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Database (Oxford). 2016 May 12;2016. pii: baw073. doi: 10.1093/database/baw073. Print 2016.

The Chinchilla Research Resource Database: resource for an otolaryngology disease model.

Author information

1
Rat Genome Database, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
2
Rat Genome Database, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA jrsmith@mcw.edu.
3
Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, USA.
4
Department of Microbiology and Immunology Department of Otolaryngology-Head and Neck Surgery, Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, Philadelphia, PA, USA.
5
Center for Microbial Pathogenesis, the Research Institute at Nationwide Children's Hospital and the Ohio State University College of Medicine, Columbus, OH, USA.
6
Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, USA Division of Pediatric Otolaryngology, Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, WI, USA.

Abstract

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease.Database URL: http://crrd.mcw.edu.

PMID:
27173523
PMCID:
PMC4865329
DOI:
10.1093/database/baw073
[Indexed for MEDLINE]
Free PMC Article

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