Tag Archives: PubMed

I have to learn a little about Python and mySQL. . .

Lindsay Cowell, who works on the Infectious Disease Ontology, was kind enough to share a script her group used to create a local mySQL database of PubMed records. It’s in Python, and Changqing Li wrote it. In order to use the script, I have to learn about Python and also more about sql databases.  I found a Python tutorial, written by the creator of Python himself! Most likely I will rely on the kindness of my friends to help coach me through the Python scripting, and once it’s in mySQL form, I can take it from there. There’s an issue about where the data is going to go, but Chanqing tells me that the whole thing requires at least 60GB. I hope it doesn’t come to this, but the best (cheapest) course of action might be to create the database on a local disk.  The records I’ll eventually want to incorporate into the Literature of Evolution database will not, I imagine, require so much disk space. I have a few GB’s at geekisp, and maybe the Darwin Manuscripts Project can spare a few.