About
The Combat-TB eXplorer web application, developed under the auspices of the Computational Bacterial Analytical Toolkit for TB (COMBAT-TB) COMBAT-TB, serves as a front-end to the Combat-TB-NeoDB which integrates M.tuberculosis (M.tb) ‘omics’ data in a Graph database enabling M.tb researchers to execute ad hoc complex federated queries with the ability to explore data interactively by linking well-known, curated and widely used biological data resources, and supplementary TB variants data from published literature tuberculosis.
Data Sources
Biological Databases
Prominent biological resources were used to build a database containing the most updated functional genome annotation information with bi-monthly updates.
| # | Database | URL |
|---|---|---|
| 1 | EnsemblBacteria | https://bacteria.ensembl.org/ |
| 2 | UniProt | https://www.uniprot.org/ |
| 3 | QuickGo | https://www.ebi.ac.uk/QuickGO/ |
| 4 | InterPro | https://www.ebi.ac.uk/interpro/ |
| 5 | KEGG | https://www.kegg.jp/ |
| 6 | Reactome | https://reactome.org/ |
| 7 | STRING (v11.0) | https://string-db.org/ |
| 8 | DrugBank (v5.1.4) | https://www.drugbank.ca/ |
| 9 | PubMed | https://www.ncbi.nlm.nih.gov/pubmed/ |
Reference Genome
Annotation of M.tb is done primarily using the H37Rv strain, the most studied strain, as a starting point with additional strains to be added in subsequent releases of the database. A tool called tb2neo was developed to integrate and import M.tb data from the above mentioned biological resources into Neo4j. tb2neo takes the H37Rv GFF3 file from EnsemblBacteria as input and generates the Combat-TB-NeoDB reference Graph database.
M.tb Variants Libraries
To integrate known drug resistance-conferring variants, we utilised libraries curated by resources in the table below.
| # | Source | Reference |
|---|---|---|
| 1 | TBProfiler | https://dio.org/10.1186/s13073-015-0164-0 |
| 2 | PhyResSe | https://dio.org/10.1128/JCM.00025-15 |
Combat-TB-NeoDB
The Combat-TB-NeoDB Graph Database models the M.tb `omics` as an interconnected graph database. For more information on the installation of the Graph database, please refer to the Installation section of the documentation.
