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Enter neutralization data (mAb)

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Kaiming Tao edited this page Jun 18, 2022 · 22 revisions

For monoclonal antibodies (mAbs), the most important drugs are the mAbs in clinical trials or under Emergency Use Authorization (EUA).

Steps

  1. Read the paper and annotate key information
  2. Extract neutralization data
  1. Format data
  1. Submit data

Read the paper and annotate key information

Please pay attention to the information below in Abstract, Methods and materials, Result, or supplementary content:

  • Paper metadata
    • first author's name
    • DOI, for publications without DOI, please provide the URL
    • year of publication
  • mAb metadata
    • name or synonyms
    • PDB files, epitope
    • clinical trial stages
  • Neutralizing potency
    • the most important data is 50% neutralization concentration (IC50)
    • we also record IC80, IC90... etc if available
  • Neutralization assay
    • Variants and mutations of SARS-CoV-2 used in the assay
    • assay type, for example live virus, pseudovirus

Extract neutralization data

Heterogeneous data represetation

Different papers are using different methods to represent the neutralization data. Some of them are easy for extracting, others need more work. Also, some papers don't provide IC50 data but fold change only. The IC50 data are considered finer than fold change data.

Here is a list of different representations:

  • Table of mAbs, IC50, and variants
  • Dose-responsive curve of mAb and variants
  • Figure of mAbs, IC50, and variants for comparing different mAbs
  • IC50 value from the body text
  • IC50 fold change between control and test variants

Despite different representations, the key information is the same:

  • mAb or treatment name
  • control and test variants and their mutations
  • neutralization assay type
  • IC50, or IC80, IC90 values
  • ULOQ (upper limit of quantification)

Comment: If the paper reports IC50 data, they should be stored in the rx_potency table, the fold change will be calculated by our program. If the paper only provides fold changes, they should be stored in the rx_fold table.

Comment: Some papers may repeatedly report the same data using different representations. To reduce the duplication, we require to enter the data with finer granularity.

A note on figures

Given the variety of data-processing and data-visualization programs available to researchers, the figures in papers differ in their style. The format of a figure can be rasterized or vectorized, which results in the need for data extraction techniques particular to each paper.

For rasterized figures, you can extract data using image editors (Adobe Illustrator, Adobe Photoshop). First, mark the points and measure the x-y coordinates. Second, use a formula to calculate actually IC50 values. You can also use the same method to get ULOQ from the figure if provided.

For vectorized figures, you can use the same method as rasterized figures. You can also find individual pars of each point in the layers panel, which will save you time to measure the x-y coordinates. You can also write scripts for image editors to measure and calculate data automatically.

Dose-responsive curve

Please pay attention to the value at 50% neutralization. If the curve doesn't cross the 50% neutralization, that means the neutralization was not detected in the assay, please use ULOQ as the neutralization potency data.

Format data

Please use this Excel template specifically for mAb to format the data.

In this section, we describe each table and its columns. The primary key or joint primary keys of a table are highlighted in bold.

Metadata tables

Common tables

Please read Enter neutralization data (metadata tables)

antibodies

Column name Description Format Default Comment
ab_name mAb main name
abbreviation_name NULL
availability Please see Steps for updating an mAb's availability and priority NULL
mature_month NULL
institute NULL
origin NULL
priority Please see Steps for updating an mAb's availability and priority 5000
visibility NULL
date_added the date the antibody is entered YYYY-MM-DD

Neutralization potency tables

rx_potency

Column name Description Format Default Comment
ref_name RefID
rx_name mAb name in the study, a combination of mAbs should be concatenated using the symbol "+"
iso_name iso_name of tested virus, the name should be in isolates table
section Figure, table, supplementary content or paragraph number from where the data are extracted
assay_name Must be a value from the assay_name column in the assays.csv table
potency_type IC50, IC80, etc
potency Neutralization data
cumulative_count number of data points share the same value
potency_upper_limit ULOQ (upper limit of quantification)
potency_lower_limit LLOQ (lower limit of quantification)
potency_unit ng/ml
date_added YYYY-MM-DD

rx_fold

Column name Description Format Default Comment
ref_name RefID
rx_name mAb name in the study, a combination of mAbs should be concatenated using the symbol "+"
control_iso_name iso_name of control virus, the name should be in isolates table
iso_name iso_name of test virus, the name should be in isolates table
section Figure, table, supplementary content or paragraph number from where the data are extracted
assay_name Must be a value from the assay_name column in the assays.csv table
potency_type IC50, IC80, etc
fold_cmp IF control IC50 > ULOQ then use ">", else use "="
fold Fold change (test IC50 / control IC50)
resistance_level NULL
ineffective NULL
cumulative_count number of data points share the same value
date_added YYYY-MM-DD

rx_antibodies

Column name Description Format Default Comment
ref_name RefID
rx_name rx_name in rx_potency table
ab_name mAb main name All mAb main names are listed in antibodies table. Synonyms should be converted to main name, please see antibody_synonyms table. A combination of mAbs should be recorded in multiple rows, one row for one main name.

ref_isolate_pairs

This table records which isolate is the control, and which isolate is the test. This table is used with the rx_potency table, if all data are in the rx_fold table, this table can be ignored.

Column name Description Format Default Comment
ref_name RefID
control_iso_name control iso_name from rx_potency table Most of time it's wild type virus or virus with D614G mutation
iso_name test iso_name from rx_potency table

Submit data

If you're not familiar with programming, please skip this step and save the Excel file to the issue page. Please also mention to the admin the data file is ready to use. We will convert the data file into the database-friendly format, and check the consistency.

Please see how to submit the data in Enter neutralization data (submit data)

If you have any issues or questions, please create a new issue.

Enter neutralization data

Data analysis

Prevalence

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