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Big anatomy: he new views from integrated anatomy, development, and genes (338.6)
Author(s) -
Mabee Paula
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.338.6
Subject(s) - ontology , biology , focus (optics) , genomics , computational biology , evolutionary developmental biology , evolutionary biology , phenotype , data science , computer science , bioinformatics , gene , genome , genetics , philosophy , physics , epistemology , optics
Comparative anatomical data are increasingly sought after to guide computational genomics work, to develop evo‐devo hypotheses, and to inform interpretation of organismal evolution in light of molecular phylogenies. Anatomical data, however, are embedded in the literature and uncomputable, thus impairing the ability of investigators to find, aggregate, or link them to other data types. By using ontology‐based methods to represent anatomical features, the Phenoscape team has developed a knowledgebase where the morphological variation of vertebrates, with a specific focus on for fin and limb phenotypes, is linked to genes and phenotypes of zebrafish, Xenopus, mouse and human through their community databases. Using the reasoning enabled by the ontology structure, and assuming a high‐level of conservation of developmental processes, candidate genes can be automatically inferred for morphological features that characterize clades and species. Two such predictions were tested in the wet‐lab, and the results support the broad‐scale utility of this approach. Morphological data in this computable format can be browsed, sorted and aggregated in ways that present unprecedented possibilities for data mining and discovery. Current work by the team includes development of methods for rapid retrieval of similar phenotypes and a focus on the fin/limb skeletal transition.