ArticleJournal of biomedical semantics2013
The Drosophila phenotype ontology.
Article in Journal of biomedical semantics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.Genetics · 2025Article
- The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.bioRxiv : the preprint server for biology · 2024Article
- Contribution of model organism phenotypes to the computational identification of human disease genes.Disease models & mechanisms · 2022Article
- Article
- The Human Phenotype Ontology in 2021.Nucleic acids research · 2021Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.Nucleic acids research · 2020Article
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.Journal of integrative bioinformatics · 2017Review
- FlyBase at 25: looking to the future.Nucleic acids research · 2017Article
- The OWL Reasoner Evaluation (ORE) 2015 Competition Report.Journal of automated reasoning · 2017Article
- Exploring FlyBase Data Using QuickSearch.Current protocols in bioinformatics · 2016Article
- Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila.Nature communications · 2016Article
- Using FlyBase, a Database of Drosophila Genes and Genomes.Methods in molecular biology (Clifton, N.J.) · 2016Review
- Cross-organism analysis using InterMine.Genesis (New York, N.Y. : 2000) · 2015Review
- My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.Journal of biomedical semantics · 2015Article
- Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens.Journal of biomedical semantics · 2015Article
- Patterns of positive selection in seven ant genomes.Molecular biology and evolution · 2014Article
- Phenotype ontologies and cross-species analysis for translational research.PLoS genetics · 2014Review
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Authors and funding
9 authors.
Funding
Abstract
backgroundPhenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions.
resultsWe have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable.
conclusionsThe DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila community, which may ultimately result in its extension to cover a broader range of phenotypes.
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Registered trials
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