Thoba Lose1, Peter van Heusden1, Alan Christoffels1. 1. South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape, Bellville, 7535, South Africa.
Abstract
MOTIVATION: Recent advancements in genomic technologies have enabled high throughput cost-effective generation of 'omics' data from M.tuberculosis (M.tb) isolates, which then gets shared via a number of heterogeneous publicly available biological databases. Albeit useful, fragmented curation negatively impacts the researcher's ability to leverage the data via federated queries. RESULTS: We present Combat-TB-NeoDB, an integrated M.tb 'omics' knowledge-base. Combat-TB-NeoDB is based on Neo4j and was created by binding the labeled property graph model to a suitable ontology namely Chado. Combat-TB-NeoDB enables researchers to execute complex federated queries by linking prominent biological databases, and supplementary M.tb variants data from published literature. AVAILABILITY AND IMPLEMENTATION: The Combat-TB-NeoDB (https://neodb.sanbi.ac.za) repository and all tools mentioned in this manuscript are freely available at https://github.com/COMBAT-TB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Recent advancements in genomic technologies have enabled high throughput cost-effective generation of 'omics' data from M.tuberculosis (M.tb) isolates, which then gets shared via a number of heterogeneous publicly available biological databases. Albeit useful, fragmented curation negatively impacts the researcher's ability to leverage the data via federated queries. RESULTS: We present Combat-TB-NeoDB, an integrated M.tb 'omics' knowledge-base. Combat-TB-NeoDB is based on Neo4j and was created by binding the labeled property graph model to a suitable ontology namely Chado. Combat-TB-NeoDB enables researchers to execute complex federated queries by linking prominent biological databases, and supplementary M.tb variants data from published literature. AVAILABILITY AND IMPLEMENTATION: The Combat-TB-NeoDB (https://neodb.sanbi.ac.za) repository and all tools mentioned in this manuscript are freely available at https://github.com/COMBAT-TB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.