Gathering Tagged Pubmed Copora

[danich1]

The goal here is to have a full listing of tagged pubmed abstracts (full text down the road). A few key issues to sort out are:

• [ ] What tagging resources are the best for tagging abstracts? (currently using Pubtator, but skeptical of its scaling abilities)
• [ ] What is the best format to parse these tagged abstracts? (currently using Pubtator's xml format, but amenable to other formats)

If I am missing anything, feel free to let me know: @dhimmel or @cgreene.

[ajratner]

Hey @dhimmel @danich1 I just added you to a repo I had started for preprocessing the PubTator tags and storing in snorkel format. It's not finished yet unfortunately...

• It needs to be updated for the newest release
• Has a few lingering parsing bugs (extremely minimal effect, but easy to correct)
• Need to set up some way to share the parsed files like Git LFS

I still plan to do this stuff, I'm just very behind on stuff for an upcoming deadline, so I figured I'd add you to the repo in case you want to take a look at before then!