Publication and GISAID number annotation of mutation_calls.csv

[philiptzou]

Hello, we are the Stanford HIVDB team and we are building an open source SARS-CoV-2 in vivo selection research database. The database so far collected mutations, timepoints and treatments data of 70 individual patients from 44 publications. All the summary data and raw data are available for public to view and reuse under a CC-BY SA 4.0 open source license. Contributions are also very welcome to this database and we are currently building and improving our collaboration tools for inside and outside contributors.

We came across your paper and repository and found that you have summarized these mutations for 28 patients. These would be a great add on to our database. However, we'd like to ask a favor from you for us to enter these data more easily. Since we have trouble to tell if the patient data are from previous publication or from COG-UK, would it be possible for you to annotate this table by adding the publication (usually DOIs are sufficient), and the GISAID numbers if exist? Thank you!

[BioWilko]

Sorry for the (extreme) delay in replying.

I would not recommend including the raw mutation calls if at all possible, I only provided those for transparency rather than expecting other people to use them.

I am now maintaining a summary table containing both DOIs and accessions (where available).
I encourage people to utilise this for further work in this area and will be updating as papers are suggested to me via a github issue.

Is this sufficient for your uses?