COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies

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.

The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible

“…Detailed output from this pipeline is made available in a per-sample analysis report ( Fig. S1 ) that includes a full report on variants identified in the sample (annotated using information from the COMBAT-TB NeoDB [ 29 ]), drug resistance prediction (from TB-Profiler), and quality control information on read mapping.…”

“…Finally the filtered, annotated variants and the TBProfiler results are fed to tb_vcf_report (v. 0.1.7), which produces a report further annotated with information from the COMBAT-TB eXplorer database ( 29 ) in both text and HTML formats.…”

The COMBAT-TB Workbench: Making powerful TB bioinformatics accessible

“…The M. tuberculosis Sample Report pipeline (see Materials and Methods) was run on all 30 samples. Detailed output from this pipeline is made available in a per-sample analysis report (Supplementary Figure 1) that includes a full report on variants identified in the sample (annotated using information from the COMBAT-TB NeoDB (28)), drug resistance prediction (from TB-Profiler) and quality control information on read mapping.…”

“…Finally the filtered, annotated variants and the TBProfiler results are fed to tb_vcf_report (v. 0.1.7) which produces a report further annotated with information from the COMBAT-TB eXplorer database (28) in both text and HTML formats.…”

Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic

“…The talks began with Peter van Heusden (South African National Bioinformatics Institute, South Africa ) who presented his work on the COMBAT-TB workbench [17], a high-throughput web-based tool for routine Mycobacterium tuberculosis analysis, accessible to non-specialist users. This tool improves the disjointed nature of using individual programmes for genomic analysis, and provides a comprehensive breakdown of data, using visual aids such as graphs.…”