Defining standards for the annotation and integration of disease relevant data across the model organism databases of the Alliance of Genome Resources (AGR)
Year: 2017
Type: other
Abstract: Model organisms are widely used to augment investigation into the etiopathogenesis of human disease. Coupling human sequence, phenotypes, pathogenicity variant calls and other biological evidence with experimental data from tractable model organisms can accelerate the identification of causative disease variants and the testing of therapeutic candidates. At present, disease relevant data reside in different formats within multiple independent databases, making data extraction and synthesis difficult and time consuming. The Alliance of Genome Resources (AGR) seeks to standardize and integrate these data in order to facilitate the search and retrieval of disease information from a single interface. Six model organism databases (MODs), including the Saccharomyces Genome Database (SGD), WormBase (WB), FlyBase (FB), the Zebrafish Information Network (ZFIN), the Rat Genome Database (RGD) and Mouse Genome Informatics (MGI), have collaborated to create annotation standards for model organism disease model data. We have converged upon using the Disease Ontology (DO) as a common source of disease terms and definitions, and we are actively working with the DO group to enhance the content and structure of the ontology so that it may be fully adopted by all MODs. We have created specifications for a common data exchange file, the Disease Association File (DAF), to standardize disease model annotation data for integration into the AGR unified resource. This specification includes: the ID of the object being annotated, such as a genotype, strain, allele or gene; experimental conditions required for the model, such as chemical exposure or dietary modification; the associated disease identifier (DO ID); the identity and effects of modifiers of the disease model, such as treatments; evidence codes for these assertions; and an attributed reference. DAF data sets from the MODs have been created and are currently being pulled into a common resource. We will show examples of the first beta version of gene pages in the unified AGR interface showing model organism disease data, together with our plans for disease reports that will integrate MOD data with human gene-to-disease associations.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W2625668296