# TB Online Data Resources This repository contains a list of online resources and datasets for computational analysis relating to Mycobacterium tuberculosis. It is hoped to make this an exhaustive 'living resource'. If you find this resource useful, please share it with your colleagues and consider adding to it!

Organisation

List is structured as follows:
1. General Resources 2. Genomics-related resources 3. Proteomics-related resources 4. Drug-related resources

Entries are formatted as follows:
Hyperlink - Resource Name Description of resource contents Reference

General

PATRIC - Pathosystems Resource Integration Center
PATRIC provides data and analysis tools for multiple omics data types:
* Antibiotic Resistance
* Genomes
* Genomic Features
* Pathways
* Protein Families
* Specialty Genes
* Transcriptomes

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL. Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

Data Sources

Genomics

GMTV Database Project - Genome-based Mycobacterium Tuberculosis Variation Database

Integrates clinical, epidemiological and microbiological description with genome variations based on whole genome sequencing data. Currently the database contains genomic information on 2819 Mycobacterium tuberculosis strains.

Ekaterina N Chernyaeva, Marina V Shulgina, Mikhail S Rotkevich, Pavel V Dobrynin, Serguei A Simonov, Egor A Shitikov, Dmitry S Ischenko, Irina Y Karpova, Elena S Kostryukova, Elena N Ilina, Vadim M Govorun, Vyacheslav Y Zhuravlev, Olga A Manicheva, Peter K Yablonsky, Yulia D Isaeva, Elena Y Nosova, Igor V Mokrousov, Anna A Vyazovaya, Olga V Narvskaya, Alla L Lapidus and Stephen J O’Brien (2014). Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics. 201415:308 https://doi.org/10.1186/1471-2164-15-308

PathogenSeq - LSHTM - WGS & Omics

Collection of tools and data; Use of WGS and Omics to better understand the biology and behaviour of Mycobacterium tuberculosis

• Poly TB - Web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale.
  
• Global Drug Resistance Study - A study to investigate drug resistance in Mycobacterium tuberculosis (Mtb).
  
• Karonga Diversity Study - Karonga Diversity Study
  
• Kampala Study - Analysis of the genome of 51 clinical isolates of M. tuberculosis including drug resistant strains and longitudinal samples from individual patients from Kampala.
  
• TDR TB Strain Bank - The Strain Bank is a collection of well characterized strains of M. tuberculosis that are available to the TB research community
• Rapid DR Study - Web tool that rapidly analyses raw sequence data and predicts resistance and lineage in M. tuberculosis.
  
• Molecular Barcode - SNP barcode for typing Mycobacterium tuberculosis.
  
• PhyTB - Web-based tool to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphisms.
  
• M.aurum - The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae
  
• PE/PPE - PE/PPE gene diversity project
  
• Sequencing Variability - Mtb sequencing variability project
  
• Philippines TB Drug resistance study - Whole genome sequencing to detect durg resistance in the Philippines
• Detecting mixed TB infections
  
• Karonga Methylation study - Karonga integrated DNA-RNA-Methylation study
  
• Mtb integrated ‘omics - An integrated ‘omics investigation of M. tuberculosis lineages
  
• TB host-pathogen analysis - TB Host-pathogen genetic interactions using genome-to-genome analysis
  
• Thailand - TB - Thailand TB drug resistance outbreak study

tbvar | Mycobacterium tuberculosis Variome Resource - TB Variome

In this report, we have re-analyzed data sets corresponding to over 400 isolates of Mtb available in public domain to reveal a comprehensive variome of Mtb comprising of over 29,000 single nucleotide variations, which has been deposited into a database (tbVar). Using a systematic computational pipeline, we have annotated potential functional variants and drug-resistance associated variants. Apart from a user-friendly interface, the database has a novel option to annotate variants from clinical re-sequencing of Mtb. To the best of our knowledge tbvar is the largest and most comprehensive genome variation resources for Mycobacterium tuberculosis.

Joshi,K.R. et. al. tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. Database (2013) Vol. 2013: article ID bat083; doi:10.1093/database/bat083.

Drug-related Databases

MtbVeb: A web portal for designing vaccine for mycobacterium tuberculosis - Vaccine Strain Data
MtbVeb is a web-based platform developed for designing vaccines against existing and emerging strains of mycobacterium tuberculosis. This includes drug resistant and extreme drug resistant M.Tb strains. It also allow users to design vaccines against M.tb using all three appraoches (strain, antigen and epitope based vaccines).

The current version of portal maintain comprehensive genomic information about 59 mycobacterium strains that includes 4 vaccine strains, 6 clinical isolates, drug resistant strains. In this study, we provides comprehensive information in the term of antigenicity of about 178 potential vaccine candidates in each of the strain.

Dhanda SK, Vir P, Singla D, Gupta S, Kumar S, Raghava GPS (2016) A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PLoS ONE 11(4): e0153771*

TBDREAM - TB Drug Resistance Mutations

In response to this urgent need to improve diagnostics of resistant TB, we have compiled a comprehensive list of the genetic polymorphisms associated with first and second line drug resistance in clinical M. tuberculosis isolates throughout the world. We have reviewed the most common mutations found for the major groups of anti-tuberculosis drugs, establishing a database that we hope will enable the development of sequence based tools for diagnosis and surveillance of drug resistance in tuberculosis.

Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. (2009) Tuberculosis Drug Resistance Mutation Database. PLoS Med 6(2): e1000002. doi:10.1371/journal.pmed.1000002.

Collaborative Drug Discovery: Drug Research Informatics

Proteomics

SInCRe - Structural Interactome Computational Resource

Structural Interactome Computational Resource is a Open Source Integrated Computational Resource for the Analysis of the Structural Interactome of Mycobacterium tuberculosis to predict Off-Site Interactions of Drug Candidates

Metri, Rahul et al. “SInCRe-structural interactome computational resource for Mycobacterium tuberculosis” Database : the journal of biological databases and curation vol. 2015 bav060. 30 Jun. 2015, doi:10.1093/database/bav060

Deprecated/Non-Functional

~~TBDB - TBDB~~
~~Proteome Comparison Database - MTB - PCDB @ BIC, JBTDRC~~
~~MyBASE Home - Genome Polymorphism and Gene Functionin Mycobacteria~~