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BMC Genomics

, 14:129

Human and rodent genomics

Abstract

BackgroundUnderstanding 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.

DescriptionNeurocarta 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.

ConclusionsNeurocarta 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.

KeywordsPhenotype Genes Knowledgebase Brain development AbbreviationsADHDgeneAttention deficit hyperactivity disorder gene database

AlzGeneAlzheimer’s disease gene database

ASDAutism spectrum disorder

CPCerebral palsy

CTDComparative toxicogenomics database

FASDFetal alcohol spectrum disorder

GADGenetic association database

GOGene ontology

GWASdbGenome-wide association study database

IEAInferred from electronic annotation

ISSInferred from sequence or structural similarity

MSGeneMultiple sclerosis gene database

NASNon-traceable author statement

NCBINational Center for Biotechnology Information

OMIMOnline mendelian inheritance in man

PDGeneParkinson’s disease gene database

RGDRat genome database

SFARISimons Foundation Autism Research Initiative.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-129 contains supplementary material, which is available to authorized users.

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Author: Elodie Portales-Casamar - Carolyn Ch’ng - Frances Lui - Nicolas St-Georges - Anton Zoubarev - Artemis Y Lai - Mark Lee -

Source: https://link.springer.com/



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