nodrogluap / pokay Goto Github PK

The link to Tchesnokov et al. (2020) (https://www.jbc.org/content/early/2020/09/23/jbc.AC120.015720.short) appears to be broken; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7681019/ works for the same article.

There are linebreaks in some updated files where a line breaks after a certain character length, causing an issue in parsing files. For example, in S_antibody_epitope_effects.txt (Line 366,375, 384, 406...) S_pharmaceutical_effectiveness.txt (Line 5,12,18...)

Pronu^n^ciation :)

nirmatrelvir resistance - Zhou et al. (2022) https://www.science.org/doi/10.1126/sciadv.add7197
S:T572I and friends - https://www.nature.com/articles/s41467-020-20321-x
S:T572I:

• https://www.biorxiv.org/content/10.1101/2023.01.30.526314v2.full
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10154619/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8567936/
• https://pubmed.ncbi.nlm.nih.gov/36690780/
• https://pubmed.ncbi.nlm.nih.gov/34307771/
• https://www.biorxiv.org/content/10.1101/2023.10.10.561643v2.full
• https://www.biorxiv.org/content/10.1101/2023.06.22.546079v1
• https://www.biorxiv.org/content/10.1101/2021.08.19.456973v1.full
• https://www.biorxiv.org/content/10.1101/2022.11.24.515932v1.full

https://www.novavax.com/sites/default/files/2021-02/20210202-NYAS-Novavax-Final.pdf in S_vaccine_neutralization_efficacy.txt

At a few places in the function description, Twitter/website URLs are used.
Example: In file S_vaccine_neutralization_efficacy.txt,
Function: All vaccinees were on a strict 3-week interval for second dose (https://twitter.com/supermarioelia/status/1390362358971781122), therefore 1st dose efficacy is likely underestimated.

Should we keep any social media links or should we only keep articles/studies?
If yes, should they be marked as an opinion? As many social media opinions could be contrasting.

Solution: If we want to keep any social media link for the purpose of cross-reference, then one way could be to use a specific character before adding any social media link, and the social media link can then be parsed and added in a separate column.

Any thoughts? @nodrogluap @miseminger @Khushivora

Hi Paul,

I am trying to parse the information in data files and came across a couple of variations in the use of separator between mutations. I was just wondering if there is a difference in interpretation of information separated by commas (,) and semi colons (;), or if it's just a typo?
For example:
Case1: Mutations in the file S_monoclonal_antibody_serial_passage_escape.txt are separated out with comma.
Case2: In S_transmissibility.txt few mutations are separated out with comma, and few with semi colon.
Case3: In S_antibody_epitope_effects.txt line#357, both separators ( , ; ) are used.
Could you please help with this?