What tools are useful for text mining of pdf-based literature? For example, suppose I had a list of several genes and several phenotypes, and wanted to look for associations between those genes and phenotypes in literature for which a PDF is available, but HTML of the full text is not. Are there tools to efficiently do this type of search?
Something like https://github.com/kermitt2/grobid perhaps?
There are lots of PDF mining repos on github that I’d suggest having a mooch through.
I’ve definitely come across libraries for extracting data from graphs too but can’t for the life of me find the repos now...
I have installed - but never used - Xapers, which can index pdf files and other sources. I don't know if you are looking for a fancy machine-learning kind of stuff, or simple indexing and searching are good enough for your purposes.
There is also pdfgrep, which could be nice for quickly searching a few pdfs.
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version 2.3.6
pdftotext is the best soln I have tried so far.
not a direct answer to your request but perhaps this resource might be of use EVEX (not sure though how well maintained it still is)