roncv / auto-db-pipeline

Automated antibody database.

Auto-AbDab

Auto-AbDab is a Pathogen-Specific Automated Antibody Database Builder​.

The pipeline works as follows:

1. The user inputs keywords related to a disease. (Eg. 'SARS-CoV-2', 'COVID-19', 'coronavirus', 'SARS-CoV', ​ 'MERS-CoV', and 'SARS'.)
2. The pipeline scrapes the following for antibodies:
   1. the full-texts and supplementary data of publications associated with PubMed or BioRxiv,
   2. the Protein Data Bank (PDB),
   3. the National Genetic Sequence Data Base (GenBank),
   4. Patents.
3. The pipeline obtains biological information for each antibody such as its sequence, germline, and structure using ANARCI and SAbDab.
4. The pipeline returns the pathogen-specific antibody database to the user.

The pipeline is demonstrated for SARS-CoV-2, though antibody databases for other pathogens may be generated as well.