COVIBASE - An information resource for the COVID-19 pandemic.

BRIEF SUMMARY:

COVIBASE will be an ongoing information and surveillance resource to track, monitor and research the current SARS-CoV-2 pandemic caused by the novel coronavirus. The database will be hosted on a website http://www.covibase.org .

There will be two parts to this database. 1) A compilation of all existing literature and information relating to COVID-19, SARS and related viruses 2) A Real-Time Database of Covid-19 mortalities (RT-docom) w.r.t a) Demographics b) Diagnostics c) Clinical characteristics d) Viral isolate details Query interface will have 3 components to it 1) Search terms 2) Sequence Profiling Interface like Sequerome 3) 3D Visualization to query for small molecule inhibitors

PERSONNEL:

Queromatics

APPROACH:

• Link up with different databases in NCBI and connect with information related to coronavirus, and create a repository

• Prepare an entity relationship diagram connecting them

• Compile them into one Comprehensive Database

  • Medical Literature - Pubmed

  • Clinical Trials (from different registries - in style of Panregia)

  • DNA/RNA sequences - NCBI nucleotide

  • Protein motif data - NCBI domain

  • PDB structures - PDB

  • Protein Sequence - NCBI Protein

  • Viral genomes - NCBI genome

  • Pubchem

  • Bioassays

  • Immune Epitope Database (IEDB)

This will be supplemented with another real-time database of cases and fatalities from COVID-19 - RT-docom

DEMOGRAPHICS

City, Date Age, Gender, Was positive diagnosis before death OR after death

DIAGNOSTICS

Test used, Culture test PCR - i) Number of primers used ii) Primer sequence iii) Company/Institution making the kit, Presumptive diagnosis

CLINICAL Clinical presentation details (List sub fields), Clinical progression details (list sub fields), Cause of death details, Underlying Co-morbid condition

VIRAL ISOLATE

PATIENT VIRAL ISOLATE Viral Isolate obtained (Y/N), Details of Virus isolated (separate database tied to the Patient) a) Viral sequence b) Protein Sequence c) Protein structure (with a 3D emulator like Cn3D OR Pymol)

ANIMAL VIRAL ISOLATE - Same as fields in 'Patient viral isolate' and Animal isolated from e.g. Bat, Snake, Pangolin (including genus and species)

USER INTERFACE

Types of queries

1) Search terms to mine

a) NCBI, ClinicalTrials.gov

b) Real time database of Covid-19 mortalities (RT-docom)

2) Sequerome style sequence profiling query. Database queried against to include genbank as well

3) 3D visualization interface for active sites of domains and run queries against custom drugbank resource. Identify the antigen by ELISA (only when infection is there) Identify Antibodies Identify Surrogate biomarkers