These scripts are used to pull information from Pubmed such as Journal Name, First Author Name, Date Paper was published and Paper Title.
To setup these scripts you must have Jupyter Notebook installed. Anaconda Navigator is highly recommended for Jupyter Notebook installation but not required.
Make sure to copy the scripts into your
If you do not have any of these packages then you must install them before running the scripts.
Get an API key from Pubmed. Read "How to obtain an API Key Through an NCBI Account".
You must input your API key into the api_key = '&exampleAPiKey' variable to gain access to Pubmed API.
Change the variables that contain Paths to point the script toward the files you want it to read.
ie: default location variable is: location = os.listdir(r'Directory of files you want to read')
I would change this to location = os.listdir(r'C:\Users\Natei\Desktop\folder_with_my_files')
Do this for all paths that reference where your files are being read from. Do this for all paths that reference where your resulting export files will be saved from.
Pulls the relevant first author name from Pubmed for each PMID.
Pulls the relevant Journal that each PMID was published in.
Pulls the title of each Paper from the given PMID.
Pulls the date that each paper was published using the given PMID.
User provides Biolegend Catalog Numbers and is returned Biolegend WebIDs necessary for their data export.