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

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 2500 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.

Pheno2GRN

“…S1. Phenotype Keyword AutoCompletion: Query phenomics databases and ontologies, currently Phenoscape KB [14], to extract all genes related to a phenotype keyword. Examples of such keywords include "fin", "limb", and "CNS interneuron".…”

“…We utilized the Phenoscape KB, a phenotype repository containing ontologyannotated phenotype data [2] [14], to obtain links between phenotypes and their associated genes. Interactor data is gathered by submitting multiple REST queries to the 31 molecular interaction databases conforming to the PSICQUIC standard.…”

“…Phenotype to genotype research has produced informatics resources such as the Phenoscape Knowledgebase (Phenoscape KB; http://kb.phenoscape.org) [14] and the Phenotype-Genotype Integrator (PhenGenI; www.ncbi.nlm.nih.gov/gap/phegeni) [20]; researchers using these resources have been able to verify key phenotype-genotype relationships [19]. Many tools also exist for the reverse engineering of GRNs from microarray datasets [15][25] [16].…”

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

“…With the success of the Gene Ontology (GO) [14], ontologies have become common in biology [15–17] and more recently the systematics and evolutionary phenotype communities have begun to use them for character description [18–20]. Through the use of description logic formalisms underpinning the Web Ontology Language (OWL) [21] (a World Wide Web Consortium standard) they facilitate semantic reasoning within and across domains that can be performed by computers.…”

Evolutionary phenomics and the emerging enlightenment of arthropod systematics

“…the character states) queryable. The most successful deployment of this approach, at least in an evolutionary biology context, is found in the world of ichthyology (Phenoscape project; see Mabee et al 2012). Phenoscape combines morphological data from fish phylogenetic matrices with data from mutant model organisms (primarily Danio rerio; http://zfin.org) and uses the logic inherent in ontologies to inform, in part, hypotheses about genotypephenotype interactions.…”