ArticleZeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology2012
500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.
Article in Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Taxonomic inflation in fish systematics: A critical review with illustrative evidence assessment and integrative case study of the Salmo trutta Complex.Journal of fish biology · 2026Review
- Connecting links with code: AI in morphological evolution.Frontiers in bioinformatics · 2026Review
- The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.bioRxiv : the preprint server for biology · 2023Article
- Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.Systematic biology · 2022Article
- Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees.Systematic biology · 2021Article
- Article
- Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.Database : the journal of biological databases and curation · 2018Article
- Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes.PLoS genetics · 2017Article
- Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes.Molecular biology and evolution · 2017Article
- The digital revolution in phenotyping.Briefings in bioinformatics · 2016Article
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.Journal of biomedical semantics · 2016Article
- Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices.PloS one · 2016Article
- The role of ontologies in biological and biomedical research: a functional perspective.Briefings in bioinformatics · 2015Article
- Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.Systematic biology · 2015Article
- A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2015Review
- Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.Database : the journal of biological databases and curation · 2015Article
- A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices.Plant methods · 2015Article
- An ontology approach to comparative phenomics in plants.Plant methods · 2015Article
- Finding our way through phenotypes.PLoS biology · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.
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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.