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.
- Section
- Applications
- Keywords
- biomedical knowledge base, PathoPhenoDB, PhenomeBrowser, text mining, biomedical NLP, clinical informatics, EHR analytics, phenotype standardization
Connections
related papers borg:linkedPaper
- DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
- BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
- Aber-OWL: a framework for ontology-based data access in biology
- Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
- Ontology-based prediction of cancer driver genes
- Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
- Predicting candidate genes from phenotypes, functions and anatomical site of expression
- Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
- Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
- Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
- Age-related differences in gene expression and pathway activation following heatstroke
- Ranking Adverse Drug Reactions With Crowdsourcing
- VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
- Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
- The role of ontologies in biological and biomedical research: a functional perspective
- Usage of cell nomenclature in biomedical literature
- Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
- The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
- A reference quality, fully annotated diploid genome from a Saudi individual
- Combining lexical and context features for automatic ontology extension
- Ontology based mining of pathogen--disease associations from literature
- PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
- Multi-faceted semantic clustering with text-derived phenotypes
- Towards similarity-based differential diagnostics for common diseases
- A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text
- Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
- Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
- BioHackathon 2015: Semantics of data for life sciences and reproducible research
- INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
- The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
- The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
- Ontology design patterns to disambiguate relations between genes and gene products in GENIA
- OBML - Ontologies in Biomedicine and Life Sciences
- An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
- Evaluation of research in biomedical ontologies
- Text-mining solutions for biomedical research: enabling integrative biology
- Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
- Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
- Analyzing gene expression data in mice with the Neuro Behavior Ontology
- Enriched biodiversity data as a resource and service
- Ontology based mining of pathogen-disease associations from literature
- Ontology-Based Concept Recognition by Using Word Embeddings
- A translational medicine approach to orphan diseases
- Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
- Datamining with Ontologies
- The informatics of developmental phenotypes
related people borg:linkedPerson
related courses borg:linkedCourse
media coverage borg:linkedMedia
- Database to support infectious disease research
- Disease researchers have a way with words
- AI tool maps hidden links between diseases
- AI tool maps hidden links between diseases
- AI tool maps hidden links between diseases
- Scientists link 8,000+ diseases in one giant web
- Database to support infectious disease research
- Sci-Café: Can big data solve my health problems?
- Robert Hoehndorf at the KAUST-MBSC Healthcare Analytics and Data Science Workshop
Referenced by
research topics borg:topic
- Robert Hoehndorf
- Imane Boudellioua
- Maxat Kulmanov
- Sarah Alghamdi
- Azza Althagafi
- Sumyyah Toonsi
- Rund Tawfiq
- Yang Liu
- Sara Althubaiti
- Ontology-based prediction of cancer driver genes
- Combining lexical and context features for automatic ontology extension
- The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
- Ontology based mining of pathogen--disease associations from literature
- PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
- Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes
- Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
- DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
- BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
- Aber-OWL: a framework for ontology-based data access in biology
- Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing
- Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
- Predicting candidate genes from phenotypes, functions and anatomical site of expression
- Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice
- Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics
- Age-related differences in gene expression and pathway activation following heatstroke
- Ranking Adverse Drug Reactions With Crowdsourcing
- VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale
- Genomic landscape in Saudi patients with hepatocellular carcinoma using whole-genome sequencing: a pilot study
- The role of ontologies in biological and biomedical research: a functional perspective
- Usage of cell nomenclature in biomedical literature
- A reference quality, fully annotated diploid genome from a Saudi individual
- Multi-faceted semantic clustering with text-derived phenotypes
- Towards similarity-based differential diagnostics for common diseases
- A fast, accurate, and generalisable heuristic-based negation detection algorithm for clinical text
- Taxon and trait recognition from digitized herbarium specimens using deep convolutional neural networks
- Causal relationships between diseases mined from the literature improve the use of polygenic risk scores
- BioHackathon 2015: Semantics of data for life sciences and reproducible research
- INDIGENA: inductive prediction of disease–gene associations using phenotype ontologies
- The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
- The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.
- Ontology design patterns to disambiguate relations between genes and gene products in GENIA
- OBML - Ontologies in Biomedicine and Life Sciences
- An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
- Evaluation of research in biomedical ontologies
- Text-mining solutions for biomedical research: enabling integrative biology
- Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
- Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources
- Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)
- Analyzing gene expression data in mice with the Neuro Behavior Ontology
- Enriched biodiversity data as a resource and service
- Ontology based mining of pathogen-disease associations from literature
- Ontology-Based Concept Recognition by Using Word Embeddings
- A translational medicine approach to orphan diseases
- Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study
- Datamining with Ontologies
- The informatics of developmental phenotypes
- Application of AI in Bioinformatics
- Algorithms in Bioinformatics
- Data Analytics
- Algorithms in Bioinformatics
- Data Analytics
- Algorithms in Bioinformatics
covers topic borg:aboutTopic
- Database to support infectious disease research
- Disease researchers have a way with words
- AI tool maps hidden links between diseases
- AI tool maps hidden links between diseases
- AI tool maps hidden links between diseases
- Scientists link 8,000+ diseases in one giant web
- Database to support infectious disease research
- Sci-Café: Can big data solve my health problems?
- Robert Hoehndorf at the KAUST-MBSC Healthcare Analytics and Data Science Workshop
Open in the interactive graph →
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