AI-tailored soil microbiome fortification
from project: A public Saudi pangenome as reference for genomics in the Middle East
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Evolutionary potential of corals to adapt to climate warming
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
acknowledges external grant: EP/S019111/1
acknowledges external grant: EP/V050869/1
acknowledges external grant: EP/Y017706/1
date published: 2025
venue: IEEE Transactions on Knowledge and Data Engineering
bib key: Chen2025
bib type: article
author raw: Chen, Jiaoyan
author raw: Mashkova, Olga
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author raw: He, Yuan
author raw: Horrocks, Ian
author: Robert Hoehndorf
keyword: ontology embeddings
keyword: survey
keyword: description logic
keyword: knowledge graph embedding
keyword: machine learning with ontologies
tag rationale: A survey of ontology-embedding methods — the core neuro-symbolic contribution. Not Applied Ontology.
topic: Neuro-symbolic methods in Bioinformatics

Ontology based mining of pathogen--disease associations from literature
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2019
venue: Journal of Biomedical Semantics
bib key: padimi2019
bib type: article
author raw: Senay Kafkas
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: pathogen-disease associations
keyword: literature mining
keyword: ontology-based mining
keyword: infectious disease
keyword: text mining
tag rationale: This paper focuses on text mining for pathogen-disease associations using ontologies, aligning with biomedical informatics and applied ontology.
topic: Biomedical informatics
topic: Applied Ontology

PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease
date published: 2019
venue: Scientific Data
bib key: pathophenodb
bib type: article
author raw: Kafkas, Senay
author raw: Abdelhakim, Marwa
author raw: Hashish, Yasmeen
author raw: Kulmanov, Maxat
author raw: Abdellatif, Marwa
author raw: Schofield, Paul N
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: PathoPhenoDB
keyword: pathogen-disease phenotypes
keyword: infectious disease research
keyword: biomedical knowledge base
keyword: phenotype data
tag rationale: This paper describes a biomedical knowledge base linking pathogens to disease phenotypes, supporting infectious disease research and rare disease diagnostics.
topic: Biomedical informatics
topic: Rare disease diagnostic support

Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: CompleX: Variant Prioritization in Complex Disease
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Data integration and ontologies for microbial cell factories
from project: CompleX: Variant Prioritization in Complex Disease
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
date published: 2022
venue: Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022
bib key: Syed2022UsingST
bib type: inproceedings
author raw: Ali Syed
author raw: Senay Kafkas
author raw: Maxat Kulmanov
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: SPARQL
keyword: PhenomeBrowser
keyword: unified queries
keyword: machine learning model query
keyword: knowledge base
tag rationale: Uniform SPARQL access over data + ontologies + ML; ontology engineering with an applied-ontology slant.
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Integrating phenotype ontologies with PhenomeNET
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
from project: Data integration and ontologies for microbial cell factories
acknowledges external grant: BB/J004464/1
date published: 2016
venue: Proceedings of Ontology Matching Workshop 2016
bib key: Miguel2016
bib type: inproceedings
author raw: Miguel Rodriguez-Garcia
author raw: Georgios V. Gkoutos
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Miguel Angel Rodriguez Garcia
author: Robert Hoehndorf
keyword: PhenomeNET
keyword: phenotype ontologies
keyword: ontology integration
keyword: disease diagnosis
keyword: semantic similarity
tag rationale: The paper describes integrating phenotype ontologies with PhenomeNET, a system used for rare disease diagnostic support and phenotype analysis.
topic: Rare disease diagnostic support
topic: Phenotype informatics

Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
type: ScholarlyArticle
acknowledges: Development of Algorithms for Biotechnology and Biomedical Applications
acknowledges: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
acknowledges: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
from project: Development of Algorithms for Biotechnology and Biomedical Applications
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions
date published: 2023
venue: BMC Bioinformatics
bib key: Kafkas2023
bib type: article
author raw: Senay Kafkas
author raw: Marwa Abdelhakim
author raw: Mahmut Uludag
author raw: Azza Althagafi
author raw: Malak Alghamdi
author raw: Robert Hoehndorf
author: Azza Althagafi
author: Robert Hoehndorf
keyword: Starvar
keyword: symptom-based ranking
keyword: variant prioritization
keyword: literature evidence
keyword: genomic evidence
keyword: rare disease
tag rationale: This paper describes Starvar, a tool for symptom-based variant prioritization in rare diseases, integrating evidence from literature and genomes.
topic: Rare disease diagnostic support
topic: Biomedical informatics

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2019
venue: Database
bib key: database2019
bib type: article
author raw: Kafkas, Senay
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: ontology-based text mining
keyword: gene-phenotype associations
keyword: candidate gene prediction
keyword: biomedical literature
keyword: Human Phenotype Ontology
tag rationale: 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.
topic: Biomedical informatics
topic: Rare disease diagnostic support

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
type: ScholarlyArticle
acknowledges: Data integration and ontologies for microbial cell factories
acknowledges: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
date published: 2018
venue: Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018.
bib key: vec2sparql
bib type: inproceedings
author raw: Maxat Kulmanov
author raw: Senay Kafkas
author raw: Andreas Karwath
author raw: Alexander Malic
author raw: Georgios V. Gkoutos
author raw: Michel Dumontier
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: Vec2SPARQL
keyword: SPARQL queries
keyword: knowledge graph embeddings
keyword: semantic web
keyword: data integration
tag rationale: 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.
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability

Improved characterisation of clinical text through ontology-based vocabulary expansion
type: ScholarlyArticle
acknowledges: CompleX: Variant Prioritization in Complex Disease
from project: CompleX: Variant Prioritization in Complex Disease
date published: 2021
venue: Journal of Biomedical Semantics
bib key: Slater2021b
bib type: article
author raw: Luke T. Slater
author raw: William Bradlow
author raw: Simon Ball
author raw: Robert Hoehndorf
author raw: Georgios V Gkoutos
author: Robert Hoehndorf
keyword: clinical text characterisation
keyword: ontology-based vocabulary expansion
keyword: biomedical NLP
keyword: text mining
keyword: phenotype extraction
tag rationale: This paper improves clinical text characterization using ontology-based vocabulary expansion, aligning with biomedical informatics and phenotype informatics.
topic: Biomedical informatics
topic: Phenotype informatics

Semantic similarity and machine learning with ontologies
type: ScholarlyArticle
date published: 2020
venue: Briefings in Bioinformatics
bib key: 10.1093/bib/bbaa199
bib type: article
author raw: Kulmanov, Maxat
author raw: Smaili, Fatima Zohra
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: semantic similarity
keyword: ontology embeddings
keyword: machine learning
keyword: biomedical ontologies
keyword: Resnik
keyword: Lin
tag rationale: This paper focuses on semantic similarity measures, their application with machine learning, and the use of ontology embeddings.
topic: Semantic similarity
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
type: ScholarlyArticle
date published: 2021
venue: Bioinformatics
bib key: 10.1093/bioinformatics/btab147
bib type: article
author raw: Liu-Wei, Wang
author raw: Kafkas, Senay
author raw: Chen, Jun
author raw: Dimonaco, Nicholas J
author raw: Tegner, Jesper
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: virus-host interactions
keyword: protein sequences
keyword: infectious disease phenotypes
keyword: DeepViral
keyword: prediction
tag rationale: This paper describes a prediction system for virus-host interactions, which falls under drug mechanisms and systems biology, and general biomedical informatics.
topic: Drug mechanisms and systems biology
topic: Biomedical informatics

Predicting protein functions using positive-unlabeled ranking with ontology-based priors
type: ScholarlyArticle
date published: 2024
venue: Bioinformatics
bib key: 10.1093/bioinformatics/btae237
bib type: article
author raw: Zhapa-Camacho, Fernando
author raw: Tang, Zhenwei
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Zhenwei Tang
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: protein function prediction
keyword: positive-unlabeled learning
keyword: PU ranking
keyword: ontology priors
keyword: Gene Ontology
tag rationale: Protein function prediction is the application; using ontology axioms as PU priors makes it neuro-symbolic.
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
type: ScholarlyArticle
date published: 2019
venue: F1000Research
bib key: 10.12688
bib type: article
author raw: Katayama, T
author raw: Kawashima, S
author raw: Micklem, G
author raw: Kawano, S
author raw: Kim, JD
author raw: Kocbek, S
author raw: Okamoto, S
author raw: Wang, Y
author raw: Wu, H
author raw: Yamaguchi, A
author raw: Yamamoto, Y
author raw: Antezana, E
author raw: Aoki-Kinoshita, KF
author raw: Arakawa, K
author raw: Banno, M
author raw: Baran, J
author raw: Bolleman, JT
author raw: Bonnal, RJP
author raw: Bono, H
author raw: Fernandez-Breis, JT
author raw: Buels, R
author raw: Campbell, MP
author raw: Chiba, H
author raw: Cock, PJA
author raw: Cohen, KB
author raw: Dumontier, M
author raw: Fujisawa, T
author raw: Fujiwara, T
author raw: Garcia, L
author raw: Gaudet, P
author raw: Hattori, E
author raw: Hoehndorf, R
author raw: Itaya, K
author raw: Ito, M
author raw: Jamieson, D
author raw: Jupp, S
author raw: Juty, N
author raw: Kalderimis, A
author raw: Kato, F
author raw: Kawaji, H
author raw: Kawashima, T
author raw: Kinjo, AR
author raw: Komiyama, Y
author raw: Kotera, M
author raw: Kushida, T
author raw: Malone, J
author raw: Matsubara, M
author raw: Mizuno, S
author raw: Mizutani, S
author raw: Mori, H
author raw: Moriya, Y
author raw: Murakami, K
author raw: Nakazato, T
author raw: Nishide, H
author raw: Nishimura, Y
author raw: Ogishima, S
author raw: Ohta, T
author raw: Okuda, S
author raw: Ono, H
author raw: Perez-Riverol, Y
author raw: Shinmachi, D
author raw: Splendiani, A
author raw: Strozzi, F
author raw: Suzuki, S
author raw: Takehara, J
author raw: Thompson, M
author raw: Tokimatsu, T
author raw: Uchiyama, I
author raw: Verspoor, K
author raw: Wilkinson, MD
author raw: Wimalaratne, S
author raw: Yamada, I
author raw: Yamamoto, N
author raw: Yarimizu, M

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
type: ScholarlyArticle
date published: 2020
venue: PLOS Computational Biology
bib key: 10.1371/journal.pcbi.1008453
bib type: article
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DeepPheno
keyword: gene loss-of-function
keyword: phenotype prediction
keyword: ontology-aware classifier
keyword: Human Phenotype Ontology
tag rationale: This paper focuses on predicting gene loss-of-function phenotypes using an ontology-aware classifier, directly supporting rare disease diagnostics and phenotype informatics.
topic: Rare disease diagnostic support
topic: Phenotype informatics
topic: Neuro-symbolic methods in Bioinformatics

A Machine Learning Based Approach for Similarity Search on Biodiversity Knowledge Graphs
type: ScholarlyArticle
date published: 2019
venue: Biodiversity Information Science and Standards
bib key: 10.3897/biss.3.37048
bib type: article
author raw: Claus Weiland
author raw: Maxat Kulmanov
author raw: Marco Schmidt
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: machine learning
keyword: similarity search
keyword: biodiversity knowledge graphs
keyword: ontology embeddings
keyword: semantic similarity
tag rationale: This paper applies machine learning for similarity search on knowledge graphs, using semantic similarity and implicitly ontology embeddings.
topic: Semantic similarity
topic: Neuro-symbolic methods in Bioinformatics

The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds
type: ScholarlyArticle
date published: 2023
venue: ACS Nano
bib key: Abdelrahman2023
bib type: article
author raw: Sherin Abdelrahman
author raw: Rui Ge
author raw: Hepi H. Susapto
author raw: Yang Liu
author raw: Faris Samkari
author raw: Manola Moretti
author raw: Xinzhi Liu
author raw: Robert Hoehndorf
author raw: Abdul-Hamid Emwas
author raw: Mariusz Jaremko
author raw: Ranim H. Rawas
author raw: Charlotte A. E. Hauser
author: Yang Liu
author: Robert Hoehndorf
keyword: mechanotransduction
keyword: metabolomics
keyword: transcriptomics
keyword: human dermal fibroblasts
keyword: peptide scaffolds
keyword: tissue engineering
tag rationale: This paper analyzes transcriptomic and metabolomic responses in a bioengineering context, fitting bioengineering and genomics.
topic: Bioengineering
topic: Genomics

Aber-OWL: a framework for ontology-based data access in biology
type: ScholarlyArticle
date published: 2015
venue: BMC Bioinformatics
bib key: aberowl
bib type: article
author raw: Robert Hoehndorf
author raw: Luke Slater
author raw: Paul N Schofield
author raw: Georgios V Gkoutos
author: Robert Hoehndorf
keyword: AberOWL
keyword: ontology-based data access
keyword: biomedical ontologies
keyword: Semantic Web
keyword: OWL
tag rationale: This paper introduces AberOWL, a framework for ontology-based data access, which is a core component of ontology engineering and biomedical informatics infrastructure.
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
type: ScholarlyArticle
date published: 2025
venue: Microbial Genomics
bib key: Alarawi2025
bib type: article
author raw: Alarawi, Mohammed S.
author raw: Altammami, Musaad
author raw: Abutarboush, Mohammed
author raw: Kulmanov, Maxat
author raw: Alkuraithy, Dalal M.
author raw: Kafkas, Senay
author raw: Radley, Robert
author raw: Abdelhakim, Marwa
author raw: Aldakhil, Hind
author raw: Bawazeer, Reema A.
author raw: Alolayan, Mohammed A.
author raw: Alnafjan, Basel M.
author raw: Huraysi, Abdulaziz A.
author raw: Almaabadi, Amani
author raw: Suliman, Bandar A.
author raw: Aljohani, Areej G.
author raw: Hemeg, Hassan A.
author raw: Almogbel, Mohammed S.
author raw: Alazmi, Meshari
author raw: Bazaid, Abdulrahman S.
author raw: Abujamel, Turki S.
author raw: Hashem, Anwar M.
author raw: Al-Zahrani, Ibrahim A.
author raw: Abdoh, Mohammed S.
author raw: Hobani, Haya I.
author raw: Felemban, Rakan F.
author raw: Alhazmi, Wafaa A.
author raw: Hong, Pei-Ying
author raw: Alghoribi, Majed F.
author raw: Aljohani, Sameera
author raw: Balkhy, Hanan
author raw: Alswaji, Abdulrahman
author raw: Alzayer, Maha
author raw: Alalwan, Bassam
author raw: Kaaki, Mai M.
author raw: Hala, Sharif M.
author raw: Fallatah, Omniya Ahmad
author raw: Bahitham, Wesam
author raw: Zakri, Samer
author raw: Alshehri, Mohammad A.
author raw: Kameli, Nader
author raw: Algaissi, Abdullah
author raw: Alamer, Edrous
author raw: Alhazmi, Abdulaziz
author raw: Shajri, Amjad A.
author raw: Darraj, Majid Ahmed
author raw: Kameli, Bandar
author raw: Sufyani, O. O.
author raw: Rahama, Badreldin S.
author raw: Bakr, Abrar A.
author raw: Alhoshani, Fahad M.
author raw: Alquait, Azzam A.
author raw: Somily, Ali M.
author raw: Albarrag, Ahmed M.
author raw: Alosaimi, Lamia
author raw: Aldakeel, Sumayh A.
author raw: Bahwerth, Fayez S.
author raw: Khan, Mushtaq A.
author raw: Abdelrahman, Tamir T.
author raw: Fanning, Seamus
author raw: Tawfik, Essam A.
author raw: Alyamani, Essam J.
author raw: Gojobori, Takashi
author raw: Miyazaki, Satoru
author raw: Al-Fageeh, Mohammed B.
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: genomic diversity
keyword: antimicrobial resistance
keyword: Staphylococcus aureus
keyword: whole-genome sequencing
keyword: Saudi Arabia
tag rationale: 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
type: ScholarlyArticle
date published: 2020
venue: BMC Medical Genomics
bib key: Alfares2020
bib type: article
author raw: Ahmed Alfares
author raw: Lamia Alsubaie
author raw: Taghrid Aloraini
author raw: Aljoharah Alaskar
author raw: Azza Althagafi
author raw: Ahmed Alahmad
author raw: Mamoon Rashid
author raw: Abdulrahman Alswaid
author raw: Ali Alothaim
author raw: Wafaa Eyaid
author raw: Faroug Ababneh
author raw: Mohammed Albalwi
author raw: Raniah Alotaibi
author raw: Mashael Almutairi
author raw: Nouf Altharawi
author raw: Alhanouf Alsamer
author raw: Marwa Abdelhakim
author raw: Senay Kafkas
author raw: Katsuhiko Mineta
author raw: Nicole Cheung
author raw: Abdallah M. Abdallah
author raw: Stine B\"uchmann-M\oller
author raw: Yoshinori Fukasawa
author raw: Xiang Zhao
author raw: Issaac Rajan
author raw: Robert Hoehndorf
author raw: Fuad Al Mutairi
author raw: Takashi Gojobori
author raw: Majid Alfadhel
author: Azza Althagafi
author: Robert Hoehndorf
keyword: sequencing approach
keyword: consanguineous populations
keyword: variant calling
keyword: rare disease diagnosis
keyword: whole-exome sequencing
tag rationale: This paper discusses sequencing approaches for consanguineous populations, relevant to genomics and rare disease diagnosis.
topic: Genomics
topic: Rare disease diagnostic support

Contribution of model organism phenotypes to the computational identification of human disease genes
type: ScholarlyArticle
date published: 2022
venue: Disease Models \& Mechanisms
bib key: Alghamdi2022
bib type: article
author raw: Sarah Alghamdi
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Sarah Alghamdi
author: Robert Hoehndorf
keyword: model organism phenotypes
keyword: human disease genes
keyword: computational identification
keyword: phenotype similarity
keyword: Human Phenotype Ontology
tag rationale: 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.
topic: Rare disease diagnostic support
topic: Phenotype informatics
topic: Semantic similarity

Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications
type: ScholarlyArticle
date published: 2022
venue: PeerJ
bib key: Alshahrani2022
bib type: article
author raw: Mona Alshahrani
author raw: Abdullah Almansour
author raw: Asma Alkhaldi
author raw: Maha A. Thafar
author raw: Mahmut Uludag
author raw: Magbubah Essack
author raw: Robert Hoehndorf
author: Mona Alshahrani
author: Robert Hoehndorf
keyword: drug-target interaction
keyword: drug-indication
keyword: biomedical knowledge graph
keyword: text mining
keyword: DTI
tag rationale: Drug-target / drug-indication prediction by combining KG + text. Drug mechanisms with neuro-symbolic methods.
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics

Neuro-symbolic representation learning on biological knowledge graphs
type: ScholarlyArticle
date published: 2017
venue: Bioinformatics
bib key: alsharani17
bib type: article
author raw: Alshahrani, Mona
author raw: Khan, Mohammad Asif
author raw: Maddouri, Omar
author raw: Kinjo, Akira R.
author raw: Queralt-Rosinach, Nuria
author raw: Hoehndorf, Robert
author: Mona Alshahrani
author: Robert Hoehndorf
keyword: neuro-symbolic representation learning
keyword: biological knowledge graphs
keyword: ontology embeddings
keyword: Description Logics
keyword: EL++
tag rationale: This paper directly addresses neuro-symbolic representation learning on biological knowledge graphs, a core area of neuro-symbolic AI and ontology engineering.
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability

LEP-AD: language embedding of proteins and attention to drugs predicts drug-target interactions
type: ScholarlyArticle
date published: 2026
venue: Journal of Cheminformatics
bib key: Alsulami2026
bib type: article
author raw: Alsulami, Reem
author raw: Lehmann, Robert
author raw: Daga, Anuj
author raw: Khan, Sumeer A.
author raw: Gr\"unberg, Raik
author raw: Abogosh, Ahmed
author raw: Cabrero, David Gomez
author raw: Arold, Stefan T.
author raw: Hoehndorf, Robert
author raw: Tegner, Jesper
author raw: Kiani, Narsis A.
author: Robert Hoehndorf
keyword: protein language model
keyword: drug-target interaction
keyword: attention
keyword: protein embedding
tag rationale: LEP-AD predicts drug-target binding by combining protein language-model embeddings with attention over drugs — a drug-mechanisms application of representation learning.
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics

DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
type: ScholarlyArticle
date published: 2022
venue: Bioinformatics
bib key: Althagafi2021
bib type: article
author raw: Azza Althagafi
author raw: Lamia Alsubaie
author raw: Nagarajan Kathiresan
author raw: Katsuhiko Mineta
author raw: Taghrid Aloraini
author raw: Fuad Al Mutairi
author raw: Majid Alfadhel
author raw: Takashi Gojobori
author raw: Ahmad Alfares
author raw: Robert Hoehndorf
author: Azza Althagafi
author: Robert Hoehndorf
keyword: DeepSVP
keyword: structural variant prioritization
keyword: deep learning
keyword: genotype-phenotype integration
keyword: Human Phenotype Ontology
tag rationale: This paper focuses on prioritizing structural variants for rare disease diagnosis using deep learning and integrating genotype and phenotype data.
topic: Rare disease diagnostic support
topic: Genomics

Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
type: ScholarlyArticle
date published: 2024
venue: Bioinformatics
bib key: Althagafi2024
bib type: article
author raw: Althagafi, Azza
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Azza Althagafi
author: Robert Hoehndorf
keyword: variant prioritization
keyword: neuro-symbolic
keyword: knowledge-enhanced learning
keyword: PhenomeNET
keyword: deep learning
tag rationale: Variant prioritization for rare disease, leveraging neuro-symbolic methods. Dual-topic.
topic: Rare disease diagnostic support
topic: Neuro-symbolic methods in Bioinformatics

CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
type: ScholarlyArticle
date published: 2025
venue: Human Genetics
bib key: Aspromonte2025
bib type: article
author raw: Aspromonte, Maria Cristina
author raw: Del Conte, Alessio
author raw: Zhu, Shaowen
author raw: Tan, Wuwei
author raw: Shen, Yang
author raw: Zhang, Yexian
author raw: Li, Qi
author raw: Wang, Maggie Haitian
author raw: Babbi, Giulia
author raw: Bovo, Samuele
author raw: Martelli, Pier Luigi
author raw: Casadio, Rita
author raw: Althagafi, Azza
author raw: Toonsi, Sumyyah
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author raw: Katsonis, Panagiotis
author raw: Williams, Amanda
author raw: Lichtarge, Olivier
author raw: Xian, Su
author raw: Surento, Wesley
author raw: Pejaver, Vikas
author raw: Mooney, Sean D.
author raw: Sunderam, Uma
author raw: Srinivasan, Rajgopal
author raw: Murgia, Alessandra
author raw: Piovesan, Damiano
author raw: Tosatto, Silvio C. E.
author raw: Leonardi, Emanuela
author: Azza Althagafi
author: Sumyyah Toonsi
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: CAGI6 ID panel challenge
keyword: neurodevelopmental disorders
keyword: phenotype prediction
keyword: variant prediction
keyword: human genetics
tag rationale: This paper describes a challenge focused on phenotype and variant predictions for neurodevelopmental disorders, directly supporting rare disease diagnostics.
topic: Rare disease diagnostic support
topic: Phenotype informatics

GFVO: the Genomic Feature and Variation Ontology
type: ScholarlyArticle
date published: 2015
venue: PeerJ
bib key: Baran2015
bib type: article
author raw: Baran, Joachim
author raw: Durgahee, Bibi Sehnaaz Begum
author raw: Eilbeck, Karen
author raw: Antezana, Erick
author raw: Hoehndorf, Robert
author raw: Dumontier, Michel
author: Robert Hoehndorf
keyword: Genomic Feature and Variation Ontology
keyword: GFVO
keyword: genomic features
keyword: genetic variation
keyword: ontology development
tag rationale: This paper introduces a new ontology for genomic features and variation, fitting applied ontology and genomics.
topic: Applied Ontology
topic: Genomics

Best behaviour? Ontologies and the formal description of animal behaviour
type: ScholarlyArticle
date published: 2015
venue: Mammalian Genome
bib key: bestbehavior
bib type: article
author raw: Gkoutos, Georgios V
author raw: Hoehndorf, Robert
author raw: Tsaprouni, Loukia
author raw: Schofield, Paul N
author: Robert Hoehndorf
keyword: animal behavior
keyword: formal description
keyword: ontology
keyword: behavior ontology
keyword: phenotype standardization
tag rationale: This paper discusses the formal description of animal behavior using ontologies, aligning with applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation
type: ScholarlyArticle
date published: 2016
venue: Journal of Biomedical Semantics
bib key: Bolleman2016
bib type: article
author raw: Bolleman, Jerven T.
author raw: Mungall, Christopher J.
author raw: Strozzi, Francesco
author raw: Baran, Joachim
author raw: Dumontier, Michel
author raw: Bonnal, Raoul P. J.
author raw: Buels, Robert
author raw: Hoehndorf, Robert
author raw: Fujisawa, Takatomo
author raw: Katayama, Toshiaki
author raw: Cock, Peter A. J.
author: Robert Hoehndorf
keyword: FALDO
keyword: semantic standard
keyword: nucleotide feature annotation
keyword: protein feature annotation
keyword: ontology development
tag rationale: This paper introduces FALDO, a semantic standard for biological feature annotation, which is a clear example of applied ontology and semantic interoperability.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke
type: ScholarlyArticle
date published: 2025
venue: Journal of Applied Physiology
bib key: Bouchama2025
bib type: article
author raw: Bouchama, Abderrezak
author raw: Gomez, Maria
author raw: Abdullah, Mashan L.
author raw: Al Mahri, Saeed
author raw: Malik, Shuja Shafi
author raw: Yezli, Saber
author raw: Mohammad, Sameer
author raw: Lehe, Cynthia
author raw: Abuyassin, Bisher
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: whole genome transcriptomics
keyword: sex-specific responses
keyword: heat stroke
keyword: transcriptomic profiling
keyword: systems biology
tag rationale: This paper focuses on whole-genome transcriptomic profiling, which is a genomics method, and its application to physiological responses, linking to bioengineering.
topic: Genomics
topic: Bioengineering

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
type: ScholarlyArticle
date published: 2016
venue: PLoS ONE
bib key: Boudellioua2016
bib type: article
author raw: Boudellioua, Imane
author raw: Saidi, Rabie
author raw: Hoehndorf, Robert
author raw: Martin, Maria J.
author raw: Solovyev, Victor
author: Imane Boudellioua
author: Robert Hoehndorf
keyword: metabolic pathway prediction
keyword: prokaryotic UniProtKB
keyword: association rule mining
keyword: protein function
keyword: data mining
tag rationale: This paper describes predicting metabolic pathway involvement, which is a form of protein function prediction, using data mining techniques.
topic: Protein function prediction
topic: Biomedical informatics

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
type: ScholarlyArticle
date published: 2019
venue: Genome Biology
bib key: cafa3
bib type: article
author raw: Zhou, Naihui
author raw: Jiang, Yuxiang
author raw: Bergquist, Timothy R
author raw: Lee, Alexandra J
author raw: Kacsoh, Balint Z
author raw: Crocker, Alex W
author raw: Lewis, Kimberley A
author raw: Georghiou, George
author raw: Nguyen, Huy N
author raw: Hamid, Md Nafiz
author raw: Davis, Larry
author raw: Dogan, Tunca
author raw: Atalay, Volkan
author raw: Rifaioglu, Ahmet S
author raw: Dalkiran, Alperen
author raw: Cetin-Atalay, Rengul
author raw: Zhang, Chengxin
author raw: Hurto, Rebecca L
author raw: Freddolino, Peter L
author raw: Zhang, Yang
author raw: Bhat, Prajwal
author raw: Supek, Fran
author raw: Fern\'andez, Jos\'e M
author raw: Gemovic, Branislava
author raw: Perovic, Vladimir R
author raw: Davidovi\'c, Radoslav S
author raw: Sumonja, Neven
author raw: Veljkovic, Nevena
author raw: Asgari, Ehsaneddin
author raw: Mofrad, Mohammad RK
author raw: Profiti, Giuseppe
author raw: Savojardo, Castrense
author raw: Martelli, Pier Luigi
author raw: Casadio, Rita
author raw: Boecker, Florian
author raw: Kahanda, Indika
author raw: Thurlby, Natalie
author raw: McHardy, Alice C
author raw: Renaux, Alexandre
author raw: Saidi, Rabie
author raw: Gough, Julian
author raw: Freitas, Alex A
author raw: Antczak, Magdalena
author raw: Fabris, Fabio
author raw: Wass, Mark N
author raw: Hou, Jie
author raw: Cheng, Jianlin
author raw: Wang, Zheng
author raw: Romero, Alfonso E
author raw: Paccanaro, Alberto
author raw: Yang, Haixuan
author raw: Goldberg, Tatyana
author raw: Zhao, Chenguang
author raw: Holm, Liisa
author raw: T\"or\"onen, Petri
author raw: Medlar, Alan J
author raw: Zosa, Elaine
author raw: Borukhov, Itamar
author raw: Novikov, Ilya
author raw: Wilkins, Angela
author raw: Lichtarge, Olivier
author raw: Chi, Po-Han
author raw: Tseng, Wei-Cheng
author raw: Linial, Michal
author raw: Rose, Peter W
author raw: Dessimoz, Christophe
author raw: Vidulin, Vedrana
author raw: Dzeroski, Saso
author raw: Sillitoe, Ian
author raw: Das, Sayoni
author raw: Lees, Jonathan Gill
author raw: Jones, David T
author raw: Wan, Cen
author raw: Cozzetto, Domenico

An open source knowledge graph ecosystem for the life sciences
type: ScholarlyArticle
date published: 2024
venue: Scientific Data
bib key: Callahan2024
bib type: article
author raw: Callahan, Tiffany J.
author raw: Tripodi, Ignacio J.
author raw: Stefanski, Adrianne L.
author raw: Cappelletti, Luca
author raw: Taneja, Sanya B.
author raw: Wyrwa, Jordan M.
author raw: Casiraghi, Elena
author raw: Matentzoglu, Nicolas A.
author raw: Reese, Justin
author raw: Silverstein, Jonathan C.
author raw: Hoyt, Charles Tapley
author raw: Boyce, Richard D.
author raw: Malec, Scott A.
author raw: Unni, Deepak R.
author raw: Joachimiak, Marcin P.
author raw: Robinson, Peter N.
author raw: Mungall, Christopher J.
author raw: Cavalleri, Emanuele
author raw: Fontana, Tommaso
author raw: Valentini, Giorgio
author raw: Mesiti, Marco
author raw: Gillenwater, Lucas A.
author raw: Santangelo, Brook
author raw: Vasilevsky, Nicole A.
author raw: Hoehndorf, Robert
author raw: Bennett, Tellen D.
author raw: Ryan, Patrick B.
author raw: Hripcsak, George
author raw: Kahn, Michael G.
author raw: Bada, Michael
author raw: Baumgartner, William A.
author raw: Hunter, Lawrence E.
author: Robert Hoehndorf
keyword: knowledge graph
keyword: PheKnowLator
keyword: life sciences KG
keyword: open source
keyword: data integration
tag rationale: An ecosystem paper about KGs for the life sciences. Engineering infrastructure, not applied ontology.
topic: Ontology engineering and semantic interoperability

Predicting candidate genes from phenotypes, functions and anatomical site of expression
type: ScholarlyArticle
date published: 2021
venue: Bioinformatics
bib key: Chen2020
bib type: article
author raw: Jun Chen
author raw: Azza Althagafi
author raw: Robert Hoehndorf
author: Azza Althagafi
author: Robert Hoehndorf
keyword: candidate gene prediction
keyword: phenotypes
keyword: functions
keyword: anatomical site
keyword: disease gene prioritization
tag rationale: This paper focuses on predicting candidate genes from phenotypic and functional data, which is crucial for rare disease diagnosis.
topic: Rare disease diagnostic support
topic: Biomedical informatics

Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates
type: ScholarlyArticle
date published: 2026
venue: Communications Biology
bib key: Colombo2026
bib type: article
author raw: Colombo, Giovanni
author raw: Salem, Israa
author raw: Szczepski, Kacper
author raw: Yu, Piao
author raw: Alfaiyz, Shaden
author raw: Guzman-Vega, Francisco Javier
author raw: Abogosh, Ahmed
author raw: Kulmanov, Maxat
author raw: Al-Harthi, Samah
author raw: Kadare, Gress
author raw: Hoehndorf, Robert
author raw: Girault, Jean-Antoine
author raw: Jaremko, Łukasz
author raw: Momin, Afaque A.
author raw: Arold, Stefan T.
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: PYK2 coacervates
keyword: molecular basis
keyword: cellular effects
keyword: Janus-class
keyword: systems biology
tag rationale: This paper investigates the molecular and cellular mechanisms of PYK2 coacervates, which relates to understanding drug mechanisms and systems biology.
topic: Drug mechanisms and systems biology
topic: Bioengineering

Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
type: ScholarlyArticle
date published: 2019
venue: Veterinary Pathology
bib key: Cooper2019
bib type: article
author raw: Timothy K. Cooper
author raw: Kathleen A. Silva
author raw: Victoria E. Kennedy
author raw: Sarah M. Alghamdi
author raw: Robert Hoehndorf
author raw: Beth A. Sundberg
author raw: Paul N. Schofield
author raw: John P. Sundberg
author: Sarah Alghamdi
author: Robert Hoehndorf
keyword: hyaline arteriolosclerosis
keyword: aged inbred mice
keyword: phenotype analysis
keyword: mouse models
keyword: pathology
tag rationale: This paper describes the analysis of a specific phenotype in mouse models, aligning with phenotype informatics and biomedical informatics.
topic: Phenotype informatics
topic: Biomedical informatics

Data science and symbolic AI: Synergies, challenges and opportunities
type: ScholarlyArticle
date published: 2017
venue: Data Science
bib key: datascience
bib type: article
author raw: Hoehndorf, Robert
author raw: Queralt-Rosinach, Nuria
author: Robert Hoehndorf
keyword: data science
keyword: symbolic AI
keyword: synergies
keyword: challenges
keyword: opportunities
tag rationale: This paper explicitly discusses the intersection of data science and symbolic AI, which is the core of neuro-symbolic AI.
topic: Neuro-symbolic methods in Bioinformatics

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
type: ScholarlyArticle
date published: 2015
venue: Nature Genetics
bib key: deAngelis2015
bib type: article
author raw: Martin Hrab\ve de Angelis
author raw: George Nicholson
author raw: Mohammed Selloum
author raw: Jacqueline K White
author raw: Hugh Morgan
author raw: Ramiro Ramirez-Solis
author raw: Tania Sorg
author raw: Sara Wells
author raw: Helmut Fuchs
author raw: Martin Fray
author raw: David J Adams
author raw: Niels C Adams
author raw: Thure Adler
author raw: Antonio Aguilar-Pimentel
author raw: Dalila Ali-Hadji
author raw: Gregory Amann
author raw: Philippe Andr\'e
author raw: Sarah Atkins
author raw: Aurelie Auburtin
author raw: Abdel Ayadi
author raw: Julien Becker
author raw: Lore Becker
author raw: Elodie Bedu
author raw: Raffi Bekeredjian
author raw: Marie-Christine Birling
author raw: Andrew Blake
author raw: Joanna Bottomley
author raw: Michael R Bowl
author raw: V\'eronique Brault
author raw: Dirk H Busch
author raw: James N Bussell
author raw: Julia Calzada-Wack
author raw: Heather Cater
author raw: Marie-France Champy
author raw: Philippe Charles
author raw: Claire Chevalier
author raw: Francesco Chiani
author raw: Gemma F Codner
author raw: Roy Combe
author raw: Roger Cox
author raw: Emilie Dalloneau
author raw: Andr\'e Dierich
author raw: Armida Di Fenza
author raw: Brendan Doe
author raw: Arnaud Duchon
author raw: Oliver Eickelberg
author raw: Chris T Esapa
author raw: Lahcen El Fertak
author raw: Tanja Feigel
author raw: Irina Emelyanova
author raw: Jeanne Estabel
author raw: Jack Favor
author raw: Ann Flenniken
author raw: Alessia Gambadoro
author raw: Lilian Garrett
author raw: Hilary Gates
author raw: Anna-Karin Gerdin
author raw: George Gkoutos
author raw: Simon Greenaway
author raw: Lisa Glasl
author raw: Patrice Goetz
author raw: Isabelle Goncalves Da Cruz
author raw: Alexander G\"otz
author raw: Jochen Graw
author raw: Alain Guimond
author raw: Wolfgang Hans
author raw: Geoff Hicks
author raw: Sabine M H\"olter
author raw: Heinz H\"ofler
author raw: John M Hancock
author raw: Robert Hoehndorf
author raw: Tertius Hough
author raw: Richard Houghton
author raw: Anja Hurt

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
type: ScholarlyArticle
date published: 2017
venue: Bioinformatics
bib key: deepgo
bib type: article
author raw: Kulmanov, Maxat
author raw: Khan, Mohammed Asif
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DeepGO
keyword: protein function prediction
keyword: Gene Ontology
keyword: deep learning
keyword: ontology-aware classifier
tag rationale: This paper introduces DeepGO, a system for protein function prediction that uses deep learning and is aware of ontology structure.
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics

DeepPVP: phenotype-based prioritization of causative variants using deep learning
type: ScholarlyArticle
date published: 2019
venue: BMC Bioinformatics
bib key: deeppvp
bib type: article
author raw: Boudellioua, Imane
author raw: Kulmanov, Maxat
author raw: Schofield, Paul N
author raw: Gkoutos, Georgios V
author raw: Hoehndorf, Robert
author: Imane Boudellioua
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DeepPVP
keyword: variant prioritization
keyword: phenotype-based
keyword: deep learning
keyword: Human Phenotype Ontology
tag rationale: This paper describes DeepPVP, a deep learning approach for prioritizing causative variants based on patient phenotypes, relevant for rare disease diagnostics.
topic: Rare disease diagnostic support
topic: Neuro-symbolic methods in Bioinformatics

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
type: ScholarlyArticle
date published: 2017
venue: Scientific Reports
bib key: destomato
bib type: article
author raw: Salhi, Adil
author raw: Negrao, Sonia
author raw: Essack, Magbubah
author raw: Morton, Mitchell J. L.
author raw: Bougouffa, Salim
author raw: Mohamad Razali, Rozaimi
author raw: Radovanovic, Aleksandar
author raw: Marchand, Benoit
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author raw: Tester, Mark A.
author raw: Bajic, Vladimir B.
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DES-TOMATO
keyword: knowledge exploration system
keyword: tomato species
keyword: ontology-based data access
keyword: Semantic Web
tag rationale: This paper describes DES-TOMATO, a knowledge exploration system for tomato species, which involves applied ontology and semantic interoperability.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

DermO; an ontology for the description of dermatologic disease
type: ScholarlyArticle
date published: 2016
venue: Journal of Biomedical Semantics
bib key: Fisher2016
bib type: article
author raw: Fisher, Hannah M.
author raw: Hoehndorf, Robert
author raw: Bazelato, Bruno S.
author raw: Dadras, Soheil S.
author raw: King, Lloyd E.
author raw: Gkoutos, Georgios V.
author raw: Sundberg, John P.
author raw: Schofield, Paul N.
author: Robert Hoehndorf
keyword: DermO
keyword: dermatologic disease
keyword: ontology development
keyword: phenotype description
keyword: disease ontology
tag rationale: This paper focuses on the development of DermO, an ontology for dermatologic diseases, which falls under applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration
type: ScholarlyArticle
date published: 2018
venue: Science of Food
bib key: foodon
bib type: article
author raw: Damion M. Dooley
author raw: Emma J. Griffiths
author raw: Gurinder S. Gosal
author raw: Pier L. Buttigieg
author raw: Robert Hoehndorf
author raw: Matthew C. Lange
author raw: Lynn M. Schriml
author raw: Fiona S. L. Brinkman
author raw: William W. L. Hsiao
author: Robert Hoehndorf
keyword: FoodOn
keyword: food ontology
keyword: traceability
keyword: quality control
keyword: data integration
keyword: OWL
tag rationale: This paper introduces FoodOn, a harmonized food ontology designed for global food traceability and data integration, indicating both applied ontology and semantic interoperability.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Age-related differences in gene expression and pathway activation following heatstroke
type: ScholarlyArticle
date published: 2025
venue: Physiological Genomics
bib key: Gomez2025
bib type: article
author raw: Gomez, Maria
author raw: Al Mahri, Saeed
author raw: Abdullah, Mashan
author raw: Malik, Shuja Shafi
author raw: Yezli, Saber
author raw: Yassin, Yara
author raw: Khan, Anas
author raw: Lehe, Cynthia
author raw: Mohammad, Sameer
author raw: Hoehndorf, Robert
author raw: Bouchama, Abderrezak
author: Robert Hoehndorf
keyword: gene expression
keyword: pathway activation
keyword: heatstroke
keyword: age-related differences
keyword: transcriptomics
keyword: systems biology
tag rationale: This paper analyzes gene expression and pathway activation in response to heatstroke, which is a biomedical informatics application with bioengineering relevance.
topic: Biomedical informatics
topic: Bioengineering

Ranking Adverse Drug Reactions With Crowdsourcing
type: ScholarlyArticle
date published: 2015
venue: J Med Internet Res
bib key: Gottlieb2015
bib type: article
author raw: Gottlieb, Assaf
author raw: Hoehndorf, Robert
author raw: Dumontier, Michel
author raw: Altman, B. Russ
author: Robert Hoehndorf
keyword: adverse drug reactions
keyword: crowdsourcing
keyword: drug safety
keyword: pharmacovigilance
keyword: drug mechanisms
tag rationale: This paper focuses on ranking adverse drug reactions using crowdsourcing, which is relevant to drug mechanisms and biomedical informatics.
topic: Drug mechanisms and systems biology
topic: Biomedical informatics

VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
type: ScholarlyArticle
date published: 2026
venue: Journal of Biological Chemistry
bib key: GuzmnVega2026
bib type: article
author raw: Guzman-Vega, Francisco J.
author raw: Cardona-Londono, Kelly J.
author raw: Gonzalez-Alvarez, Ana C.
author raw: Pena-Guerra, Karla A.
author raw: Althagafi, Azza
author raw: Khan, Tanisha
author raw: Hoehndorf, Robert
author raw: Arold, Stefan T.
author: Azza Althagafi
author: Robert Hoehndorf
keyword: VarLand
keyword: missense variants
keyword: proteome scale
keyword: structural landscape
keyword: variant analysis
keyword: genomic pipeline
tag rationale: This paper describes VarLand, a pipeline for mapping missense variants at the proteome scale, which is a genomics and biomedical informatics topic.
topic: Genomics
topic: Biomedical informatics

Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
type: ScholarlyArticle
date published: 2023
venue: Frontiers in Gastroenterology
bib key: Hassanain2023
bib type: article
author raw: Mazen Hassanain
author raw: Yang Liu
author raw: Weam Hussain
author raw: Albandri Binowayn
author raw: Duna Barakeh
author raw: Ebtehal Alsolme
author raw: Faisal AlSaif
author raw: Ghaida Almasaad
author raw: Mohammed AlSwayyed
author raw: Maram Alaqel
author raw: Rana Aljunidel
author raw: Sherin Abdelrahman
author raw: Charlotte A. E. Hauser
author raw: Saleh Alqahtani
author raw: Robert Hoehndorf
author raw: Malak Abedalthagafi
author: Yang Liu
author: Robert Hoehndorf
keyword: genomic landscape
keyword: hepatocellular carcinoma
keyword: Saudi patients
keyword: whole-genome sequencing
keyword: variant calling
keyword: cancer genomics
tag rationale: This paper investigates the genomic landscape of hepatocellular carcinoma in Saudi patients using whole-genome sequencing, falling under genomics and biomedical informatics.
topic: Genomics
topic: Biomedical informatics

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
type: ScholarlyArticle
date published: 2022
venue: Journal of Biomedical Semantics
bib key: He2022
bib type: article
author raw: Yongqun He
author raw: Hong Yu
author raw: Anthony Huffman
author raw: Asiyah Yu Lin
author raw: Darren A. Natale
author raw: John Beverley
author raw: Ling Zheng
author raw: Yehoshua Perl
author raw: Zhigang Wang
author raw: Yingtong Liu
author raw: Edison Ong
author raw: Yang Wang
author raw: Philip Huang
author raw: Long Tran
author raw: Jinyang Du
author raw: Zalan Shah
author raw: Easheta Shah
author raw: Roshan Desai
author raw: Hsin-hui Huang
author raw: Yujia Tian
author raw: Eric Merrell
author raw: William D. Duncan
author raw: Sivaram Arabandi
author raw: Lynn M. Schriml
author raw: Jie Zheng
author raw: Anna Maria Masci
author raw: Liwei Wang
author raw: Hongfang Liu
author raw: Fatima Zohra Smaili
author raw: Robert Hoehndorf
author raw: Zoe May Pendlington
author raw: Paola Roncaglia
author raw: Xianwei Ye
author raw: Jiangan Xie
author raw: Yi-Wei Tang
author raw: Xiaolin Yang
author raw: Suyuan Peng
author raw: Luxia Zhang
author raw: Luonan Chen
author raw: Junguk Hur
author raw: Gilbert S. Omenn
author raw: Brian Athey
author raw: Barry Smith
author: Yang Liu
author: Robert Hoehndorf
author: Zhenwei Tang
author: Xi Peng
keyword: CIDO
keyword: coronavirus
keyword: infectious disease ontology
keyword: COVID-19
keyword: domain ontology
tag rationale: Updating the CIDO domain ontology; canonical Applied Ontology.
topic: Applied Ontology

Notions of similarity for systems biology models
type: ScholarlyArticle
date published: 2018
venue: Briefings in Bioinformatics
bib key: Henkel2016
bib type: article
author raw: Ron Henkel
author raw: Robert Hoehndorf
author raw: Tim Kacprowski
author raw: Christian Knupfer
author raw: Wolfgang Liebermeister
author raw: Dagmar Waltemath
author: Robert Hoehndorf
keyword: similarity measures
keyword: systems biology models
keyword: ontology-based similarity
keyword: model comparison
keyword: semantic comparison
tag rationale: This paper reviews notions of similarity for systems biology models, directly addressing semantic similarity and its application in an ontological context.
topic: Semantic similarity
topic: Applied Ontology

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug\textendashtarget interactions
type: ScholarlyArticle
date published: 2021
venue: Bioinformatics
bib key: Hinnerichs2021
bib type: article
author raw: Tilman Hinnerichs
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: DTI-Voodoo
keyword: drug-target interaction
keyword: interaction network
keyword: ontology-based background knowledge
keyword: GNN
tag rationale: Drug-target prediction over interaction networks + ontology priors; drug mechanisms with neuro-symbolic methods.
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals
type: ScholarlyArticle
date published: 2018
venue: ILAR Journal
bib key: histopathology
bib type: article
author raw: Keenan, Charlotte M
author raw: McKerlie, Colin
author raw: Gkoutos, Georgios V
author raw: Ward, Jerrold M
author raw: Sundberg, John P
author raw: Cesta, Mark F
author raw: Schofield, Paul N
author raw: Cardiff, Robert
author raw: Hoehndorf, Robert
author raw: Elmore, Susan A
author: Robert Hoehndorf
keyword: histopathology nomenclature
keyword: laboratory animals
keyword: ontology standards
keyword: semantic interoperability
keyword: pathology ontology
tag rationale: This paper reviews standards and evolution of histopathology nomenclature, which involves applied ontology and efforts towards semantic interoperability.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Similarity-based search of model organism, disease and drug effect phenotypes
type: ScholarlyArticle
date published: 2015
venue: Journal of Biomedical Semantics
bib key: Hoehndorf2015phenome2
bib type: article
author raw: Hoehndorf, Robert
author raw: Gruenberger, Michael
author raw: Gkoutos, Georgios
author raw: Schofield, Paul
author: Robert Hoehndorf
keyword: phenotype similarity
keyword: model organism
keyword: disease phenotypes
keyword: drug effect phenotypes
keyword: semantic search
keyword: phenomeNET
tag rationale: 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.
topic: Semantic similarity
topic: Rare disease diagnostic support
topic: Drug mechanisms and systems biology

The role of ontologies in biological and biomedical research: a functional perspective
type: ScholarlyArticle
date published: 2015
venue: Briefings in Bioinformatics
bib key: Hoehndorf2015role
bib type: article
author raw: Hoehndorf, Robert
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: ontologies
keyword: biological research
keyword: biomedical research
keyword: functional perspective
keyword: knowledge representation
tag rationale: 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.
topic: Applied Ontology
topic: Biomedical informatics

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases
type: ScholarlyArticle
date published: 2015
venue: Scientific Reports
bib key: Hoehndorf2015srep
bib type: article
author raw: Robert Hoehndorf
author raw: Paul N Schofield
author raw: Georgios V Gkoutos
author: Robert Hoehndorf
keyword: human diseasome
keyword: phenotype similarity
keyword: genetic diseases
keyword: infectious diseases
keyword: disease analysis
keyword: HPO
tag rationale: This paper analyzes the human diseasome using phenotype similarity, which is a key aspect of rare disease diagnostic support and semantic similarity.
topic: Rare disease diagnostic support
topic: Semantic similarity

Usage of cell nomenclature in biomedical literature
type: ScholarlyArticle
date published: 2017
venue: BMC Bioinformatics
bib key: Kafkas2017
bib type: article
author raw: Kafkas, \cSenay
author raw: Sarntivijai, Sirarat
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: cell nomenclature
keyword: biomedical literature
keyword: text mining
keyword: ontology mapping
keyword: semantic interoperability
tag rationale: This paper focuses on the usage of cell nomenclature in biomedical literature, which involves text mining and mapping to ontologies for semantic interoperability.
topic: Biomedical informatics
topic: Ontology engineering and semantic interoperability

Evaluating the effect of annotation size on measures of semantic similarity
type: ScholarlyArticle
date published: 2017
venue: Journal of Biomedical Semantics
bib key: Kulmanov2017
bib type: article
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: semantic similarity
keyword: annotation size
keyword: Gene Ontology
keyword: ontology evaluation
keyword: biomedical ontologies
tag rationale: This paper evaluates the impact of annotation size on semantic similarity measures, a core topic in semantic similarity research.
topic: Semantic similarity
topic: Applied Ontology

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
type: ScholarlyArticle
date published: 2021
venue: Nucleic Acids Research
bib key: Kulmanov2021
bib type: article
author raw: Maxat Kulmanov
author raw: Fernando Zhapa-Camacho
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DeepGOWeb
keyword: protein function prediction
keyword: Gene Ontology
keyword: Semantic Web
keyword: OWL
keyword: deep learning
tag rationale: This paper introduces DeepGOWeb for protein function prediction using Gene Ontology and Semantic Web technologies.
topic: Protein function prediction
topic: Ontology engineering and semantic interoperability

DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
type: ScholarlyArticle
date published: 2022
venue: Bioinformatics
bib key: Kulmanov2022
bib type: article
author raw: Maxat Kulmanov
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: DeepGOZero
keyword: protein function prediction
keyword: zero-shot learning
keyword: ontology axioms
keyword: Gene Ontology
tag rationale: Protein function prediction with zero-shot from ontology axioms; PFP + neuro-symbolic.
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics

A reference quality, fully annotated diploid genome from a Saudi individual
type: ScholarlyArticle
date published: 2024
venue: Scientific Data
bib key: Kulmanov2024
bib type: article
author raw: Kulmanov, Maxat
author raw: Tawfiq, Rund
author raw: Liu, Yang
author raw: Al Ali, Hatoon
author raw: Abdelhakim, Marwa
author raw: Alarawi, Mohammed
author raw: Aldakhil, Hind
author raw: Alhattab, Dana
author raw: Alsolme, Ebtehal A.
author raw: Althagafi, Azza
author raw: Angelov, Angel
author raw: Bougouffa, Salim
author raw: Driguez, Patrick
author raw: Park, Changsook
author raw: Putra, Alexander
author raw: Reyes-Ramos, Ana M.
author raw: Hauser, Charlotte A. E.
author raw: Cheung, Ming Sin
author raw: Abedalthagafi, Malak S.
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Rund Tawfiq
author: Yang Liu
author: Azza Althagafi
author: Robert Hoehndorf
keyword: Saudi genome
keyword: reference genome
keyword: diploid assembly
keyword: population genomics
keyword: Middle East
tag rationale: Pure genome-resource paper. Not Applied Ontology.
topic: Genomics

Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
type: ScholarlyArticle
date published: 2025
venue: Scientific Data
bib key: Kulmanov2025
bib type: article
author raw: Kulmanov, Maxat
author raw: Ashouri, Saeideh
author raw: Liu, Yang
author raw: Abdelhakim, Marwa
author raw: Alsolme, Ebtehal
author raw: Nagasaki, Masao
author raw: Ohkawa, Yasuyuki
author raw: Suzuki, Yutaka
author raw: Tawfiq, Rund
author raw: Tokunaga, Katsushi
author raw: Katayama, Toshiaki
author raw: Abedalthagafi, Malak S.
author raw: Hoehndorf, Robert
author raw: Kawai, Yosuke
author: Maxat Kulmanov
author: Yang Liu
author: Rund Tawfiq
author: Robert Hoehndorf
keyword: phased genome assemblies
keyword: pangenome graphs
keyword: human populations
keyword: Japan
keyword: Saudi Arabia
keyword: genomic resources
tag rationale: This paper focuses on the development of phased genome assemblies and pangenome graphs for specific human populations, which is a core genomics topic.
topic: Genomics

Nail abnormalities identified in an ageing study of 30 inbred mouse strains
type: ScholarlyArticle
date published: 2019
venue: Experimental Dermatology
bib key: Linn2018
bib type: article
author raw: Linn, Sarah C.
author raw: Mustonen, Allison M.
author raw: Silva, Kathleen A.
author raw: Kennedy, Victoria E.
author raw: Sundberg, Beth A.
author raw: Bechtold, Lesley S.
author raw: Alghamdi, Sarah M.
author raw: Hoehndorf, Robert
author raw: Schofield, Paul N.
author raw: Sundberg, John P.
author: Sarah Alghamdi
author: Robert Hoehndorf
keyword: nail abnormalities
keyword: aging study
keyword: inbred mouse strains
keyword: phenotype characterization
keyword: mouse models
tag rationale: This paper describes the identification and characterization of phenotypes (nail abnormalities) in mouse models, aligning with phenotype informatics.
topic: Phenotype informatics

Genomic landscape of retinoblastoma: Insights into risk stratification and precision pediatric Neuro-Oncology
type: ScholarlyArticle
date published: 2025
venue: Neuro-Oncology Pediatrics
bib key: Maktabi2025
bib type: article
author raw: Maktabi, Azza
author raw: Liu, Yang
author raw: Almesfer, Saleh
author raw: Abdelhakim, Marwa
author raw: Aldakhil, Hind
author raw: Kulmanov, Maxat
author raw: Edward, Deepak P
author raw: Hoehndorf, Robert
author raw: Abedalthagafi, Malak
author: Yang Liu
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: genomic landscape
keyword: retinoblastoma
keyword: risk stratification
keyword: precision pediatric neuro-oncology
keyword: variant analysis
keyword: cancer genomics
tag rationale: This paper investigates the genomic landscape of retinoblastoma for risk stratification and precision medicine, combining genomics with diagnostic support.
topic: Genomics
topic: Rare disease diagnostic support

DELE: Deductive EL++ Embeddings for Knowledge Base Completion
type: ScholarlyArticle
date published: 2026
venue: Neurosymbolic Artificial Intelligence
bib key: Mashkova2026
bib type: article
author raw: Mashkova, Olga
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: ontology embedding
keyword: EL++ description logic
keyword: deductive closure
keyword: knowledge base completion
keyword: negative sampling
tag rationale: DELE learns ontology embeddings for EL++ with explicit use of the deductive closure to construct negatives — a neuro-symbolic ontology-embedding contribution.
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
type: ScholarlyArticle
date published: 2017
venue: BMC Genomics
bib key: Motwalli2017
bib type: article
author raw: Motwalli, Olaa
author raw: Essack, Magbubah
author raw: Jankovic, Boris R.
author raw: Ji, Boyang
author raw: Liu, Xinyao
author raw: Ansari, Hifzur Rahman
author raw: Hoehndorf, Robert
author raw: Gao, Xin
author raw: Arold, Stefan T.
author raw: Mineta, Katsuhiko
author raw: Archer, John A. C.
author raw: Gojobori, Takashi
author raw: Mijakovic, Ivan
author raw: Bajic, Vladimir B.
author: Robert Hoehndorf
keyword: in silico screening
keyword: chassis strains
keyword: free fatty acid
keyword: cyanobacteria
keyword: microbial engineering
keyword: bioprospecting
tag rationale: This paper describes in silico screening for microbial chassis strains, which falls under metagenomics and microbial function, particularly bioprospecting.
topic: Metagenomics and microbial community function

An ontology approach to comparative phenomics in plants
type: ScholarlyArticle
date published: 2015
venue: Plant Methods
bib key: Oellrich2015
bib type: article
author raw: Oellrich, Anika
author raw: Walls, Ramona
author raw: Cannon, Ethalinda
author raw: Cannon, Steven
author raw: Cooper, Laurel
author raw: Gardiner, Jack
author raw: Gkoutos, Georgios
author raw: Harper, Lisa
author raw: He, Mingze
author raw: Hoehndorf, Robert
author raw: Jaiswal, Pankaj
author raw: Kalberer, Scott
author raw: Lloyd, John
author raw: Meinke, David
author raw: Menda, Naama
author raw: Moore, Laura
author raw: Nelson, Rex
author raw: Pujar, Anuradha
author raw: Lawrence, Carolyn
author raw: Huala, Eva
author: Robert Hoehndorf
keyword: ontology approach
keyword: comparative phenomics
keyword: plants
keyword: plant ontology
keyword: phenotype standardization
keyword: FLOPO
tag rationale: This paper applies an ontology-based approach to comparative phenomics in plants, directly aligning with applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants
type: ScholarlyArticle
date published: 2018
venue: Scientific Reports
bib key: oligopvp
bib type: article
author raw: Boudellioua, Imane
author raw: Kulmanov, Maxat
author raw: Schofield, Paul N
author raw: Gkoutos, Georgios V
author raw: Hoehndorf, Robert
author: Imane Boudellioua
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: OligoPVP
keyword: phenotype-driven analysis
keyword: genomic information
keyword: oligogenic disease
keyword: variant prioritization
keyword: rare disease
tag rationale: This paper introduces OligoPVP for phenotype-driven prioritization of oligogenic disease variants, a key aspect of rare disease diagnostic support and genomics.
topic: Rare disease diagnostic support
topic: Genomics

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
bib key: onto2vec
bib type: article
author raw: Smaili, Fatima Zohra
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: Onto2Vec
keyword: vector-based representation
keyword: ontology embeddings
keyword: biological entities
keyword: ontology annotations
keyword: neuro-symbolic AI
tag rationale: This paper introduces Onto2Vec for generating vector-based representations (embeddings) of biological entities and their ontology annotations, which is a neuro-symbolic AI method.
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
bib key: opa2vec
bib type: article
author raw: Smaili, Fatima Zohra
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: OPA2Vec
keyword: formal content
keyword: informal content
keyword: biomedical ontologies
keyword: similarity-based prediction
keyword: ontology embeddings
keyword: neuro-symbolic AI
tag rationale: 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.
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters
type: ScholarlyArticle
date published: 2018
venue: BMC Genomics
bib key: Othoum2018
bib type: article
author raw: Othoum, Ghofran
author raw: Bougouffa, Salim
author raw: Razali, Rozaimi
author raw: Bokhari, Ameerah
author raw: Alamoudi, Soha
author raw: Antunes, Andr\'e
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author raw: Arold, Stefan T.
author raw: Gojobori, Takashi
author raw: Hirt, Heribert
author raw: Mijakovic, Ivan
author raw: Bajic, Vladimir B.
author raw: Lafi, Feras F.
author raw: Essack, Magbubah
author: Robert Hoehndorf
keyword: in silico exploration
keyword: Red Sea Bacillus
keyword: natural product
keyword: biosynthetic gene clusters
keyword: microbial genomics
keyword: bioprospecting
tag rationale: This paper involves in silico exploration of microbial genomes for natural product biosynthetic gene clusters, fitting into metagenomics and microbial function.
topic: Metagenomics and microbial community function

The anatomy of phenotype ontologies: principles, properties and applications
type: ScholarlyArticle
date published: 2018
venue: Briefings in Bioinformatics
bib key: pato-paper
bib type: article
author raw: Georgios V. Gkoutos
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: phenotype ontologies
keyword: PATO
keyword: ontology principles
keyword: ontology applications
keyword: phenotype standardization
tag rationale: This paper discusses the principles and applications of phenotype ontologies, directly fitting applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

Semantic prioritization of novel causative genomic variants
type: ScholarlyArticle
date published: 2017
venue: PLOS Computational Biology
bib key: pvp-main
bib type: article
author raw: Boudellioua, Imane
author raw: Mahamad Razali, Rozaimi B.
author raw: Kulmanov, Maxat
author raw: Hashish, Yasmeen
author raw: Bajic, Vladimir B.
author raw: Goncalves-Serra, Eva
author raw: Schoenmakers, Nadia
author raw: Gkoutos, Georgios V.
author raw: Schofield, Paul N.
author raw: Hoehndorf, Robert
author: Imane Boudellioua
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: genomic variants
keyword: variant prioritization
keyword: semantic similarity
keyword: Human Phenotype Ontology
keyword: HPO
keyword: disease gene prioritization
tag rationale: This paper focuses on semantic prioritization of genomic variants using phenotype information, which is central to rare disease diagnostic support and semantic similarity.
topic: Rare disease diagnostic support
topic: Semantic similarity

Nanodesigner: resolving the complex-CDR interdependency with iterative refinement
type: ScholarlyArticle
date published: 2025
venue: Journal of Cheminformatics
bib key: RiosZertuche2025
bib type: article
author raw: Rios Zertuche, Melissa Maria
author raw: Kafkas, Senay
author raw: Renn, Dominik
author raw: Rueping, Magnus
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: nanodesigner
keyword: CDR interdependency
keyword: iterative refinement
keyword: drug design
keyword: computational chemistry
tag rationale: This paper describes a computational tool for designing complex molecules, which aligns with bioengineering and drug mechanisms.
topic: Bioengineering
topic: Drug mechanisms and systems biology

Ontology-based validation and identification of regulatory phenotypes
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
bib key: rule-phenotype
bib type: article
author raw: Kulmanov, Maxat
author raw: Schofield, Paul N
author raw: Gkoutos, Georgios V
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: regulatory phenotypes
keyword: ontology-based validation
keyword: phenotype identification
keyword: phenotype standardization
keyword: formal ontology
tag rationale: This paper uses ontologies for validating and identifying regulatory phenotypes, directly aligning with applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

DESM: portal for microbial knowledge exploration systems
type: ScholarlyArticle
date published: 2016
venue: Nucleic Acids Research
bib key: Salhi2016
bib type: article
author raw: Salhi, Adil
author raw: Essack, Magbubah
author raw: Radovanovic, Aleksandar
author raw: Marchand, Benoit
author raw: Bougouffa, Salim
author raw: Antunes, Andre
author raw: Simoes, Marta Filipa
author raw: Lafi, Feras F.
author raw: Motwalli, Olaa A.
author raw: Bokhari, Ameerah
author raw: Malas, Tariq
author raw: Amoudi, Soha Al
author raw: Othum, Ghofran
author raw: Allam, Intikhab
author raw: Mineta, Katsuhiko
author raw: Gao, Xin
author raw: Hoehndorf, Robert
author raw: C. Archer, John A.
author raw: Gojobori, Takashi
author raw: Bajic, Vladimir B.
author: Robert Hoehndorf
keyword: DESM portal
keyword: microbial knowledge
keyword: knowledge exploration systems
keyword: microbial communities
keyword: semantic web
tag rationale: This paper describes a portal for microbial knowledge exploration, linking to metagenomics and microbial function, and involving knowledge systems.
topic: Metagenomics and microbial community function
topic: Ontology engineering and semantic interoperability

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning
type: ScholarlyArticle
date published: 2016
venue: 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
bib key: Slater2016
bib type: inbook
author raw: Slater, Luke
author raw: Rodriguez-Garcia, Miguel
author raw: O'Shea, Keiron
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author raw: Hoehndorf, Robert
author: Miguel Angel Rodriguez Garcia
author: Robert Hoehndorf
keyword: AberOWL
keyword: ontology repository
keyword: OWL EL reasoning
keyword: semantic web
keyword: ontology infrastructure
tag rationale: This paper discusses experiences with AberOWL, an ontology repository with OWL EL reasoning, directly related to ontology engineering and semantic interoperability.
topic: Ontology engineering and semantic interoperability

Multi-faceted semantic clustering with text-derived phenotypes
type: ScholarlyArticle
date published: 2021
venue: Computers in Biology and Medicine
bib key: Slater2021
bib type: article
author raw: Luke T. Slater
author raw: John A. Williams
author raw: Andreas Karwath
author raw: Hilary Fanning
author raw: Simon Ball
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: semantic clustering
keyword: text-derived phenotypes
keyword: clinical text
keyword: phenotype extraction
keyword: patient profiles
tag rationale: This paper focuses on semantic clustering using text-derived phenotypes, which falls under biomedical informatics and phenotype informatics.
topic: Biomedical informatics
topic: Phenotype informatics

Effects of Negation and Uncertainty Stratification on Text-Derived Patient Profile Similarity
type: ScholarlyArticle
date published: 2021
venue: Frontiers in Digital Health
bib key: Slater2021c
bib type: article
author raw: Luke T. Slater
author raw: Andreas Karwath
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: negation stratification
keyword: uncertainty stratification
keyword: text-derived patient profiles
keyword: patient profile similarity
keyword: clinical text
keyword: semantic similarity
tag rationale: This paper investigates the effects of negation and uncertainty on patient profile similarity from clinical text, fitting biomedical informatics and semantic similarity.
topic: Biomedical informatics
topic: Semantic similarity

Evaluating semantic similarity methods for comparison of text-derived phenotype profiles
type: ScholarlyArticle
date published: 2022
venue: BMC Medical Informatics and Decision Making
bib key: Slater2022b
bib type: article
author raw: Luke T. Slater
author raw: Sophie Russell
author raw: Silver Makepeace
author raw: Alexander Carberry
author raw: Andreas Karwath
author raw: John A. Williams
author raw: Hilary Fanning
author raw: Simon Ball
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: semantic similarity
keyword: phenotype profile
keyword: text-derived phenotype
keyword: benchmarking
keyword: HPO
tag rationale: Direct semantic-similarity evaluation paper. Move out of Applied Ontology.
topic: Semantic similarity

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
bib key: smudge
bib type: article
author raw: Alshahrani, Mona
author raw: Hoehndorf, Robert
author: Mona Alshahrani
author: Robert Hoehndorf
keyword: SmuDGE
keyword: semantic disease gene embeddings
keyword: phenotype-based prioritization
keyword: disease gene prioritization
keyword: ontology embeddings
keyword: neuro-symbolic AI
tag rationale: This paper introduces semantic disease gene embeddings for prioritization, which is a neuro-symbolic AI approach applied to rare disease diagnostic support.
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
type: ScholarlyArticle
date published: 2018
venue: Botany Letters
bib key: Sohaib2018
bib type: article
author raw: Sohaib Younis
author raw: Claus Weiland
author raw: Robert Hoehndorf
author raw: Stefan Dressler
author raw: Thomas Hickler
author raw: Bernhard Seeger
author raw: Marco Schmidt
author: Robert Hoehndorf
keyword: herbarium specimens
keyword: deep convolutional neural networks
keyword: taxon recognition
keyword: trait recognition
keyword: digitized images
tag rationale: This paper focuses on recognizing biological traits and taxa from images, which aligns with phenotype informatics and uses biomedical informatics methods.
topic: Phenotype informatics
topic: Biomedical informatics

Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
type: ScholarlyArticle
date published: 2024
venue: Human Genomics
bib key: Stenton2024
bib type: article
author raw: Stenton, Sarah L.
author raw: O’Leary, Melanie C.
author raw: Lemire, Gabrielle
author raw: VanNoy, Grace E.
author raw: DiTroia, Stephanie
author raw: Ganesh, Vijay S.
author raw: Groopman, Emily
author raw: O’Heir, Emily
author raw: Mangilog, Brian
author raw: Osei-Owusu, Ikeoluwa
author raw: Pais, Lynn S.
author raw: Serrano, Jillian
author raw: Singer-Berk, Moriel
author raw: Weisburd, Ben
author raw: Wilson, Michael W.
author raw: Austin-Tse, Christina
author raw: Abdelhakim, Marwa
author raw: Althagafi, Azza
author raw: Babbi, Giulia
author raw: Bellazzi, Riccardo
author raw: Bovo, Samuele
author raw: Carta, Maria Giulia
author raw: Casadio, Rita
author raw: Coenen, Pieter-Jan
author raw: De Paoli, Federica
author raw: Floris, Matteo
author raw: Gajapathy, Manavalan
author raw: Hoehndorf, Robert
author raw: Jacobsen, Julius O. B.
author raw: Joseph, Thomas
author raw: Kamandula, Akash
author raw: Katsonis, Panagiotis
author raw: Kint, Cyrielle
author raw: Lichtarge, Olivier
author raw: Limongelli, Ivan
author raw: Lu, Yulan
author raw: Magni, Paolo
author raw: Mamidi, Tarun Karthik Kumar
author raw: Martelli, Pier Luigi
author raw: Mulargia, Marta
author raw: Nicora, Giovanna
author raw: Nykamp, Keith
author raw: Pejaver, Vikas
author raw: Peng, Yisu
author raw: Pham, Thi Hong Cam
author raw: Podda, Maurizio S.
author raw: Rao, Aditya
author raw: Rizzo, Ettore
author raw: Saipradeep, Vangala G.
author raw: Savojardo, Castrense
author raw: Schols, Peter
author raw: Shen, Yang
author raw: Sivadasan, Naveen
author raw: Smedley, Damian
author raw: Soru, Dorian
author raw: Srinivasan, Rajgopal
author raw: Sun, Yuanfei
author raw: Sunderam, Uma
author raw: Tan, Wuwei
author raw: Tiwari, Naina
author raw: Wang, Xiao
author raw: Wang, Yaqiong
author raw: Williams, Amanda
author raw: Worthey, Elizabeth A.
author raw: Yin, Rujie
author raw: You, Yuning
author raw: Zeiberg, Daniel
author raw: Zucca, Susanna
author raw: Bakolitsa, Constantina
author raw: Brenner, Steven E.
author raw: Fullerton, Stephanie M.
author raw: Radivojac, Predrag
author raw: Rehm, Heidi L.
author raw: O’Donnell-Luria, Anne

DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
type: ScholarlyArticle
date published: 2024
venue: Scientific Reports
bib key: Tawfiq2024
bib type: article
author raw: Tawfiq, Rund
author raw: Niu, Kexin
author raw: Hoehndorf, Robert
author raw: Kulmanov, Maxat
author: Rund Tawfiq
author: Kexin Niu
author: Robert Hoehndorf
author: Maxat Kulmanov
keyword: DeepGOMeta
keyword: microbial communities
keyword: protein function prediction
keyword: deep learning
keyword: functional insights
keyword: metagenomics
tag rationale: 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.
topic: Metagenomics and microbial community function
topic: Protein function prediction

Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
type: ScholarlyArticle
date published: 2024
venue: Bioinformatics
bib key: Toonsi2024
bib type: article
author raw: Toonsi, Sumyyah
author raw: Gauran, Iris Ivy
author raw: Ombao, Hernando
author raw: Schofield, Paul N
author raw: Hoehndorf, Robert
author: Sumyyah Toonsi
author: Robert Hoehndorf
keyword: causal relationships
keyword: literature mining
keyword: polygenic risk scores
keyword: disease prediction
keyword: text mining
tag rationale: 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.
topic: Biomedical informatics
topic: Rare disease diagnostic support

Causal knowledge graph analysis identifies adverse drug effects
type: ScholarlyArticle
date published: 2025
venue: Bioinformatics
bib key: Toonsi2025
bib type: article
author raw: Toonsi, Sumyyah
author raw: Schofield, Paul N
author raw: Hoehndorf, Robert
author: Sumyyah Toonsi
author: Robert Hoehndorf
keyword: causal knowledge graph
keyword: causality
keyword: adverse drug effect
keyword: drug safety
keyword: knowledge graph reasoning
tag rationale: About discovering adverse drug effects via causal KG analysis. Not ontology engineering.
topic: Drug mechanisms and systems biology

EMC10 homozygous variant identified in a family with global developmental delay, mild intellectual disability, and speech delay
type: ScholarlyArticle
date published: 2020
venue: Clinical Genetics
bib key: Umair2020
bib type: article
author raw: Muhammad Umair
author raw: Mariam Ballow
author raw: Abdulaziz Asiri
author raw: Yusra Alyafee
author raw: Abeer Tuwaijri
author raw: Kheloud M. Alhamoudi
author raw: Taghrid Aloraini
author raw: Marwa Abdelhakim
author raw: Azza Thamer Althagafi
author raw: Senay Kafkas
author raw: Lamia Alsubaie
author raw: Muhammad Talal Alrifai
author raw: Robert Hoehndorf
author raw: Ahmed Alfares
author raw: Majid Alfadhel
author: Azza Althagafi
author: Robert Hoehndorf
keyword: EMC10 variant
keyword: global developmental delay
keyword: intellectual disability
keyword: speech delay
keyword: homozygous variant
keyword: clinical genetics
tag rationale: 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.
topic: Rare disease diagnostic support
topic: Genomics

Semantic units: organizing knowledge graphs into semantically meaningful units of representation
type: ScholarlyArticle
date published: 2024
venue: Journal of Biomedical Semantics
bib key: Vogt2024
bib type: article
author raw: Vogt, Lars
author raw: Kuhn, Tobias
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: semantic units
keyword: knowledge graph
keyword: representation
keyword: modular KG
keyword: RDF
tag rationale: Genuinely Applied Ontology: organising KGs into semantically meaningful units.
topic: Applied Ontology

BioHackathon 2015: Semantics of data for life sciences and reproducible research
type: ScholarlyArticle
date published: 2020
venue: F1000Research
bib key: Vos2020
bib type: article
author raw: Rutger A. Vos
author raw: Toshiaki Katayama
author raw: Hiroyuki Mishima
author raw: Shin Kawano
author raw: Shuichi Kawashima
author raw: Jin-Dong Kim
author raw: Yuki Moriya
author raw: Toshiaki Tokimatsu
author raw: Atsuko Yamaguchi
author raw: Yasunori Yamamoto
author raw: Hongyan Wu
author raw: Peter Amstutz
author raw: Erick Antezana
author raw: Nobuyuki P. Aoki
author raw: Kazuharu Arakawa
author raw: Jerven T. Bolleman
author raw: Evan Bolton
author raw: Raoul J. P. Bonnal
author raw: Hidemasa Bono
author raw: Kees Burger
author raw: Hirokazu Chiba
author raw: Kevin B. Cohen
author raw: Eric W. Deutsch
author raw: Jesualdo T. Fern\'andez-Breis
author raw: Gang Fu
author raw: Takatomo Fujisawa
author raw: Atsushi Fukushima
author raw: Alexander Garc\'\ia
author raw: Naohisa Goto
author raw: Tudor Groza
author raw: Colin Hercus
author raw: Robert Hoehndorf
author raw: Kotone Itaya
author raw: Nick Juty
author raw: Takeshi Kawashima
author raw: Jee-Hyub Kim
author raw: Akira R. Kinjo
author raw: Masaaki Kotera
author raw: Kouji Kozaki
author raw: Sadahiro Kumagai
author raw: Tatsuya Kushida
author raw: Thomas L\"utteke
author raw: Masaaki Matsubara
author raw: Joe Miyamoto
author raw: Attayeb Mohsen
author raw: Hiroshi Mori
author raw: Yuki Naito
author raw: Takeru Nakazato
author raw: Jeremy Nguyen-Xuan
author raw: Kozo Nishida
author raw: Naoki Nishida
author raw: Hiroyo Nishide
author raw: Soichi Ogishima
author raw: Tazro Ohta
author raw: Shujiro Okuda
author raw: Benedict Paten
author raw: Jean-Luc Perret
author raw: Philip Prathipati
author raw: Pjotr Prins
author raw: N\'uria Queralt-Rosinach
author raw: Daisuke Shinmachi
author raw: Shinya Suzuki
author raw: Tsuyosi Tabata
author raw: Terue Takatsuki
author raw: Kieron Taylor
author raw: Mark Thompson
author raw: Ikuo Uchiyama
author raw: Bruno Vieira
author raw: Chih-Hsuan Wei
author raw: Mark Wilkinson
author raw: Issaku Yamada
author raw: Ryota Yamanaka
author raw: Kazutoshi Yoshitake
author raw: Akiyasu C. Yoshizawa

mOWL: Python library for machine learning with biomedical ontologies
type: ScholarlyArticle
date published: 2023
venue: Bioinformatics
bib key: ZhapaCamacho2022
bib type: article
author raw: Fernando Zhapa-Camacho
author raw: Maxat Kulmanov
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: mOWL
keyword: library
keyword: OWL ontology embedding
keyword: machine learning with ontologies
keyword: Python
tag rationale: mOWL is the library underpinning ontology embedding work; neuro-symbolic, not applied ontology.
topic: Neuro-symbolic methods in Bioinformatics

LLM Agent Based Protein Function Prediction
type: ScholarlyArticle
date published: 2025
venue: Biocomputing 2026
bib key: ZhapaCamacho2025
bib type: inproceedings
author raw: Zhapa-Camacho, Fernando
author raw: Mashkova, Olga
author raw: Hoehndorf, Robert
author raw: Kulmanov, Maxat
author: Robert Hoehndorf
author: Maxat Kulmanov
keyword: large language model
keyword: LLM agent
keyword: protein function
keyword: autonomous agent
keyword: Gene Ontology
tag rationale: LLM-agent-based protein function prediction at PSB 2026. The contribution is the agent.
topic: Protein function prediction

INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
type: ScholarlyArticle
date published: 2026
venue: Bioinformatics
bib key: ZhapaCamacho2026indigena
bib type: article
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Robert Hoehndorf

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
type: ScholarlyArticle
date published: 2014
venue: Journal of Biomedical Semantics
bib key: sio
bib type: article
author raw: Dumontier, Michel
author raw: Baker, Christopher
author raw: Baran, Joachim
author raw: Callahan, Alison
author raw: Chepelev, Leonid
author raw: Cruz-Toledo, Jose
author raw: Del Rio, Nicholas
author raw: Duck, Geraint
author raw: Furlong, Laura
author raw: Keath, Nichealla
author raw: Klassen, Dana
author raw: McCusker, James
author raw: Queralt-Rosinach, Nuria
author raw: Samwald, Matthias
author raw: Villanueva-Rosales, Natalia
author raw: Wilkinson, Mark
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: Semanticscience Integrated Ontology
keyword: SIO
keyword: biomedical research
keyword: knowledge discovery
keyword: ontology development
tag rationale: 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.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Statistical tests for associations between two directed acyclic graphs.
type: ScholarlyArticle
venue: PloS ONE
bib key: h3
bib type: article
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Dannemann, Michael
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

Applying the functional abnormality ontology pattern to anatomical functions.
type: ScholarlyArticle
venue: Journal of biomedical semantics
bib key: h7
bib type: article
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

The ontology of biological sequences.
type: ScholarlyArticle
venue: BMC Bioinformatics
bib key: h10
bib type: article
author raw: Hoehndorf, Robert
author raw: Kelso, Janet
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
type: ScholarlyArticle
venue: BMC Bioinformatics
bib key: h15
bib type: article
author raw: Hoehndorf, Robert
author raw: Bacher, Joshua
author raw: Backhaus, Michael
author raw: Gregorio, Sergio E.
author raw: Loebe, Frank
author raw: Pr\"ufer, Kay
author raw: Uciteli, Alexandr
author raw: Visagie, Johann
author raw: Herre, Heinrich
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

Relations as patterns: bridging the gap between OBO and OWL.
type: ScholarlyArticle
venue: BMC Bioinformatics
bib key: h20
bib type: article
author raw: Hoehndorf, Robert
author raw: Oellrich, Anika
author raw: Dumontier, Michel
author raw: Kelso, Janet
author raw: Rebholz-Schuhmann, Dietrich
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

GFO-Bio: A biomedical core ontology
type: ScholarlyArticle
venue: Applied Ontology
bib key: h23
bib type: article
author raw: Hoehndorf, Robert
author raw: Loebe, Frank
author raw: Poli, Roberto
author raw: Kelso, Janet
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies
type: ScholarlyArticle
venue: BMC Bioinformatics
bib key: h25
bib type: article
author raw: Hoehndorf, Robert
author raw: Loebe, Frank
author raw: Kelso, Janet
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

A top-level ontology of functions and its application in the Open Biomedical Ontologies.
type: ScholarlyArticle
venue: Bioinformatics
bib key: h26
bib type: article
author raw: Burek, Patryk
author raw: Hoehndorf, Robert
author raw: Loebe, Frank
author raw: Visagie, Johann
author raw: Herre, Heinrich
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

Interoperability between phenotype and anatomy ontologies
type: ScholarlyArticle
venue: Bioinformatics
bib key: h29
bib type: article
author raw: Hoehndorf, Robert
author raw: Oellrich, Anika
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
keyword: phenotype ontology
keyword: anatomy ontology
keyword: interoperability
keyword: ontology alignment
keyword: cross-species phenotypes
tag rationale: This paper focuses on achieving interoperability between phenotype and anatomy ontologies, which is a core aspect of applied ontology, ontology engineering, and phenotype informatics.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
topic: Phenotype informatics

A common layer of interoperability for biomedical ontologies based on OWL EL
type: ScholarlyArticle
venue: Bioinformatics
bib key: elvira
bib type: article
author raw: Robert Hoehndorf
author raw: Michel Dumontier
author raw: Anika Oellrich
author raw: Sarala Wimalaratne
author raw: Dietrich Rebholz-Schuhmann
author raw: Paul N. Schofield
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: biomedical ontologies
keyword: OWL EL
keyword: interoperability layer
keyword: automated reasoning
keyword: ontology integration
tag rationale: This paper describes a common interoperability layer for biomedical ontologies based on OWL EL, directly fitting ontology engineering and applied ontology.
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
type: ScholarlyArticle
venue: Applied Ontology
bib key: rnao
bib type: article
author raw: Robert Hoehndorf
author raw: Colin Batchelor
author raw: Thomas Bittner
author raw: Michel Dumontier
author raw: Karen Eilbeck
author raw: Rob Knight
author raw: Chris J. Mungall
author raw: Jane S. Richardson
author raw: Jesse Stombaugh
author raw: Eric Westhof
author raw: Craig L. Zirbel
author raw: Neocles B. Leontis
author: Robert Hoehndorf
keyword: RNA Ontology
keyword: RNAO
keyword: RNA sequence
keyword: RNA structure
keyword: ontology integration
keyword: biomedical data
tag rationale: 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.
topic: Applied Ontology
topic: Biomedical informatics

PhenomeNET: a whole-phenome approach to disease gene discovery
type: ScholarlyArticle
venue: Nucleic Acids Research
bib key: Hoehndorf2011phenome
bib type: article
author raw: Hoehndorf, Robert
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: PhenomeNET
keyword: disease gene discovery
keyword: whole-phenome approach
keyword: phenotype similarity
keyword: Human Phenotype Ontology
tag rationale: 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.
topic: Rare disease diagnostic support
topic: Semantic similarity
topic: Phenotype informatics

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning
type: ScholarlyArticle
venue: PLOS ONE
bib key: Hoehndorf2011incon
bib type: article
author raw: Robert Hoehndorf
author raw: Michel Dumontier
author raw: Anika Oellrich
author raw: Dietrich Rebholz-Schuhmann
author raw: Paul N. Schofield
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: biomedical ontologies
keyword: interoperability
keyword: relation expansion
keyword: upper-level ontologies
keyword: automatic reasoning
keyword: ontology integration
tag rationale: This paper addresses interoperability between biomedical ontologies through relation expansion and automated reasoning, which is central to ontology engineering and applied ontology.
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Integrating systems biology models and biomedical ontologies
type: ScholarlyArticle
venue: BMC Systems Biology
bib key: Hoehndorf2011models
bib type: article
author raw: Hoehndorf, Robert
author raw: Dumontier, Michel
author raw: Gennari, John H.
author raw: Wimalaratne, Sarala
author raw: de Bono, Bernard
author raw: Cook, Daniel L.
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
topic: Applied Ontology

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
type: ScholarlyArticle
venue: BMC Research Notes
bib key: ricordovision
bib type: article
author raw: de Bono, Bernard
author raw: Hoehndorf, Robert
author raw: Wimalaratne, Sarala
author raw: Gkoutos, Georgios V.
author raw: Grenon, Pierre
author: Robert Hoehndorf
keyword: RICORDO
keyword: semantic interoperability
keyword: biomedical data
keyword: biomedical models
keyword: standards
keyword: linked data
tag rationale: 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.
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

PIDO: The Primary Immunodeficiency Disease Ontology
type: ScholarlyArticle
venue: Bioinformatics
bib key: Adams2011
bib type: article
author raw: Adams, Nico
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author raw: Hansen, Gesine
author raw: Hennig, Christian
author: Robert Hoehndorf
keyword: PIDO
keyword: Primary Immunodeficiency Disease Ontology
keyword: immunodeficiency diseases
keyword: ontology development
keyword: disease classification
tag rationale: 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.
topic: Applied Ontology
topic: Rare disease diagnostic support

Ontology design patterns to disambiguate relations between genes and gene products in GENIA
type: ScholarlyArticle
venue: Journal of Biomedical Semantics
bib key: Hoehndorf2011genia
bib type: article
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Pyysalo, Sampo
author raw: Ohta, Tomoko
author raw: Oellrich, Anika
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
keyword: ontology design patterns
keyword: GENIA
keyword: gene relations
keyword: gene products
keyword: disambiguation
keyword: text mining
tag rationale: 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.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models
type: ScholarlyArticle
venue: Briefings in Functional Genomics
bib key: Schofield2011
bib type: article
author raw: Schofield, Paul N.
author raw: Sundberg, John P.
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: phenotype representation
keyword: human diseases
keyword: animal models
keyword: phenotype analysis
keyword: ontology application
tag rationale: 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.
topic: Applied Ontology
topic: Phenotype informatics
topic: Rare disease diagnostic support

OBML - Ontologies in Biomedicine and Life Sciences
type: ScholarlyArticle
venue: Journal of Biomedical Semantics
bib key: Hoehndorf2010obml
bib type: article
author raw: Herre, Heinrich
author raw: Hoehndorf, Robert
author raw: Kelso, Janet
author raw: Loebe, Frank
author raw: Schulz, Stefan
author: Robert Hoehndorf
keyword: ontologies
keyword: biomedicine
keyword: life sciences
keyword: knowledge representation
keyword: semantic integration
tag rationale: This paper discusses ontologies in biomedicine and life sciences, fitting applied ontology and biomedical informatics.
topic: Applied Ontology
topic: Biomedical informatics

Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing
type: ScholarlyArticle
venue: Pacific Symposium on Biocomputing (PSB)
bib key: Hoehndorf2012psb
bib type: article
author raw: Robert Hoehndorf
author raw: Anika Oellrich
author raw: Dietrich Rebholz-Schuhmann
author raw: Paul N. Schofield
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: PharmGKB
keyword: phenotype studies
keyword: animal models
keyword: drug repurposing
keyword: disease models
tag rationale: This paper links PharmGKB to phenotype studies and animal models for drug repurposing, directly addressing drug mechanisms, rare disease support, and applied ontology.
topic: Drug mechanisms and systems biology
topic: Rare disease diagnostic support
topic: Applied Ontology

Mouse genetic and phenotypic resources for human genetics
type: ScholarlyArticle
venue: Human Mutation
bib key: Schofield2012
bib type: article
author raw: Schofield, Paul N.
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: mouse genetics
keyword: phenotypic resources
keyword: human genetics
keyword: disease modeling
keyword: phenotype analysis
tag rationale: This paper discusses mouse genetic and phenotypic resources for human genetics, which is relevant to rare disease diagnostic support and phenotype informatics.
topic: Rare disease diagnostic support
topic: Phenotype informatics

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
type: ScholarlyArticle
venue: Journal of Biomedical Semantics
bib key: Jupp2012
bib type: article
author raw: Jupp, Simon
author raw: Stevens, Robert
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: Gene Ontology
keyword: GOAL
keyword: OWL
keyword: gene annotations
keyword: logical representation
tag rationale: This paper explores Gene Ontology annotations using OWL, aligning with applied ontology, protein function prediction, and ontology engineering.
topic: Applied Ontology
topic: Protein function prediction
topic: Ontology engineering and semantic interoperability

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
type: ScholarlyArticle
date published: 2012
venue: Bioinformatics
bib key: Hoehndorf2012cpo
bib type: article
author raw: Hoehndorf, Robert
author raw: Harris, Midori A.
author raw: Herre, Heinrich
author raw: Rustici, Gabriella
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: physiology phenotypes
keyword: Cellular Phenotype Ontology
keyword: semantic integration
keyword: OWL
keyword: phenotype standardization
tag rationale: This paper focuses on semantic integration of physiology phenotypes using the Cellular Phenotype Ontology, fitting applied ontology, phenotype informatics, and ontology engineering.
topic: Applied Ontology
topic: Phenotype informatics
topic: Ontology engineering and semantic interoperability

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
type: ScholarlyArticle
venue: Bioinformatics
bib key: Wimalaratne2012
bib type: article
author raw: Wimalaratne, Sarala M.
author raw: Grenon, Pierre
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author raw: de Bono, Bernard
author: Robert Hoehndorf
keyword: ontology-based information systems
keyword: biomedicine
keyword: RICORDO
keyword: infrastructure
keyword: semantic integration
tag rationale: This paper describes an infrastructure for ontology-based information systems in biomedicine, which is a core aspect of ontology engineering and biomedical informatics.
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
type: ScholarlyArticle
date published: 2012
venue: Bioinformatics
bib key: Hoehndorf2012pharmgkb
bib type: article
author raw: Hoehndorf, Robert
author raw: Dumontier, Michel
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: aberrant pathways
keyword: pharmacogenomics
keyword: knowledge integration
keyword: systems biology
keyword: drug mechanisms
tag rationale: This paper focuses on identifying aberrant pathways through integrated analysis in pharmacogenomics, directly relating to drug mechanisms and biomedical informatics.
topic: Drug mechanisms and systems biology
topic: Biomedical informatics

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
type: ScholarlyArticle
date published: 2012
venue: Journal of Biomedical Semantics
bib key: Oellrich2012
bib type: article
author raw: Oellrich, Anika
author raw: Gkoutos, Georgios V.
author raw: Hoehndorf, Robert
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
keyword: Human Phenotype Ontology
keyword: Mammalian Phenotype Ontology
keyword: mapping methods
keyword: phenotype comparison
keyword: ontology alignment
tag rationale: This paper quantitatively compares mapping methods between HPO and MPO, which is a form of semantic similarity and phenotype informatics within applied ontology.
topic: Semantic similarity
topic: Phenotype informatics
topic: Applied Ontology

Towards improving phenotype representation in OWL
type: ScholarlyArticle
date published: 2012
venue: Journal of Biomedical Semantics
bib key: Loebe2012
bib type: article
author raw: Loebe, Frank
author raw: Stumpf, Frank
author raw: Hoehndorf, Robert
author raw: Herre, Heinrich
author: Robert Hoehndorf
keyword: phenotype representation
keyword: OWL
keyword: ontology development
keyword: formal ontology
keyword: phenotype standardization
tag rationale: This paper aims to improve phenotype representation in OWL, directly aligning with applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
type: ScholarlyArticle
date published: 2012
venue: Journal of Biomedical Semantics
bib key: Gkoutos2012yeast
bib type: article
author raw: Gkoutos, Georgios V.
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: Saccharomyces cerevisiae
keyword: phenotypes
keyword: cross-species integration
keyword: ontology-based analysis
keyword: yeast models
tag rationale: This paper focuses on ontology-based cross-species integration and analysis of yeast phenotypes, fitting applied ontology, phenotype informatics, and ontology engineering.
topic: Applied Ontology
topic: Phenotype informatics
topic: Ontology engineering and semantic interoperability

Evaluation of research in biomedical ontologies
type: ScholarlyArticle
date published: 2012
venue: Briefings in Bioinformatics
bib key: Hoehndorf2012eval
bib type: article
author raw: Hoehndorf, Robert
author raw: Dumontier, Michel
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: biomedical ontologies
keyword: research evaluation
keyword: ontology quality
keyword: ontology metrics
keyword: knowledge representation
tag rationale: This paper evaluates research in biomedical ontologies, which is a meta-level topic for applied ontology and biomedical informatics.
topic: Applied Ontology
topic: Biomedical informatics

The Units Ontology: a tool for integrating units of measurement in science
type: ScholarlyArticle
date published: 2012
venue: Database
bib key: Gkoutos2012units
bib type: article
author raw: Gkoutos, Georgios V.
author raw: Schofield, Paul N.
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: Units Ontology
keyword: units of measurement
keyword: science integration
keyword: data standardization
keyword: formal ontology
tag rationale: This paper introduces the Units Ontology for integrating units of measurement, which is a clear example of applied ontology and ontology engineering.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Text-mining solutions for biomedical research: enabling integrative biology
type: ScholarlyArticle
date published: 2012
venue: Nature Reviews Genetics
bib key: Hoehndorf2012nrg
bib type: article
author raw: Dietrich Rebholz-Schuhmann
author raw: Anika Oellrich
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: text-mining
keyword: biomedical research
keyword: integrative biology
keyword: biomedical NLP
keyword: information extraction
tag rationale: This paper discusses text-mining solutions for biomedical research, directly falling under biomedical informatics.
topic: Biomedical informatics

Chapter Four - The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes
type: ScholarlyArticle
date published: 2012
venue: Bioinformatics of Behavior: Part 1
bib key: Gkoutos2012behavior
bib type: incollection
author raw: Georgios V. Gkoutos
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: Neurobehavior Ontology
keyword: behavior annotation
keyword: behavioral phenotypes
keyword: ontology integration
keyword: neuroscience
tag rationale: This paper describes the Neurobehavior Ontology for annotating and integrating behavior and behavioral phenotypes, aligning with applied ontology, phenotype informatics, and ontology engineering.
topic: Applied Ontology
topic: Phenotype informatics
topic: Ontology engineering and semantic interoperability

An integrative, translational approach to understanding rare and orphan genetically based diseases
type: ScholarlyArticle
date published: 2013
venue: Interface Focus
bib key: Hoehndorf2013orphanet
bib type: article
author raw: Hoehndorf, Robert
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: rare diseases
keyword: Orphanet
keyword: phenotype data
keyword: disease mechanisms
keyword: semantic integration
tag rationale: This paper focuses on integrating data for rare disease understanding, aligning with rare disease diagnostic support and semantic interoperability.
topic: Rare disease diagnostic support
topic: Ontology engineering and semantic interoperability

Representing physiological processes and their participants with PhysioMaps
type: ScholarlyArticle
date published: 2013
venue: Journal of Biomedical Semantics
bib key: Cook2013
bib type: article
author raw: Cook, Daniel
author raw: Neal, Maxwell
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios
author raw: Gennari, John
author: Robert Hoehndorf
keyword: PhysioMaps
keyword: physiological processes
keyword: formal representation
keyword: ontology development
keyword: systems biology
tag rationale: The paper describes the development of PhysioMaps for representing physiological processes, which is a clear application of ontology engineering.
topic: Applied Ontology

Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
type: ScholarlyArticle
date published: 2013
venue: PLoS ONE
bib key: Hoehndorf2013p2g
bib type: article
author raw: Hoehndorf, Robert
author raw: Hardy, Nigel W.
author raw: Osumi-Sutherland, David
author raw: Tweedie, Susan
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author: Robert Hoehndorf
keyword: phenotype data
keyword: gene function
keyword: model organisms
keyword: computational analysis
keyword: phenotype-genotype association
tag rationale: This paper focuses on analyzing experimental phenotype data to reveal gene functions, which falls under phenotype informatics and general biomedical informatics.
topic: Phenotype informatics
topic: Biomedical informatics

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
type: ScholarlyArticle
date published: 2013
venue: Journal of Biomedical Semantics
bib key: Rebholz2013
bib type: article
author raw: Rebholz-Schuhmann, Dietrich
author raw: Kafkas, Senay
author raw: Kim, Jee-Hyub
author raw: Li, Chen
author raw: Jimeno Yepes, Antonio
author raw: Hoehndorf, Robert
author raw: Backofen, Rolf
author raw: Lewin, Ian
author: Robert Hoehndorf
keyword: gene/protein tagging
keyword: lexical resources
keyword: gold standard corpora
keyword: text mining
keyword: biomedical NLP
tag rationale: This paper evaluates gene/protein tagging solutions and lexical resources, which is a core task in biomedical natural language processing and informatics.
topic: Biomedical informatics

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
type: ScholarlyArticle
date published: 2013
venue: PLoS ONE
bib key: lexebi
bib type: article
author raw: Dietrich Rebholz-Schuhmann
author raw: Jee-Hyub Kim
author raw: Ying Yan
author raw: Abhishek Dixit
author raw: Caroline Friteyre
author raw: Robert Hoehndorf
author raw: Rolf Backofen
author raw: Ian Lewin
author: Robert Hoehndorf
keyword: LexEBI
keyword: lexical entities
keyword: biological interest
keyword: text mining
keyword: ontology integration
tag rationale: The paper evaluates lexical entities of biological interest, combining aspects of biomedical NLP and the use of ontologies.
topic: Biomedical informatics
topic: Applied Ontology

Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery
type: ScholarlyArticle
date published: 2013
venue: Systems Biology
bib key: dumontier2013semantic
bib type: incollection
author raw: Dumontier, Michel
author raw: Chepelev, Leonid L
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: semantic systems biology
keyword: formal knowledge representation
keyword: model construction
keyword: systems biology
keyword: ontology-driven discovery
tag rationale: This paper discusses formal knowledge representation in systems biology, which is a direct application of ontology and relevant to understanding biological mechanisms.
topic: Applied Ontology
topic: Drug mechanisms and systems biology

Mouse model phenotypes provide information about human drug targets
type: ScholarlyArticle
date published: 2013
venue: Bioinformatics
bib key: Hoehndorf2013drugs
bib type: article
author raw: Hoehndorf, Robert
author raw: Hiebert, Tanya
author raw: Hardy, Nigel W.
author raw: Schofield, Paul N.
author raw: Gkoutos, Georgios V.
author raw: Dumontier, Michel
author: Robert Hoehndorf
keyword: mouse models
keyword: human drug targets
keyword: phenotype analysis
keyword: drug repurposing
keyword: disease models
tag rationale: This paper uses mouse model phenotypes to identify human drug targets, directly linking to drug mechanisms and potential applications in rare diseases.
topic: Drug mechanisms and systems biology
topic: Rare disease diagnostic support

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
type: ScholarlyArticle
date published: 2014
venue: Journal of biomedical semantics
bib key: Katayama2014
bib type: article
author raw: Katayama, Toshiaki
author raw: Wilkinson, Mark D.
author raw: Aoki-Kinoshita, Kiyoko F.
author raw: Kawa\-shima, Shuichi
author raw: Yamamoto, Yasunori
author raw: Yamaguchi, Atsuko
author raw: Okamoto, Shinobu
author raw: Kawano, Shin
author raw: Kim, Jin-Dong
author raw: Wang, Yue
author raw: Wu, Hongyan
author raw: Kano, Yoshinobu
author raw: Ono, Hiromasa
author raw: Bono, Hidemasa
author raw: Kocbek, Simon
author raw: Aerts, Jan
author raw: Akune, Yukie
author raw: Antezana, Erick
author raw: Arakawa, Kazuharu
author raw: Aranda, Bruno
author raw: Baran, Joachim
author raw: Bolleman, Jerven
author raw: Bonnal, Raoul Jp
author raw: Buttigieg, Pier Luigi
author raw: Campbell, Matthew P.
author raw: Chen, Yi-An
author raw: Chiba, Hirokazu
author raw: Cock, Peter Ja
author raw: Cohen, Kevin B.
author raw: Constantin, Alexandru
author raw: Duck, Geraint
author raw: Dumontier, Michel
author raw: Fujisawa, Takatomo
author raw: Fujiwara, Toyofumi
author raw: Goto, Naohisa
author raw: Hoehndorf, Robert
author raw: Igarashi, Yoshinobu
author raw: Itaya, Hidetoshi
author raw: Ito, Maori
author raw: Iwasaki, Wataru
author raw: Kala, Mat\'u
author raw: Katoda, Takeo
author raw: Kim, Taehong
author raw: Kokubu, Anna
author raw: Komiyama, Yusuke
author raw: Kotera, Masaaki
author raw: Laibe, Camille
author raw: Lapp, Hilmar
author raw: L\
author: Robert Hoehndorf
topic: Applied Ontology

Thematic series on biomedical ontologies in JBMS: challenges and new directions
type: ScholarlyArticle
date published: 2014
venue: Journal of Biomedical Semantics
bib key: Hoehndorf2014thematicseries
bib type: article
author raw: Hoehndorf, Robert
author raw: Haendel, Melissa
author raw: Stevens, Robert
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
keyword: biomedical ontologies
keyword: ontology challenges
keyword: new directions
keyword: semantic web
keyword: knowledge representation
tag rationale: This paper discusses challenges and new directions in biomedical ontologies, making it a general topic in applied ontology.
topic: Applied Ontology

Analyzing gene expression data in mice with the Neuro Behavior Ontology
type: ScholarlyArticle
date published: 2014
venue: Mamm Genome
bib key: Hoehndorf2013nbo
bib type: article
author raw: Hoehndorf, R.
author raw: Hancock, J. M.
author raw: Hardy, N. W.
author raw: Mallon, A. M.
author raw: Schofield, P. N.
author raw: Gkoutos, G. V.
author: Robert Hoehndorf
keyword: Neuro Behavior Ontology
keyword: gene expression data
keyword: mouse models
keyword: phenotype analysis
keyword: neuroscience
tag rationale: This paper applies the Neuro Behavior Ontology to analyze gene expression data in mice, combining ontology application with biomedical data analysis.
topic: Applied Ontology
topic: Biomedical informatics

Enriched biodiversity data as a resource and service
type: ScholarlyArticle
date published: 2014
venue: Biodiversity Data Journal
bib key: Biosphere
bib type: article
author raw: Rutger Vos
author raw: Jordan Biserkov
author raw: Bachir Balech
author raw: Niall Beard
author raw: Matthew Blissett
author raw: Christian Brenninkmeijer
author raw: Tom van Dooren
author raw: David Eades
author raw: George Gosline
author raw: Quentin Groom
author raw: Thomas Hamann
author raw: Hannes Hettling
author raw: Robert Hoehndorf
author raw: Ayco Holleman
author raw: Peter Hovenkamp
author raw: Patricia Kelbert
author raw: David King
author raw: Don Kirkup
author raw: Youri Lammers
author raw: Thibaut DeMeulemeester
author raw: Daniel Mietchen
author raw: Jeremy Miller
author raw: Ross Mounce
author raw: Nicola Nicolson
author raw: Rod Page
author raw: Aleksandra Pawlik
author raw: Serrano Pereira
author raw: Lyubomir Penev
author raw: Kevin Richards
author raw: Guido Sautter
author raw: David Shorthouse
author raw: Marko Tahtinen
author raw: Claus Weiland
author raw: Alan Williams
author raw: Soraya Sierra
author: Robert Hoehndorf
keyword: biodiversity data
keyword: data enrichment
keyword: knowledge resource
keyword: semantic web
keyword: data integration
tag rationale: This paper focuses on enriching biodiversity data as a resource, which involves semantic integration and knowledge representation.
topic: Applied Ontology
topic: Biomedical informatics

Interactively Exploring Graph Coloring Algorithms in a Bilingual Web Platform with Gamification
type: ScholarlyArticle
date published: 2017
venue: Proceedings of EdMedia: World Conference on Educational Media and Technology 2017
bib key: AlraAlhaTala2017ll
bib type: inproceedings
author raw: Maha Alrashed
author raw: Lujain Alharbi
author raw: Omamah Talal Al-Muhammadi
author raw: Salha Bahadiq
author raw: Robert Hoehndorf
author raw: Liam Mencel
author: Robert Hoehndorf
keyword: graph coloring
keyword: algorithm visualization
keyword: bilingual learning
tag rationale: Educational graph-coloring web platform; not core research of the group — intentionally untagged.

SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
type: ScholarlyArticle
date published: 2026
venue: The Semantic Web -- ESWC 2026
bib key: Ashhad2026
bib type: inbook
author raw: Ashhad, Mohammad
author raw: Mashkova, Olga
author raw: Henao, Ricardo
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: drug knowledge graph
keyword: drug indication
keyword: adverse effect
keyword: semantic integration
keyword: pharmacovigilance
tag rationale: SIDEKICK integrates drug-related semantic resources (effects, indications, contraindications) for downstream learning and reasoning.
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics

From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings
type: ScholarlyArticle
date published: 2023
venue: Proceedings of the 17th International Workshop on Neural-Symbolic Learning and Reasoning, La Certosa di Pontignano, Siena, Italy, July 3-5, 2023
bib key: DBLP:conf/nesy/Zhapa-CamachoH23
bib type: inproceedings
author raw: Fernando Zhapa-Camacho
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: graph-based ontology embedding
keyword: axioms
keyword: evaluation
keyword: EL++
keyword: NeSy
tag rationale: Evaluating graph-based ontology embeddings; neuro-symbolic methodology.
topic: Neuro-symbolic methods in Bioinformatics

Evaluating Different Methods for Semantic Reasoning Over Ontologies
type: ScholarlyArticle
date published: 2023
venue: 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
bib key: DBLP:conf/semweb/Zhapa-CamachoH23
bib type: inproceedings
author raw: Fernando Zhapa-Camacho
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: semantic reasoning
keyword: reasoner evaluation
keyword: OWL
keyword: scholarly QALD
keyword: SemREC
tag rationale: Evaluation of semantic reasoners; ontology-engineering infrastructure.
topic: Ontology engineering and semantic interoperability

Updating the CEMO ontology for future epidemiological challenges
type: ScholarlyArticle
date published: 2023
venue: 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023
bib key: DBLP:conf/swat4ls/Queralt-Rosinach23
bib type: inproceedings
author raw: N\'uria Queralt-Rosinach
author raw: Paul N. Schofield
author raw: Marco Roos
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: CEMO
keyword: epidemiology
keyword: COVID-19
keyword: ontology update
keyword: infectious disease ontology
tag rationale: Domain-ontology update for epidemiology; Applied Ontology.
topic: Applied Ontology

Large-Scale Reasoning over Functions in Biomedical Ontologies
type: ScholarlyArticle
date published: 2016
venue: Formal Ontology in Information Systems
bib key: Hoehndorf2016fois
bib type: inproceedings
author raw: Robert Hoehndorf
author raw: Liam Mencel
author raw: Georgios V. Gkoutos
author raw: Paul N. Schofield
author: Robert Hoehndorf
keyword: formal ontology
keyword: functions
keyword: biomedical ontologies
keyword: large-scale reasoning
keyword: OWL
tag rationale: This paper focuses on large-scale reasoning over functions in biomedical ontologies, which is a core aspect of applied ontology and ontology engineering.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)
type: ScholarlyArticle
date published: 2016
venue: International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)
bib key: IT702
bib type: inproceedings
author raw: Luke Slater
author raw: Georgios V. Gkoutos
author raw: Paul N Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: MIREOT
keyword: Experimental Factor Ontology
keyword: EFO
keyword: ontology reuse
keyword: ontology modularity
keyword: ontology engineering
tag rationale: This paper investigates the impact of MIREOT in EFO, directly addressing ontology engineering practices and applied ontology.
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Ontology based mining of pathogen-disease associations from literature
type: ScholarlyArticle
date published: 2018
venue: Bio-Ontologies COSI
bib key: Kafkas2018-ismb
bib type: inproceedings
author raw: Senay Kafkas
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: pathogen-disease associations
keyword: literature mining
keyword: ontology-based mining
keyword: text mining
keyword: knowledge extraction
tag rationale: This paper uses ontology-based methods to mine pathogen-disease associations from literature, combining biomedical text mining with applied ontology.
topic: Biomedical informatics
topic: Applied Ontology

Evaluating the effect of annotation size on measures of semantic similarity
type: ScholarlyArticle
date published: 2016
venue: Proceedings of Bio-Ontologies SIG
bib key: Kulmanov2016
bib type: inproceedings
author raw: Maxat Kulmanov
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: semantic similarity
keyword: annotation size
keyword: ontology annotations
keyword: evaluation
keyword: biomedical ontologies
tag rationale: This paper directly evaluates the effect of annotation size on semantic similarity measures, making it a clear fit for the semantic similarity topic.
topic: Semantic similarity
topic: Applied Ontology

EL Embeddings: Geometric construction of models for the Description Logic EL++
type: ScholarlyArticle
date published: 2019
venue: Proceedings of IJCAI 2019
bib key: kulmanov2019el
bib type: inproceedings
author raw: Maxat Kulmanov
author raw: Wang Liu-Wei
author raw: Yuan Yan
author raw: Robert Hoehndorf
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: ontology embeddings
keyword: Description Logic
keyword: EL++
keyword: geometric construction
keyword: model theory
tag rationale: 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.
topic: Neuro-symbolic methods in Bioinformatics

Enhancing Geometric Ontology Embeddings for $\mathcalE\mathcalL^++$ with Negative Sampling and Deductive Closure Filtering
type: ScholarlyArticle
date published: 2024
venue: Neural-Symbolic Learning and Reasoning
bib key: Mashkova2024
bib type: inbook
author raw: Mashkova, Olga
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: EL++
keyword: geometric ontology embedding
keyword: negative sampling
keyword: deductive closure
keyword: description logic
tag rationale: Geometric embeddings for EL++ are the core neuro-symbolic line. Not Applied Ontology.
topic: Neuro-symbolic methods in Bioinformatics

Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference
type: ScholarlyArticle
date published: 2019
venue: The World Wide Web Conference
bib key: Pei2019
bib type: inproceedings
author raw: Pei, Shichao
author raw: Yu, Lu
author raw: Hoehndorf, Robert
author raw: Zhang, Xiangliang
author: Robert Hoehndorf
keyword: knowledge graph embedding
keyword: entity alignment
keyword: semi-supervised learning
keyword: degree difference
keyword: semantic matching
tag rationale: This paper focuses on knowledge graph embedding for entity alignment, which falls under neuro-symbolic AI methods for integrating symbolic knowledge with learning.
topic: Neuro-symbolic methods in Bioinformatics

Ontology-Based Concept Recognition by Using Word Embeddings
type: ScholarlyArticle
date published: 2018
venue: Bio-Ontologies COSI
bib key: Sara2018
bib type: inproceedings
author raw: Sara Althubaiti
author raw: Senay Kafkas
author raw: Robert Hoehndorf
author: Sara Althubaiti
author: Robert Hoehndorf
keyword: ontology-based concept recognition
keyword: word embeddings
keyword: biomedical text mining
keyword: natural language processing
tag rationale: This paper uses word embeddings for ontology-based concept recognition, combining symbolic knowledge with statistical learning, and is applied in a biomedical context.
topic: Neuro-symbolic methods in Bioinformatics
topic: Biomedical informatics

Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies
type: ScholarlyArticle
date published: 2015
venue: Proceedings of International Conference on Biomedical Ontologies (ICBO)
bib key: Slater2015
bib type: inproceedings
author raw: Luke Slater
author raw: Georgios Gkoutos
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: AberOWL
keyword: OWL reasoning
keyword: BioPortal ontologies
keyword: scalable reasoning
keyword: ontology portal
tag rationale: This paper describes the use of AberOWL for fast and scalable reasoning over BioPortal ontologies, directly addressing ontology engineering and semantic interoperability.
topic: Ontology engineering and semantic interoperability

AberOWL: an ontology portal with OWL EL reasoning
type: ScholarlyArticle
date published: 2015
venue: Proceedings of International Conference on Biomedical Ontologies (ICBO)
bib key: Slater2015b
bib type: inproceedings
author raw: Luke Slater
author raw: Georgios Gkoutos
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: AberOWL
keyword: ontology portal
keyword: OWL EL reasoning
keyword: biomedical ontologies
keyword: semantic web
tag rationale: This paper introduces AberOWL as an ontology portal with OWL EL reasoning, which is a key component of ontology engineering and semantic interoperability infrastructure.
topic: Ontology engineering and semantic interoperability

Robust Knowledge Graph Embedding via Denoising
type: ScholarlyArticle
date published: 2026
venue: The Semantic Web -- ESWC 2026
bib key: Song2026
bib type: inbook
author raw: Song, Tengwei
author raw: Ma, Xudong
author raw: Liu, Yang
author raw: Luo, Jie
author raw: Hoehndorf, Robert
author: Tengwei Song
author: Yang Liu
author: Robert Hoehndorf
keyword: knowledge graph embedding
keyword: denoising
keyword: robustness
keyword: noisy triples
keyword: representation learning
tag rationale: Robust KG embedding under triple noise — a neuro-symbolic representation-learning contribution.
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability

SPARQL2OWL: Towards Bridging the Semantic Gap Between RDF and OWL
type: ScholarlyArticle
date published: 2016
venue: Proceedings of the Joint International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016.
bib key: sparql2owl
bib type: inproceedings
author raw: Mona Alshahrani
author raw: Hussein Almashouq
author raw: Robert Hoehndorf
author: Mona Alshahrani
author: Robert Hoehndorf
keyword: SPARQL
keyword: OWL
keyword: RDF
keyword: semantic gap
keyword: knowledge representation
keyword: data integration
tag rationale: This paper focuses on bridging the semantic gap between RDF and OWL using SPARQL, which is central to semantic interoperability and ontology engineering.
topic: Ontology engineering and semantic interoperability

Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion
type: ScholarlyArticle
date published: 2022
venue: Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence
bib key: Tang2022
bib type: inproceedings
author raw: Zhenwei Tang
author raw: Shichao Pei
author raw: Zhao Zhang
author raw: Yongchun Zhu
author raw: Fuzhen Zhuang
author raw: Robert Hoehndorf
author raw: Xiangliang Zhang
author: Zhenwei Tang
author: Robert Hoehndorf
keyword: knowledge graph completion
keyword: positive-unlabeled learning
keyword: adversarial augmentation
keyword: KG embedding
keyword: IJCAI
tag rationale: KG completion methodology; neuro-symbolic, not applied ontology.
topic: Neuro-symbolic methods in Bioinformatics

Neural Multi-hop Logical Query Answering with Concept-Level Answers
type: ScholarlyArticle
venue: The Semantic Web – ISWC 2023
bib key: tang_neural_2023
bib type: inproceedings
author raw: Tang, Zhenwei
author raw: Pei, Shichao
author raw: Peng, Xi
author raw: Zhuang, Fuzhen
author raw: Zhang, Xiangliang
author raw: Hoehndorf, Robert
author: Zhenwei Tang
author: Xi Peng
author: Robert Hoehndorf
keyword: neural query answering
keyword: multi-hop logical queries
keyword: concept-level answers
keyword: knowledge graphs
keyword: symbolic reasoning
tag rationale: 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.
topic: Neuro-symbolic methods in Bioinformatics

Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
type: ScholarlyArticle
date published: 2024
venue: Neural-Symbolic Learning and Reasoning
bib key: ZhapaCamacho2024
bib type: inbook
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: ALC
keyword: lattice
keyword: ontology embedding
keyword: description logic
keyword: saturation
tag rationale: Lattice-preserving ALC ontology embeddings; clearly neuro-symbolic.
topic: Neuro-symbolic methods in Bioinformatics

Fully Geometric Multi-hop Reasoning on Knowledge Graphs with Transitive Relations
type: ScholarlyArticle
date published: 2026
venue: The Semantic Web -- ESWC 2026
bib key: ZhapaCamacho2026
bib type: inbook
author raw: Zhapa-Camacho, Fernando
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
keyword: multi-hop reasoning
keyword: geometric embedding
keyword: transitive relations
keyword: knowledge graph
keyword: description logic
tag rationale: Geometric embeddings for multi-hop reasoning that explicitly model transitive relations — neuro-symbolic graph reasoning.
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Applying ontology design patterns to the implementation of relations in GENIA
type: ScholarlyArticle
date published: 2010
venue: Proceedings of the Fourth Symposium on Semantic Mining in Biomedicine (SMBM 2010)
bib key: h1
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Pyysalo, Sampo
author raw: Ohta, Tomoko
author raw: Oellrich, Anika
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
topic: Applied Ontology

The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes
type: ScholarlyArticle
date published: 2010
venue: Proceedings of the 2nd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
bib key: h2
bib type: inproceedings
author raw: Adams, Nico
author raw: Hennig, Christian
author raw: Hoehndorf, Robert
author raw: Oellrich, Anika
author raw: Rebholz-Schuhmann, Dietrich
author raw: Hansen, Gesine
author: Robert Hoehndorf
topic: Applied Ontology

Relational patterns in OWL and their application to OBO
type: ScholarlyArticle
date published: 2010
venue: OWL: Experiences and Directions (OWLED)
bib key: h4
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Oellrich, Anika
author raw: Dumontier, Michel
author raw: Kelso, Janet
author raw: Herre, Heinrich
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
topic: Applied Ontology

OWLDEF: Integrating OBO and OWL
type: ScholarlyArticle
date published: 2010
venue: Proceedings of the 13th Annual Bio-Ontologies Meeting
bib key: h5
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Oellrich, Anika
author raw: Dumontier, Michel
author raw: Janet Kelso
author raw: Herre, Heinrich
author raw: Rebholz-Schuhmann, Dietrich
author: Robert Hoehndorf
topic: Applied Ontology

The application of an ontology design pattern for functional abnormalities to phenotype ontologies and the extraction of an ontology of anatomical functions
type: ScholarlyArticle
date published: 2009
venue: Proceedings of the The 3rd International Symposium on Languages in Biology and Medicine
bib key: h11
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

Developing Consistent and Modular Software Models with Ontologies
type: ScholarlyArticle
date published: 2009
venue: SoMeT
bib key: h12
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

Contributions to the formal ontology of functions and dispositions: an application of non-monotonic reasoning
type: ScholarlyArticle
date published: 2009
venue: Proceedings of the 12th Annual Bio-Ontologies Meeting
bib key: h13
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Kelso, Janet
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

A Formal Ontology of Sequences
type: ScholarlyArticle
date published: 2009
venue: Nature Precedings
bib key: h14
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Kelso, Janet
author raw: Herre, Heinrich
author: Robert Hoehndorf
topic: Applied Ontology

Towards Ontological Interpretations for Improved Text Mining
type: ScholarlyArticle
date published: 2008
venue: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland
bib key: h16
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Dannemann, Michael
author: Robert Hoehndorf
topic: Applied Ontology

From Terms to Categories: Testing the Significance of Co-occurrences between Ontological Categories
type: ScholarlyArticle
date published: 2008
venue: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland
bib key: h17
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Ngonga Ngomo, Axel-Cyrille
author raw: Dannemann, Michael
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology
type: ScholarlyArticle
date published: 2008
venue: Proceedings of the 11th Annual Bio-Ontologies Meeting
bib key: h18
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Bacher, Joshua
author raw: Backhaus, Michael
author raw: Gregorio, Sergio E.
author raw: Loebe, Frank
author raw: Pr\"ufer, Kay
author raw: Uciteli, Alexandr
author raw: Visagie, Johann
author raw: Herre, Heinrich
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

The design of a wiki-based curation system for the Ontology of Functions
type: ScholarlyArticle
date published: 2006
venue: Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting
bib key: h19
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Pr\"ufer, Kay
author raw: Backhaus, Michael
author raw: Visagie, Johann
author raw: Kelso, Janet
author: Robert Hoehndorf
topic: Applied Ontology

A proposal for a gene functions wiki
type: ScholarlyArticle
date published: 2006
venue: OTM Workshops 2006
bib key: h21
bib type: inproceedings
author raw: Hoehndorf, Robert
author raw: Pr\"ufer, Kay
author raw: Backhaus, Michael
author raw: Herre, Heinrich
author raw: Kelso, Janet
author raw: Loebe, Frank
author raw: Visagie, Johann
author: Robert Hoehndorf
topic: Applied Ontology

BOWiki - a collaborative annotation and ontology curation framework
type: ScholarlyArticle
date published: 2007
venue: Proceedings of Workshop on Social and Collaborative Construction of Structured Knowledge
bib key: h27
bib type: inproceedings
author raw: Backhaus, Michael
author raw: Kelso, Janet
author raw: Bacher, Joshua
author raw: Herre, Heinrich
author raw: Hoehndorf, Robert
author raw: Loebe, Frank
author raw: Visagie, Johann
author: Robert Hoehndorf
topic: Applied Ontology

Higgs bosons, mars missions, and unicorn delusions: How to deal with terms of dubious reference in scientific ontologies
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the Second International Conference on Biomedical Ontology
bib key: unicorn1
bib type: inproceedings
author raw: Stefan Schulz
author raw: Mathias Brochhausen
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: scientific ontologies
keyword: dubious reference
keyword: ontology design
keyword: foundational ontology
keyword: formal ontology
tag rationale: This paper discusses how to deal with terms of dubious reference in scientific ontologies, which is a foundational problem in applied ontology.
topic: Applied Ontology

Investigation of the fundamental strategy for interoperability of description of biological measurements
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the Second International Conference on Biomedical Ontology
bib key: icbo2
bib type: inproceedings
author raw: Hiroshi Masuya
author raw: Georgios V. Gkoutos
author raw: Nobuhiko Tanaka
author raw: Kazunori Waki
author raw: Yoshihiro Okuda
author raw: Tatsuya Kushida
author raw: Norio Kobayashi
author raw: Koji Doi
author raw: Kouji Kozaki
author raw: Robert Hoehndorf
author raw: Shigeharu Wakana
author raw: Tetsuro Toyoda
author raw: Riichiro Mizoguchi
author: Robert Hoehndorf
keyword: biological measurements
keyword: interoperability
keyword: ontology strategy
keyword: data integration
keyword: semantic standards
tag rationale: This paper investigates strategies for interoperability of biological measurements, which is a core aspect of applied ontology and semantic interoperability.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Exploring Gene Ontology Annotations with OWL
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the 13th Bio-Ontology Meeting
bib key: goannos
bib type: inproceedings
author raw: Simon Jupp
author raw: Robert Stevens
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: Gene Ontology
keyword: GO annotations
keyword: OWL
keyword: ontology exploration
keyword: protein function
tag rationale: This paper explores Gene Ontology annotations using OWL, which is an application of ontology for understanding protein function.
topic: Applied Ontology
topic: Protein function prediction

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
bib key: obml2011h1
bib type: inproceedings
author raw: Georgios V. Gkoutos
author raw: Robert Hoehndorf
author: Robert Hoehndorf
keyword: ontology-based integration
keyword: cross-species analysis
keyword: Saccharomyces cerevisiae
keyword: phenotypes
keyword: model organisms
tag rationale: This paper focuses on ontology-based cross-species integration and analysis of phenotypes, which is a key area in applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
bib key: obml2011h2
bib type: inproceedings
author raw: Anika Oellrich
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author raw: Dietrich Rebholz-Schuhmann
author: Robert Hoehndorf
keyword: Human Phenotype Ontology
keyword: Mammalian Phenotype Ontology
keyword: phenotype mapping
keyword: ontology comparison
keyword: semantic similarity measures
tag rationale: This paper focuses on comparing methods for mapping between phenotype ontologies, which falls under phenotype informatics and semantic similarity.
topic: Phenotype informatics
topic: Semantic similarity

Towards Improving Phenotype Representation in OWL
type: ScholarlyArticle
date published: 2011
venue: Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
bib key: obml2011h3
bib type: inproceedings
author raw: Frank Loebe
author raw: Frank Stumpf
author raw: Robert Hoehndorf
author raw: Heinrich Herre
author: Robert Hoehndorf
keyword: phenotype representation
keyword: OWL
keyword: ontology design patterns
keyword: Human Phenotype Ontology
keyword: formal ontology
tag rationale: The paper discusses improving phenotype representation in OWL, which is a core aspect of applied ontology and phenotype informatics.
topic: Applied Ontology
topic: Phenotype informatics

Realism for scientific ontologies
type: ScholarlyArticle
date published: 2010
venue: Formal Ontology in Information Systems, Proceedings of the Sixth International Conference, FOIS 2010
bib key: h8
bib type: inproceedings
author raw: Dumontier, Michel
author raw: Hoehndorf, Robert
author: Robert Hoehndorf
topic: Applied Ontology

Argumentation to Represent and Reason over Biological Systems
type: ScholarlyArticle
date published: 2012
venue: Proceedings of the 3rd International Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2012)
bib key: Wyner2012
bib type: inproceedings
author raw: Adam Wyner
author raw: Luke Riley
author raw: Robert Hoehndorf
author raw: Samuel Croset
author: Robert Hoehndorf
keyword: argumentation
keyword: biological systems
keyword: knowledge representation
keyword: reasoning
keyword: formal ontology
tag rationale: This paper focuses on using argumentation for representing and reasoning over biological systems, which is a method in applied ontology.
topic: Applied Ontology

A translational medicine approach to orphan diseases
type: ScholarlyArticle
date published: 2012
venue: Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012)
bib key: Hoehndorf2012vph1
bib type: inproceedings
author raw: Robert Hoehndorf
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: translational medicine
keyword: orphan diseases
keyword: phenotype-driven diagnosis
keyword: knowledge integration
keyword: patient data
tag rationale: The paper describes a translational medicine approach to orphan diseases, aligning with rare disease diagnostic support and biomedical informatics.
topic: Rare disease diagnostic support
topic: Biomedical informatics

Integration of knowledge for personalized medicine: a pharmacogenomics case-study
type: ScholarlyArticle
date published: 2012
venue: Proceedings of the Virtual Physiological Human Conference 2012 (VPH2012)
bib key: Hoehndorf2012vph2
bib type: inproceedings
author raw: Robert Hoehndorf
author raw: Michel Dumontier
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf
keyword: personalized medicine
keyword: pharmacogenomics
keyword: knowledge integration
keyword: Semantic Web
keyword: drug response
tag rationale: This paper discusses integrating knowledge for personalized medicine in pharmacogenomics, which relates to drug mechanisms and semantic interoperability.
topic: Drug mechanisms and systems biology
topic: Ontology engineering 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)
type: ScholarlyArticle
date published: 2020
venue: CEUR-WS
bib key: 1479305
bib type: proceedings
keyword: ontology workshops
keyword: knowledge representation
keyword: ontology development
keyword: semantic technologies
keyword: ontology applications
tag rationale: As proceedings of ontology workshops, this entry broadly covers applied ontology and ontology engineering.
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
type: ScholarlyArticle
date published: 2025
venue: Gastroenterology
bib key: Alhattab2025
bib type: article
author raw: Alhattab, Dana
author raw: Barakeh, Duna
author raw: Khoja, Basma
author raw: Elhadi, Ahmad
author raw: Miro, Jameel
author raw: Alessy, Saleh A.
author raw: Alharbi, Ahmed
author raw: Bokhary, Manal
author raw: Alzahrani, May
author raw: Ali, Saga
author raw: Almohamdi, Wadha
author raw: Hefni, Lama
author raw: Moretti, Manola
author raw: Liu, Yang
author raw: Abdelhakim, Marwa
author raw: Abdullah, Abeer
author raw: Alomaim, Waleed
author raw: Hoehndorf, Robert
author raw: Hauser, Charlotte
author raw: Alqahtani, Saleh A.
author: Yang Liu
author: Robert Hoehndorf
keyword: colorectal cancer
keyword: organoids
keyword: Saudi patients
keyword: disease modeling
keyword: patient-derived models
tag rationale: This paper describes the development of organoids from Saudi patients for colorectal cancer, which is a bioengineering and biomedical informatics application.
topic: Bioengineering
topic: Biomedical informatics

Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling
type: ScholarlyArticle
date published: 2025
venue: Gastroenterology
bib key: Alhattab2025b
bib type: article
author raw: Alhattab, Dana
author raw: Barakeh, Duna
author raw: Khoja, Basma
author raw: Elhadi, Ahmad
author raw: Miro, Jameel
author raw: Alessy, Saleh A.
author raw: Alharbi, Ahmed
author raw: Bokhary, Manal
author raw: Alzahrani, May
author raw: Ali, Saga
author raw: Almohamdi, Wadha
author raw: Hefni, Lama
author raw: Moretti, Manola
author raw: Abdullah, Abeer
author raw: Alomaim, Waleed
author raw: Hoehndorf, Robert
author raw: Hauser, Charlotte
author raw: Alqahtani, Saleh A.
author: Robert Hoehndorf
keyword: peptide-based matrices
keyword: colorectal organoids
keyword: therapeutic applications
keyword: disease modeling
keyword: drug screening
keyword: tissue engineering
tag rationale: This paper focuses on peptide-based matrices for organoid development and therapeutic applications, fitting bioengineering and drug mechanisms.
topic: Bioengineering
topic: Drug mechanisms and systems biology

Datamining with Ontologies
type: ScholarlyArticle
date published: 2016
venue: Data Mining Techniques for the Life Sciences
bib key: Hoehndorf2016abc
bib type: inbook
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author raw: Schofield, Paul N.
author: Robert Hoehndorf
keyword: data mining
keyword: ontologies
keyword: life sciences
keyword: knowledge-driven data analysis
keyword: semantic data mining
tag rationale: This paper discusses data mining with ontologies in life sciences, which is a key aspect of biomedical informatics and applied ontology.
topic: Biomedical informatics
topic: Applied Ontology

Computational prediction of protein functional annotations
type: ScholarlyArticle
date published: 2025
venue: Protein Function Prediction
bib key: Kulmanov2025x
bib type: inbook
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: protein function prediction
keyword: functional annotations
keyword: Gene Ontology
keyword: computational methods
keyword: deep learning
tag rationale: The paper's title explicitly states 'Computational prediction of protein functional annotations', directly aligning with protein function prediction.
topic: Protein function prediction

The informatics of developmental phenotypes
type: ScholarlyArticle
date published: 2025
venue: Kaufman’s Atlas of Mouse Development Supplement
bib key: Schofield2025
bib type: inbook
author raw: Schofield, Paul N.
author raw: Hoehndorf, Robert
author raw: Gkoutos, Georgios V.
author raw: Smith, Cynthia L.
author: Robert Hoehndorf
keyword: developmental phenotypes
keyword: phenotype informatics
keyword: phenotype standardization
keyword: mouse development
keyword: phenotype ontologies
tag rationale: This paper focuses on the informatics of developmental phenotypes, which is a core area of phenotype informatics and biomedical informatics.
topic: Phenotype informatics
topic: Biomedical informatics

Annotating genomes with DeepGO protein function prediction tools
type: ScholarlyArticle
date published: 2025
venue: Protein Function Prediction
bib key: Tawfiq2025
bib type: inbook
author raw: Tawfiq, Rund
author raw: Niu, Kexin
author raw: Kulmanov, Maxat
author raw: Hoehndorf, Robert
author: Rund Tawfiq
author: Kexin Niu
author: Maxat Kulmanov
author: Robert Hoehndorf
keyword: genome annotation
keyword: DeepGO
keyword: protein function prediction
keyword: Gene Ontology
keyword: genomic analysis
tag rationale: This paper describes annotating genomes using DeepGO tools for protein function prediction, directly linking to protein function prediction and genomics.
topic: Protein function prediction
topic: Genomics

Kaufmann's Atlas of Mouse Development Supplement
type: ScholarlyArticle
date published: 2015
venue: Elsevier Academic Press
bib key: mouseatlas
bib type: inbook
author raw: Paul N. Schofield
author raw: Robert Hoehndorf
author raw: Cynthia L. Smith
author raw: Janan T. Eppig
author raw: Georgios V. Gkoutos
author: Robert Hoehndorf

Ontologies in Biology
type: ScholarlyArticle
date published: 2010
venue: Theory and Applications of Ontology: Computer Applications
bib key: h9
bib type: incollection
author raw: Kelso, Janet
author raw: Hoehndorf, Robert
author raw: Pr\"ufer, Kay
author: Robert Hoehndorf
topic: Applied Ontology

Knowledge Representation and Reasoning
type: Course
year: 2026
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Neurosymbolic AI
type: Course
year: 2026
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 394D
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
instructor: Robert Hoehndorf

Application of AI in Bioinformatics
type: Course
year: 2025
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 321
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
instructor: Robert Hoehndorf

Algorithms in Bioinformatics
type: Course
year: 2025
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 249
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction
instructor: Robert Hoehndorf

Foundations of Bioengineering
type: Course
year: 2025
institution: KAUST
program: Bioengineering
role: Co-Instructor
course code: BioE 200
topic: Bioengineering
instructor: Robert Hoehndorf

Foundations of Bioengineering
type: Course
year: 2024
institution: KAUST
program: Bioengineering
role: Co-Instructor
course code: BioE 200
topic: Bioengineering
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2024
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Neurosymbolic AI
type: Course
year: 2024
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 394D
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
instructor: Robert Hoehndorf

Data Analytics
type: Course
year: 2023
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 220
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Algorithms in Bioinformatics
type: Course
year: 2022
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 249
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2022
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Foundations of Bioengineering
type: Course
year: 2021
institution: KAUST
program: Bioengineering
role: Co-Instructor
course code: BioE 200
topic: Bioengineering
instructor: Robert Hoehndorf

Data Analytics
type: Course
year: 2021
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 220
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2021
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Algorithms in Bioinformatics
type: Course
year: 2020
institution: KAUST
program: Computer Science / Bioengineering
role: Instructor
course code: CS 290
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2020
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Introduction to Artificial Intelligence
type: Course
year: 2019
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 290 E
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Applied Ontology
type: Course
year: 2018
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 322
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2017-2018
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
instructor: Robert Hoehndorf

Applied Ontology
type: Course
year: 2016-2017
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 390EE
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability
instructor: Robert Hoehndorf

Knowledge Representation and Reasoning
type: Course
year: 2015-2016
institution: KAUST
program: Computer Science
role: Instructor
course code: CS 213
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
instructor: Robert Hoehndorf

Computer Science Graduate Seminar
type: Course
year: 2015
institution: KAUST
program: Computer Science
role: Organizer
instructor: Robert Hoehndorf

Object-Oriented Programming
type: Course
year: 2014
institution: Northeastern University, Shenyang, China
program: Software Engineering College
role: Instructor
instructor: Robert Hoehndorf

Professional and Personal Development
type: Course
year: 2013-2014
institution: Aberystwyth University
program: Computer Science
role: Instructor
instructor: Robert Hoehndorf

Object-Oriented Programming
type: Course
year: 2013
institution: Northeastern University, Shenyang, China
program: Software Engineering College
role: Instructor
instructor: Robert Hoehndorf

Machine learning
type: Course
year: 2013
institution: Aberystwyth University
program: Computer Science
role: Co-instructor
topic: Neuro-symbolic methods in Bioinformatics
instructor: Robert Hoehndorf

Ontology in medical information systems
type: Course
year: 2005-2008
institution: University of Leipzig
program: Computer Science
role: Co-instructor
topic: Applied Ontology
instructor: Robert Hoehndorf

Computer science and society / Information
type: Course
year: 2006-2007
institution: University of Leipzig
program: Computer Science
role: Instructor and co-organizer
instructor: Robert Hoehndorf

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property ID: ROR
value: KAUST Center for Smart Health, Pathway to Impact Grant Program 2025

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value: https://doi.org/10.13039/501100004052

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