Question: Documentation on the contents of the "pubtatordb" package in R?
gravatar for mike-zx
2 days ago by
mike-zx220 wrote:

Pubtator is a text-mining tool which can be used to check for reported relationships between genes in literature (papers) among other useful things. The authors have several publications including a recent 2019 one. There is also an R package called pubtatordb which is handy as it setups a local SQLite database of papers and the genes that are mentioned in the papers. This makes it very efficient to do some basic queries from your R session. However, I have not being able to find some basic info regarding the data bundled in the package. I am using the package for an analysis which I need to document and I would like to know the following:

  • When a gene appears as mentioned in a paper, what are the fields in which the gene can appear? I'd assume the gene appears in the body of the paper OR abstract OR title, but I can't find any resource to confirm this.

  • What time frame does the bundled data consider? I'd assume that any paper published previous to the last update of the package (November 2019) is considered, but again there doesn't seem to be any documentation to confirm this.

If anyone knows or can dig additional information regarding this I would appreciate it very much.

R pubtator • 32 views
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