Data mining, mostly medline. Used to be CAOPSCI project.

For the time being we shall provide this functionality:

• update local cache, a mongo document database, from a query to PubMed
• build mesh term networks from queries to mongodb, as networkX graphs, save them to python pickle files
• plot these networks using matplotlib
• plot these networks using d3
• convert these networks to CSV files
• a CSV to networkX loader, inputs CVS, outputs pickle

These functions shall have a command line interface and those scripts shall have PSU Galaxy wrappers.

We hope to share this tool online from our own Galaxy instance.