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500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.

dc.contributor.author Balhoff, JP
dc.contributor.author Dahdul, Wasila M
dc.contributor.author Lapp, Hilmar
dc.contributor.author Mabee, BP
dc.contributor.author Midford, PE
dc.contributor.author Vision, TJ
dc.contributor.author Westerfield, M
dc.coverage.spatial Germany
dc.date.accessioned 2017-06-25T19:05:07Z
dc.date.available 2017-06-25T19:05:07Z
dc.date.issued 2012-06-01
dc.identifier https://www.ncbi.nlm.nih.gov/pubmed/22736877
dc.identifier.issn 0175-8659
dc.identifier.uri http://hdl.handle.net/10161/14954
dc.description.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.
dc.language eng
dc.relation.ispartof J Appl Ichthyol
dc.relation.isversionof 10.1111/j.1439-0426.2012.01985.x
dc.title 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.
dc.type Journal article
pubs.author-url https://www.ncbi.nlm.nih.gov/pubmed/22736877
pubs.begin-page 300
pubs.end-page 305
pubs.issue 3
pubs.organisational-group Duke
pubs.organisational-group Staff
pubs.publication-status Published
pubs.volume 28


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