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Data for antibody escape maps

This directory holds all the input data on the maps of antigenic effects of mutations.

Within this directory, there is a subdirectory for each study. The study-level subdirectories should be given short names describing the study by year, first author, and a brief descriptions, as in 2021_Starr_REGN. Each study-level subdirectory should have two files:

  1. A YAML file named study.yml that contains the following required fields (you are free to add additional fields if you'd like although they will be ignored in processing of the data):
  • study_title: title of the paper or pre-print from which the data are taken.
  • study_first_author: last name of first author of study.
  • study_year: year of study.
  • study_journal: journal of study.
  • study_url: weblink to study.
  • lab: lab that performed study.
  • notes: any relevant notes, should include specification of how data were extracted from study.
  • conditions: map antibodies or sera used (e.g., CR3022) to the following keyed attributes:
    • type: antibody, antibody cocktail, or serum. Note that data of type antibody cocktail are ignored!
    • subtype: more details about antibody or sera class:
      • if type is antibody, should be class 1, class 2, class 3, or class 4 based on the Barnes et al classification scheme.
      • if type is antibody cocktail, should be none.
      • if type is serum can be: convalescent serum, Moderna vaccine serum, Pfizer vaccine serum. Note that Pfizer vaccine serum has not been implemented yet and a new color will need to be chosen for this serum type.
    • year: year that antibody or serum was isolated.
    • eliciting_virus: list of viruses that elicited antibody / sera, if missing default to [SARS-CoV-2, pre-Omicron SARS-CoV-2]`
    • alias (optional): another name for the antibody/sera
    • notes (optional): any notes on the antibody or serum
    • known_to_neutralize (optional): list of viruses the antibody neutralizes. Entries can either by strings giving virus names, or lists of virus and IC50, as in [[Wuhan-Hu-1, 5.7]]. Assumed [Wuhan-Hu-1] if not specified.
  1. A CSV file named data.csv that contains the actual data. The required columns are listed below. Sites with no entry for a given condition are assumed to have a mut_escape value of 0.
    • condition: the antibody or sera name listed under conditions in study.yml.
    • site: the site in the spike protein (use Wuhan-Hu-1 numbering).
    • wildtype: the wildtype amino acid at the site.
    • mutation: the mutant amino acid.
    • mut_escape: the escape fraction for this mutation.