ArticleBriefings in bioinformatics2018
The anatomy of phenotype ontologies: principles, properties and applications.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 2 of them syntheses that pooled it.
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Who cites it
59 citing papers in PubMed, 2 syntheses or guidelines pooled it, 109 citations in OpenAlex.
- A systematic review to identify target genes that modulate root system architecture in response to abiotic stress.Scientific reports · 2025Pooled it
- Computational resources associating diseases with genotypes, phenotypes and exposures.Briefings in bioinformatics · 2019Pooled it
- Comparative assessment of large language models for microbial phenotype assignment.Genome biology · 2026Article
- The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.Cell genomics · 2026Article
- Ontology-driven dual-channel relational graph convolutional network (DCR-GCN) for lettuce leaf phenotype classification.Plant methods · 2026Article
- INDIGENA: inductive prediction of disease-gene associations using phenotype ontologies.Bioinformatics (Oxford, England) · 2026Article
- VO: The Vaccine Ontology.Scientific data · 2026Article
- CartograPlant: bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.Genetics · 2026Article
- Advancing the bioassay ontology through integrated PK/PD and safety pharmacology representation.Journal of biomedical semantics · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- CMEO: a metadata-centric ontology for clinical studies exploration and harmonization assessment.BMC medical informatics and decision making · 2025Article
- Nicheformer: a foundation model for single-cell and spatial omics.Nature methods · 2025Article
- Refining the diagnostic accuracy of Parkinsonian disorders using metaphenomic annotation of the clinicopathological literature.NPJ Parkinson's disease · 2025Article
- VO: The Vaccine Ontology.bioRxiv : the preprint server for biology · 2025Article
- Representation of chemistry transport models simulations using knowledge graphs.Journal of cheminformatics · 2025Article
- The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients.Scientific reports · 2025Article
- AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships.Computational and structural biotechnology journal · 2025Review
- Automated annotation of scientific texts for ML-based keyphrase extraction and validation.Database : the journal of biological databases and curation · 2024Article
- Review
- Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies. A large number of these ontologies have been developed across many domains, and we are now at a point where the knowledge captured in the structure of these ontologies can be used for the integration and analysis of large interrelated data sets. The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration and analysis of phenotype data. Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.