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.