Update Mendeley keywords from medline (pubmed)

In Windows, the Mendeley database is at %localappdata%\Mendeley Ltd\Mendeley Desktop\yourname@[email protected] where you replace [email protected] with the email you used to register Mendeley.

Use DB Browser for SQLite to access the Mendeley database.

Steps to update Mendeley database.

1. Run the code in get-pmids.sql to obtain a text file listing all the PMIDs in the database.
2. Use Batch Entrez, using the Database Pubmed to obtain a listing of all the references.
3. Change the format of the results to Medline, then select send to file.
4. Run pmid-keywords.awk with the file saved in step 3, and output to a file named pmd.csv.
5. Either run update-keywords.sql to update the database or, in DB Browser, import the csv file and go through each of the sql statements one-by-one to update the database.
6. To flag references without a PMID, run notmedline.awk on the file saved in step 3, output to a csv file. Import into the database with the table name pmnotmedline. Then run update-nopmid.sql.