todo: update literature data [web module]

[celinesin]

• [x] merge tables in sql db so publication date is not NULL
• [ ] implement way to display this from dataswimmer

Later:

• [ ] write script to auto update database (see felix instructions below)

[celinesin]

Feliksmueller commented 2 days ago Pubmed IDs and content for genes retrieved from indra.literature module. Script: get_pubmedstuff4genes.ipynb and pub2date.ipynb

It includes some nasty beautifulsoup parsing plus some indeirect watys to also get the dates and additional stuff. And it needs a long time to get all articles because the their servers have some restrictions. So there might be a way of doing it better and easier.

Check out: https://biopython.org/DIST/docs/api/Bio.Entrez-module.html Check out: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821292/

[celinesin]

db updated in menchelabdb.datadivr and asimov.ppi For some reason, db in papersimov is unusably slow. Will talk to Martin to get it fixed, but meanwhile i finally managed to update the table there too :)