Animal model integration to AutDB, a genetic database for autism

Abstract

BackgroundIn the post-genomic era, multi-faceted research on complex disorders such as autism has generated diverse types of molecular information related to its pathogenesis. The rapid accumulation of putative candidate genes/loci for Autism Spectrum Disorders (ASD) and ASD-related animal models poses a major challenge for systematic analysis of their content. We previously created the Autism Database (AutDB) to provide a publicly available web portal for ongoing collection, manual annotation, and visualization of genes linked to ASD. Here, we describe the design, development, and integration of a new module within AutDB for ongoing collection and comprehensive cataloguing of ASD-related animal models.DescriptionAs with the original AutDB, all data is extracted from published, peer-reviewed scientific literature. Animal models are annotated with a new standardized vocabulary of phenotypic terms developed by our researchers which is designed to reflect the diverse clinical manifestations of ASD. The new Animal Model module is seamlessly integrated to AutDB for dissemination of diverse information related to ASD. Animal model entries within the new module are linked to corresponding candidate genes in the original "Human Gene" module of the resource, thereby allowing for cross-modal navigation between gene models and human gene studies. Although the current release of the Animal Model module is restricted to mouse models, it was designed with an expandable framework which can easily incorporate additional species and non-genetic etiological models of autism in the future.ConclusionsImportantly, this modular ASD database provides a platform from which data mining, bioinformatics, and/or computational biology strategies may be adopted to develop predictive disease models that may offer further insights into the molecular underpinnings of this disorder. It also serves as a general model for disease-driven databases curating phenotypic characteristics of corresponding animal models.

Animal Models of Autism Spectrum Disorder

“…Autism Database (AutDB) which was created by Basu et al [68] is of great importance in this regard. A module within AutDB for ongoing collection and comprehensive cataloguing of ASD-related animal models was introduced by Kumar et al [69]. This study also should not escape the investigators' notice.…”

Production of Transgenic Nonhuman Primates

“…Indeed, this study suggests the importance of the correlation between early brain development, when brain structures and functions develop higher order abilities with the emergence of neuropsychiatric symptoms. Studies in rodents have suggested that modulation of ASD susceptibility genes can directly lead to phenotypic changes that parallel those seen in human patients (Bangash et al, 2011;Bozdagi et al, 2010;Kumar et al, 2011;Patterson, 2011;Peca et al, 2011;Wang et al, 2011). Although transgenic rodent models have been widely used for evaluating the genetic abnormalities observed in human patients, there are limitations in nonprimate models for studying psychiatric disorders.…”

Genetic Evaluation of Individuals with Autism Spectrum Disorders

“…The Animal Model module contains a comprehensive collection of mouse models linked to ASD [41]. While the Animal Model module initially contained only genetic mouse models of ASD, it has since been expanded to include induced mouse models of ASD in which a chemical or biological agent linked to ASD has been administered.…”