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Neurocarta: aggregating and sharing disease-gene relations for the neurosciences

Elodie Portales-Casamar, Carolyn Ch’ng, Frances Lui, Nicolas St-Georges, Anton Zoubarev, Artemis Y Lai, Mark Lee, Cathy Kwok, Willie Kwok, Luchia Tseng and Paul Pavlidis*

Author affiliations

Centre for High-Throughput Biology and Department of Psychiatry, University of British Columbia, 2125 East Mall, Vancouver, BC V6T1Z4, Canada

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Citation and License

BMC Genomics 2013, 14:129  doi:10.1186/1471-2164-14-129

Published: 26 February 2013

Abstract

Background

Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools.

Description

Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 7,000 genes to 2,000 different phenotypes.

Conclusions

Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they’re not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta’s in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Keywords:
Phenotype; Genes; Knowledgebase; Brain development