ArticleBMC developmental biology2008
An ontology for Xenopus anatomy and development.
Article in BMC developmental biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 58 citations in OpenAlex.
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- Foxi1 regulates multipotent mucociliary progenitors and ionocyte specification through transcriptional and epigenetic mechanisms.PLoS biology · 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
- Cellular Distribution Pattern of tjp1 (ZO-1) in Xenopus laevis Oocytes Heterologously Expressing Claudins.The Journal of membrane biology · 2023Article
- Phenotypic variation in Xenopus laevis tadpoles from contrasting climatic regimes is the result of adaptation and plasticity.Oecologia · 2022Article
- Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.Development (Cambridge, England) · 2021Article
- The skin microbiome of Xenopus laevis and the effects of husbandry conditions.Animal microbiome · 2021Article
- The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.Nucleic acids research · 2021Article
- The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX).Frontiers in cell and developmental biology · 2021Article
- Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.BMC medical informatics and decision making · 2020Article
- Where to search top-K biomedical ontologies?Briefings in bioinformatics · 2019Review
- The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.Science (New York, N.Y.) · 2018Article
- Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine.BMC bioinformatics · 2018Article
- COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.Journal of proteome research · 2018Article
- Xenbase: a genomic, epigenomic and transcriptomic model organism database.Nucleic acids research · 2018Article
- Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.Methods in molecular biology (Clifton, N.J.) · 2018Article
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.Journal of biomedical semantics · 2016Article
- Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.BMC developmental biology · 2016Article
- The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.Journal of biomedical semantics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information. Xenbase is a model organism database that provides centralized access to this information, including gene function data from high-throughput screens and the scientific literature. A controlled, structured vocabulary for Xenopus anatomy and development is essential for organizing these data.
resultsWe have constructed a Xenopus anatomical ontology that represents the lineage of tissues and the timing of their development. We have classified many anatomical features in a common framework that has been adopted by several model organism database communities. The ontology is available for download at the Open Biomedical Ontologies Foundry http://obofoundry.org.
conclusionThe Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. We encourage community recommendations for updates and improvements to the ontology.
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Registered trials
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 OpenQuestion graph.