Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
type: Project
funded by: Personalized cancer treatment prediction (KCSH Pathway to Impact 2025)
has member: Robert Hoehndorf
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
type: Project
funded by: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
has member: Robert Hoehndorf
has member: Mahdi Bu Ali
topic: Drug mechanisms and systems biology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
type: Project
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
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Semantic similarity

Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
type: Project
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
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
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
topic: Genomics
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Enabling desert revegetation by AI-tailored soil microbiome fortification
type: Project
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
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Enabling mangrove restoration by AI-tailored microbiome fortification
type: Project
funded by: Enabling mangrove restoration by AI-tailored microbiome fortification
has member: Heribert Hirt
has member: Robert Hoehndorf
topic: Genomics
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics

Metagenomics-based surface prospecting
type: Project
funded by: Metagenomics-based surface prospecting
has member: Robert Hoehndorf
has member: Takashi Gojobori
topic: Metagenomics and microbial community function

Evolutionary potential of corals to adapt to climate warming
type: Project
funded by: Evolutionary potential of corals to adapt to climate warming
has member: Manuel Aranda
has member: Robert Hoehndorf
topic: Genomics
topic: Protein function prediction

Computational methods for functional metagenomics: from protein functions to multi-scale interactions
type: Project
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
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
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
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Development of Algorithms for Biotechnology and Biomedical Applications
type: Project
funded by: Development of Algorithms for Biotechnology and Biomedical Applications
has member: Robert Hoehndorf
has member: Sumyyah Toonsi
topic: Neuro-symbolic methods in Bioinformatics

CompleX: Variant Prioritization in Complex Disease
type: Project
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
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Improving health of Saudi population
type: Project
funded by: Improving health of Saudi population
has member: Robert Hoehndorf
has member: Sakhaa Alsaedi
has member: Yang Liu
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Whole genome sequencing of rare disease patients
type: Project
funded by: Whole genome sequencing of rare disease patients
has member: Robert Hoehndorf
topic: Rare disease diagnostic support

Sequencing and computational analysis of MRSA samples
type: Project
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
topic: Genomics
topic: Metagenomics and microbial community function

Improvement of genetic variant prioritization technology
type: Project
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
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Bio2Vec: Smart analytics infrastructure for the life sciences
type: Project
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
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
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
topic: Genomics

Data integration and ontologies for microbial cell factories
type: Project
funded by: Data integration and ontologies for microbial cell factories
has member: Vladimir Bajic
has member: Robert Hoehndorf
has member: Miguel Angel Rodriguez Garcia
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
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: King Abdullah University of Science and Technology

KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)
type: Grant
funder: King Abdullah University of Science and Technology

Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)
type: Grant
funder: King Abdullah University of Science and Technology

Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications
type: Grant
funder: King Abdullah University of Science and Technology

A public Saudi pangenome as reference for genomics in the Middle East
type: Grant
funder: King Abdullah University of Science and Technology

Enabling desert revegetation by AI-tailored soil microbiome fortification
type: Grant
funder: King Abdullah University of Science and Technology

Enabling mangrove restoration by AI-tailored microbiome fortification
type: Grant
funder: King Abdullah University of Science and Technology

Metagenomics-based surface prospecting
type: Grant
funder: Saudi Aramco

Evolutionary potential of corals to adapt to climate warming
type: Grant
funder: King Abdullah University of Science and Technology

Computational methods for functional metagenomics: from protein functions to multi-scale interactions
type: Grant
funder: King Abdullah University of Science and Technology

IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information
type: Grant
funder: King Abdullah University of Science and Technology

Development of Algorithms for Biotechnology and Biomedical Applications
type: Grant
funder: King Abdullah University of Science and Technology

CompleX: Variant Prioritization in Complex Disease
type: Grant
funder: King Abdullah University of Science and Technology

Improving health of Saudi population
type: Grant
funder: King Abdullah University of Science and Technology

Whole genome sequencing of rare disease patients
type: Grant
funder: King Abdullah University of Science and Technology

Sequencing and computational analysis of MRSA samples
type: Grant
funder: King Abdulaziz City for Science and Technology

Improvement of genetic variant prioritization technology
type: Grant
funder: King Abdullah University of Science and Technology

Bio2Vec: Smart analytics infrastructure for the life sciences
type: Grant
funder: King Abdullah University of Science and Technology

The Whale Shark 100: Applying Population Genomics to Understand Mysteries of the World's Largest Fish
type: Grant
funder: King Abdullah University of Science and Technology

Data integration and ontologies for microbial cell factories
type: Grant
funder: King Abdullah University of Science and Technology

KAUST Center of Excellence for Smart Health — BCB research theme (Infectious Disease area)
type: Grant
funder: King Abdullah University of Science and Technology

Robert Hoehndorf
type: Person
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

Imane Boudellioua
type: Person
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
type: Person
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

Maxat Kulmanov
type: Person
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

Sarah Alghamdi
type: Person
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
type: Person
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
type: Person
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

Rund Tawfiq
type: Person
topic: Protein function prediction
topic: Genomics
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology

Yang Liu
type: Person
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

Fernando Zhapa-Camacho
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Ontology engineering and semantic interoperability
topic: Semantic similarity

Sakhaa Alsaedi
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Abeer Almutairi
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Sara Althubaiti
type: Person
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

Daulet Toibazar
type: Person
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Maria G Gomez Castillo
type: Person

Amal Alhelal
type: Person
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Md Nurul Muttakin
type: Person
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Hatoon Al Ali
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Shahad Qatan
type: Person
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Kexin Niu
type: Person
topic: Protein function prediction
topic: Metagenomics and microbial community function
topic: Genomics
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Xi Peng
type: Person
topic: Applied Ontology
topic: Rare disease diagnostic support
topic: Neuro-symbolic methods in Bioinformatics
topic: Genomics

Zhenwei Tang
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology
topic: Protein function prediction
topic: Rare disease diagnostic support

Safana Bakheet
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Melissa Rios Zertuche
type: Person

Sawsan Al Boeisa
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Mahdi Bu Ali
type: Person
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

Mohammad Ashhad
type: Person

Asaad Mohammedsaleh
type: Person
topic: Applied Ontology
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Miguel Angel Rodriguez Garcia
type: Person
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

Ashraf Kibraya
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Tengwei Song
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Semantic similarity

Aleksei Matveev
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Charlotte Hauser
type: Person
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Malak Althagafi
type: Person
topic: Genomics
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support

Heribert Hirt
type: Person
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction
topic: Genomics

Gabriel Wittum
type: Person
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Arne Nägel
type: Person
topic: Metagenomics and microbial community function
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Manuel Aranda
type: Person
topic: Genomics
topic: Protein function prediction

Takashi Gojobori
type: Person
topic: Metagenomics and microbial community function
topic: Genomics
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Paul N Schofield
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity
topic: Ontology engineering and semantic interoperability

Georgios V Gkoutos
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Rare disease diagnostic support
topic: Semantic similarity

Mohammed Al Fageeh
type: Person
topic: Genomics
topic: Metagenomics and microbial community function

Vladimir Bajic
type: Person
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

Xin Gao
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

Michel Dumontier
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

Jens Lehmann
type: Person
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics
topic: Semantic similarity

Michael Berumen
type: Person
topic: Genomics

mOWL
type: SoftwareApplication
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
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

catE
type: SoftwareApplication
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

DELE
type: SoftwareApplication
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

OPA2Vec
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease

Onto2Vec
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DL2Vec
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

Walking RDF and OWL
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

EL2Box
type: SoftwareApplication
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

Interpretable Learning
type: SoftwareApplication
from project: Towards sound, complete, and explainable machine learning with biomedical ontologies (CRG11)

DeepGOPlus
type: SoftwareApplication
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
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
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepGOZero
type: SoftwareApplication
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepGOMeta
type: SoftwareApplication
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
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

DeepPheno
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease

GO-Agent
type: SoftwareApplication
from project: KAUST Center of Excellence for Generative AI (Health and Wellness, BCB theme)

PhenoGoCon
type: SoftwareApplication
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

Genomic Context
type: SoftwareApplication
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

AberOWL
type: SoftwareApplication
from project: Data integration and ontologies for microbial cell factories

Onto2Graph
type: SoftwareApplication
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
from project: IBNSINA-QI: Integrating Biomedical Networks and Semantic Information for Neural network Analysis of Quantitative Information

OntoFunc
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

vec2SPARQL
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

PhenomeNET-VP
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease
from project: Sequencing and computational analysis of MRSA samples

DeepSVP
type: SoftwareApplication
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
from project: CompleX: Variant Prioritization in Complex Disease

STARVar
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease

INDIGENA
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease

GenomeLinter
type: SoftwareApplication
from project: Improvement of genetic variant prioritization technology

predCAN
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease

DeepViral
type: SoftwareApplication
from project: CompleX: Variant Prioritization in Complex Disease

SmuDGE
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
from project: CompleX: Variant Prioritization in Complex Disease

Multi-Drug Embedding
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

DeepMOCCA
type: SoftwareApplication
from project: Bio2Vec: Smart analytics infrastructure for the life sciences

PathoPhenoDB
type: SoftwareApplication
from project: Computational methods for functional metagenomics: from protein functions to multi-scale interactions

NanoDesigner
type: SoftwareApplication
from project: Disease Models from Patient-derived Leukemic Cells in Biomimetic Peptide Scaffolds for Precision Medicine Applications

Machine Learning with Ontologies
type: SoftwareApplication

Ontology Tutorial
type: SoftwareApplication

mOWL Tutorial
type: SoftwareApplication

Units of Measurement Ontology (UO)
type: SoftwareApplication

PhenomeNet
type: SoftwareApplication
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
date published: 2016
venue: Journal of Biomedical Semantics
topic: Applied Ontology
topic: Phenotype informatics

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
type: ScholarlyArticle
date published: 2019
venue: Scientific Reports
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
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
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
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)
topic: Applied Ontology

Ontology-based prediction of cancer driver genes
type: ScholarlyArticle
date published: 2019
venue: Scientific Reports
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
topic: Applied Ontology
topic: Biomedical informatics

Improving the classification of cardinality phenotypes using collections
type: ScholarlyArticle
date published: 2023
venue: Journal of Biomedical Semantics
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)
topic: Applied Ontology

Combining lexical and context features for automatic ontology extension
type: ScholarlyArticle
date published: 2020
venue: Journal of Biomedical Semantics
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

DDIEM: drug database for inborn errors of metabolism
type: ScholarlyArticle
date published: 2020
venue: Orphanet Journal of Rare Diseases
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
topic: Drug mechanisms and systems biology
topic: Rare disease diagnostic support

DeepGOPlus: improved protein function prediction from sequence
type: ScholarlyArticle
date published: 2020
venue: Bioinformatics
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
topic: Protein function prediction
topic: Neuro-symbolic methods in Bioinformatics

Phenotype-driven discovery of digenic variants in personal genome sequences
type: ScholarlyArticle
date published: 2017
venue: Proceedings of VarI-SIG
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Rare disease diagnostic support
topic: Genomics
topic: Phenotype informatics

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
type: ScholarlyArticle
date published: 2020
venue: Bioinformatics
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
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Klarigi: Characteristic explanations for semantic biomedical data
type: ScholarlyArticle
date published: 2023
venue: Computers in Biology and Medicine
from project: CompleX: Variant Prioritization in Complex Disease
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
date published: 2025
venue: Scientific Reports
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)
topic: Rare disease diagnostic support
topic: Biomedical informatics

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
type: ScholarlyArticle
date published: 2020
venue: BMC Medical Informatics and Decision Making
from project: CompleX: Variant Prioritization in Complex Disease
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Neuro-Symbolic AI in Life Sciences
type: ScholarlyArticle
date published: 2025
venue: Handbook on Neurosymbolic AI and Knowledge Graphs
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)
topic: Neuro-symbolic methods in Bioinformatics

Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction
type: ScholarlyArticle
date published: 2024
venue: Neural-Symbolic Learning and Reasoning
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)
topic: Neuro-symbolic methods in Bioinformatics

Ontology Embedding: A Survey of Methods, Applications and Resources
type: ScholarlyArticle
date published: 2025
venue: IEEE Transactions on Knowledge and Data Engineering
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)
topic: Neuro-symbolic methods in Bioinformatics

Ontology based mining of pathogen--disease associations from literature
type: ScholarlyArticle
date published: 2019
venue: Journal of Biomedical Semantics
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Biomedical informatics
topic: Applied Ontology

PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
type: ScholarlyArticle
date published: 2019
venue: Scientific Data
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
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
date published: 2022
venue: Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022
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
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Integrating phenotype ontologies with PhenomeNET
type: ScholarlyArticle
date published: 2016
venue: Proceedings of Ontology Matching Workshop 2016
from project: Data integration and ontologies for microbial cell factories
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
date published: 2023
venue: BMC Bioinformatics
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
topic: Rare disease diagnostic support
topic: Biomedical informatics

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
type: ScholarlyArticle
date published: 2019
venue: Database
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Biomedical informatics
topic: Rare disease diagnostic support

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
type: ScholarlyArticle
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.
from project: Data integration and ontologies for microbial cell factories
from project: Bio2Vec: Smart analytics infrastructure for the life sciences
topic: Neuro-symbolic methods in Bioinformatics
topic: Ontology engineering and semantic interoperability

Improved characterisation of clinical text through ontology-based vocabulary expansion
type: ScholarlyArticle
date published: 2021
venue: Journal of Biomedical Semantics
from project: CompleX: Variant Prioritization in Complex Disease
topic: Biomedical informatics
topic: Phenotype informatics

Semantic similarity and machine learning with ontologies
type: ScholarlyArticle
date published: 2020
venue: Briefings in Bioinformatics
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
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
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
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
type: ScholarlyArticle
date published: 2020
venue: PLOS Computational Biology
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
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
topic: Bioengineering
topic: Genomics

Aber-OWL: a framework for ontology-based data access in biology
type: ScholarlyArticle
date published: 2015
venue: BMC Bioinformatics
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
topic: Genomics
topic: 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
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
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
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
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
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
topic: Rare disease diagnostic support
topic: Genomics

Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
type: ScholarlyArticle
date published: 2024
venue: Bioinformatics
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
topic: Rare disease diagnostic support
topic: Phenotype informatics

GFVO: the Genomic Feature and Variation Ontology
type: ScholarlyArticle
date published: 2015
venue: PeerJ
topic: Applied Ontology
topic: Genomics

Best behaviour? Ontologies and the formal description of animal behaviour
type: ScholarlyArticle
date published: 2015
venue: Mammalian Genome
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
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
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
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
topic: Protein function prediction

An open source knowledge graph ecosystem for the life sciences
type: ScholarlyArticle
date published: 2024
venue: Scientific Data
topic: Ontology engineering and semantic interoperability

Predicting candidate genes from phenotypes, functions and anatomical site of expression
type: ScholarlyArticle
date published: 2021
venue: Bioinformatics
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
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
topic: Phenotype informatics
topic: Biomedical informatics

Data science and symbolic AI: Synergies, challenges and opportunities
type: ScholarlyArticle
date published: 2017
venue: Data Science
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
topic: Phenotype informatics
topic: Biomedical informatics

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
type: ScholarlyArticle
date published: 2017
venue: Bioinformatics
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
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
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
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
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
topic: Biomedical informatics
topic: Bioengineering

Ranking Adverse Drug Reactions With Crowdsourcing
type: ScholarlyArticle
date published: 2015
venue: J Med Internet Res
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
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
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
topic: Applied Ontology

Notions of similarity for systems biology models
type: ScholarlyArticle
date published: 2018
venue: Briefings in Bioinformatics
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
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
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
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
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
topic: Rare disease diagnostic support
topic: Semantic similarity

Usage of cell nomenclature in biomedical literature
type: ScholarlyArticle
date published: 2017
venue: BMC Bioinformatics
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
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
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
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
topic: Genomics

Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
type: ScholarlyArticle
date published: 2025
venue: Scientific Data
topic: Genomics

Nail abnormalities identified in an ageing study of 30 inbred mouse strains
type: ScholarlyArticle
date published: 2019
venue: Experimental Dermatology
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
topic: Genomics
topic: Rare disease diagnostic support

DELE: Deductive EL++ Embeddings for Knowledge Base Completion
type: ScholarlyArticle
date published: 2026
venue: Neurosymbolic Artificial Intelligence
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
topic: Metagenomics and microbial community function

An ontology approach to comparative phenomics in plants
type: ScholarlyArticle
date published: 2015
venue: Plant Methods
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
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
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
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
topic: Metagenomics and microbial community function

The anatomy of phenotype ontologies: principles, properties and applications
type: ScholarlyArticle
date published: 2018
venue: Briefings in Bioinformatics
topic: Applied Ontology
topic: Phenotype informatics

Semantic prioritization of novel causative genomic variants
type: ScholarlyArticle
date published: 2017
venue: PLOS Computational Biology
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
topic: Bioengineering
topic: Drug mechanisms and systems biology

Ontology-based validation and identification of regulatory phenotypes
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
topic: Applied Ontology
topic: Phenotype informatics

DESM: portal for microbial knowledge exploration systems
type: ScholarlyArticle
date published: 2016
venue: Nucleic Acids Research
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
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
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
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
topic: Semantic similarity

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
type: ScholarlyArticle
date published: 2018
venue: Bioinformatics
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
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
topic: Rare disease diagnostic support
topic: Genomics

DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction
type: ScholarlyArticle
date published: 2024
venue: Scientific Reports
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
topic: Biomedical informatics
topic: Rare disease diagnostic support

Causal knowledge graph analysis identifies adverse drug effects
type: ScholarlyArticle
date published: 2025
venue: Bioinformatics
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
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
topic: Applied Ontology

BioHackathon 2015: Semantics of data for life sciences and reproducible research
type: ScholarlyArticle
date published: 2020
venue: F1000Research
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

mOWL: Python library for machine learning with biomedical ontologies
type: ScholarlyArticle
date published: 2023
venue: Bioinformatics
topic: Neuro-symbolic methods in Bioinformatics

LLM Agent Based Protein Function Prediction
type: ScholarlyArticle
date published: 2025
venue: Biocomputing 2026
topic: Protein function prediction

INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
type: ScholarlyArticle
date published: 2026
venue: Bioinformatics

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
type: ScholarlyArticle
date published: 2014
venue: Journal of Biomedical Semantics
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Statistical tests for associations between two directed acyclic graphs.
type: ScholarlyArticle
venue: PloS ONE
topic: Applied Ontology

Applying the functional abnormality ontology pattern to anatomical functions.
type: ScholarlyArticle
venue: Journal of biomedical semantics
topic: Applied Ontology

The ontology of biological sequences.
type: ScholarlyArticle
venue: BMC Bioinformatics
topic: Applied Ontology

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.
type: ScholarlyArticle
venue: BMC Bioinformatics
topic: Applied Ontology

Relations as patterns: bridging the gap between OBO and OWL.
type: ScholarlyArticle
venue: BMC Bioinformatics
topic: Applied Ontology

GFO-Bio: A biomedical core ontology
type: ScholarlyArticle
venue: Applied Ontology
topic: Applied Ontology

Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies
type: ScholarlyArticle
venue: BMC Bioinformatics
topic: Applied Ontology

A top-level ontology of functions and its application in the Open Biomedical Ontologies.
type: ScholarlyArticle
venue: Bioinformatics
topic: Applied Ontology

Interoperability between phenotype and anatomy ontologies
type: ScholarlyArticle
venue: Bioinformatics
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
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
topic: Applied Ontology
topic: Biomedical informatics

PhenomeNET: a whole-phenome approach to disease gene discovery
type: ScholarlyArticle
venue: Nucleic Acids Research
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
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Integrating systems biology models and biomedical ontologies
type: ScholarlyArticle
venue: BMC Systems Biology
topic: Applied Ontology

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
type: ScholarlyArticle
venue: BMC Research Notes
topic: Ontology engineering and semantic interoperability
topic: Biomedical informatics

PIDO: The Primary Immunodeficiency Disease Ontology
type: ScholarlyArticle
venue: Bioinformatics
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
topic: Applied Ontology

Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
type: ScholarlyArticle
date published: 2013
venue: PLoS ONE
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
topic: Biomedical informatics

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
type: ScholarlyArticle
date published: 2013
venue: PLoS ONE
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
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
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
topic: Applied Ontology

Thematic series on biomedical ontologies in JBMS: challenges and new directions
type: ScholarlyArticle
date published: 2014
venue: Journal of Biomedical Semantics
topic: Applied Ontology

Analyzing gene expression data in mice with the Neuro Behavior Ontology
type: ScholarlyArticle
date published: 2014
venue: Mamm Genome
topic: Applied Ontology
topic: Biomedical informatics

Enriched biodiversity data as a resource and service
type: ScholarlyArticle
date published: 2014
venue: Biodiversity Data Journal
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

SIDEKICK: A Semantically Integrated Resource for Drug Effects, Indications, and Contraindications
type: ScholarlyArticle
date published: 2026
venue: The Semantic Web -- ESWC 2026
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
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
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
topic: Applied Ontology

Large-Scale Reasoning over Functions in Biomedical Ontologies
type: ScholarlyArticle
date published: 2016
venue: Formal Ontology in Information Systems
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)
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
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
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
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
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
topic: Neuro-symbolic methods in Bioinformatics

Ontology-Based Concept Recognition by Using Word Embeddings
type: ScholarlyArticle
date published: 2018
venue: Bio-Ontologies COSI
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)
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)
topic: Ontology engineering and semantic interoperability

Robust Knowledge Graph Embedding via Denoising
type: ScholarlyArticle
date published: 2026
venue: The Semantic Web -- ESWC 2026
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.
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
topic: Neuro-symbolic methods in Bioinformatics

Neural Multi-hop Logical Query Answering with Concept-Level Answers
type: ScholarlyArticle
venue: The Semantic Web – ISWC 2023
topic: Neuro-symbolic methods in Bioinformatics

Lattice-Preserving $\mathcal ALC$ Ontology Embeddings
type: ScholarlyArticle
date published: 2024
venue: Neural-Symbolic Learning and Reasoning
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
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)
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)
topic: Applied Ontology

Relational patterns in OWL and their application to OBO
type: ScholarlyArticle
date published: 2010
venue: OWL: Experiences and Directions (OWLED)
topic: Applied Ontology

OWLDEF: Integrating OBO and OWL
type: ScholarlyArticle
date published: 2010
venue: Proceedings of the 13th Annual Bio-Ontologies Meeting
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
topic: Applied Ontology

Developing Consistent and Modular Software Models with Ontologies
type: ScholarlyArticle
date published: 2009
venue: SoMeT
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
topic: Applied Ontology

A Formal Ontology of Sequences
type: ScholarlyArticle
date published: 2009
venue: Nature Precedings
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
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
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
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
topic: Applied Ontology

A proposal for a gene functions wiki
type: ScholarlyArticle
date published: 2006
venue: OTM Workshops 2006
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
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
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
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
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)
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)
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)
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
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)
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)
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)
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
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
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
topic: Bioengineering
topic: Drug mechanisms and systems biology

Datamining with Ontologies
type: ScholarlyArticle
date published: 2016
venue: Data Mining Techniques for the Life Sciences
topic: Biomedical informatics
topic: Applied Ontology

Computational prediction of protein functional annotations
type: ScholarlyArticle
date published: 2025
venue: 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
topic: Phenotype informatics
topic: Biomedical informatics

Annotating genomes with DeepGO protein function prediction tools
type: ScholarlyArticle
date published: 2025
venue: Protein Function Prediction
topic: Protein function prediction
topic: Genomics

Kaufmann's Atlas of Mouse Development Supplement
type: ScholarlyArticle
date published: 2015
venue: Elsevier Academic Press

Ontologies in Biology
type: ScholarlyArticle
date published: 2010
venue: Theory and Applications of Ontology: Computer Applications
topic: Applied Ontology

Neuro-symbolic methods in Bioinformatics
type: Topic

Ontology engineering and semantic interoperability
type: Topic

Applied Ontology
type: Topic

Protein function prediction
type: Topic

Rare disease diagnostic support
type: Topic

Drug mechanisms and systems biology
type: Topic

Genomics
type: Topic

Biomedical informatics
type: Topic

Semantic similarity
type: Topic

Metagenomics and microbial community function
type: Topic

Phenotype informatics
type: Topic

Bioengineering
type: Topic

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Neurosymbolic AI
type: Course
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology

Application of AI in Bioinformatics
type: Course
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics
topic: Protein function prediction

Algorithms in Bioinformatics
type: Course
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction

Foundations of Bioengineering
type: Course
topic: Bioengineering

Foundations of Bioengineering
type: Course
topic: Bioengineering

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Neurosymbolic AI
type: Course
topic: Neuro-symbolic methods in Bioinformatics
topic: Applied Ontology

Data Analytics
type: Course
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics

Algorithms in Bioinformatics
type: Course
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Foundations of Bioengineering
type: Course
topic: Bioengineering

Data Analytics
type: Course
topic: Biomedical informatics
topic: Neuro-symbolic methods in Bioinformatics

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Algorithms in Bioinformatics
type: Course
topic: Biomedical informatics
topic: Genomics
topic: Protein function prediction

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology
topic: Neuro-symbolic methods in Bioinformatics

Introduction to Artificial Intelligence
type: Course
topic: Neuro-symbolic methods in Bioinformatics

Applied Ontology
type: Course
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Applied Ontology
type: Course
topic: Applied Ontology
topic: Ontology engineering and semantic interoperability

Knowledge Representation and Reasoning
type: Course
topic: Ontology engineering and semantic interoperability
topic: Applied Ontology

Computer Science Graduate Seminar
type: Course

Object-Oriented Programming
type: Course

Professional and Personal Development
type: Course

Object-Oriented Programming
type: Course

Machine learning
type: Course
topic: Neuro-symbolic methods in Bioinformatics

Ontology in medical information systems
type: Course
topic: Applied Ontology

Computer science and society / Information
type: Course

King Abdullah University of Science and Technology
type: Organization

Saudi Aramco
type: Organization

King Abdulaziz City for Science and Technology
type: Organization