Enter neutralization data (metadata tables)

List of metadata tables

• articles
• isolates
• variants
• isolate_mutations

articles

About create a new RefID, please read here

Column name	Description	Format	Default	Comment
ref_name	RefID
doi	DOI
url				Provide URL if the reference doesn't have DOI
first_author		Surname, Initials (no dots)	NULL
year		YYYY
date_added		YYYY-MM-DD
date_updated		YYYY-MM-DD	NULL

isolates

The isolates.d is for organizing isolates by studies. All files in this folder will be merged in to isolates.csv file.

The concept of isolates in the database is for recording variants and mutations. Each neutralization data should link to an isolate. Each isolate name represents a list of mutations and an isolate may belongs to a variant. Please see Record Variants, isolates, and mutations for more details.

Please find the isolate and mutations from the paper in the orders below:

1. GISAID/GenBank. Please find the sequence by GISAID ID or GISAID name, then download the FASTA file, and upload it into SARS-CoV-2 Sequence Analysis program. You can download the mutation list by selecting Spreadsheets (CSV) > Mutation list, you can find the PANGOLIN name by clicking the button "Analyze".
2. Mutation list in paper. Some papers provide the full list of mutations for the viruses. This is our alternative source of the mutation lists if the GISAID/GenBank accessions are not available from the paper. You need to convert the genes and positions to the database format.
3. Consensus. If the paper only reports the name of the variants or PANGOLIN names. Please find the corresponding isolate in isolates table and use "[PANGOLIN NAME] full genome" for authentic virus assay or "[PANGOLIN NAME] Spike" for pseudovirus assay.

Column name	Description	Format	Default	Comment
iso_name
var_name			NULL	Please see variants table.
site_directed				TRUE for virus with single mutation created in lab, else FALSE
gisaid_id	GISAID ID without the prefix EPI_ISL_		NULL
genbank_accn	Genbank accession number		NULL
sra_accn	SRA accession number		NULL
expandable				TRUE for most case; FALSE for non-SARS-CoV-2 viruses

variants

Column name	Description	Format	Default	Comment
var_name	Variant name (naming rules)
as_wildtype	TRUE if this variant should be treated as a wild type; else FALSE
consensus_availability			FALSE

isolate_mutations

The isolate_mutations.d is for organizing isolate mutations by studies. All files in this folder will be merged in to isolate_mutations.csv file.

The isolate_mutations table stores a list of mutations for each isolate in the isolates table. If you are adding a new isolate to the isolates.csv table, then you should add the mutation list to the isolate_mutations table.

Column name	Description	Format	Default	Comment
iso_name	isolate name
gene	Gene name (see SARS-CoV-2 genome / gene position conversion table # column 4
position	Amino acid position
amino_acid	Single letter amino acid. Mixtures with two AAs should be input as two rows. Mixtures with three or more should not be entered. ins for insertion, del for deletion, stop for stop codon.
count		NULL
total		NULL