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fulltext use cases #3

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emhart opened this Issue Aug 8, 2014 · 11 comments

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emhart commented Aug 8, 2014

What are usecases for fulltext?

  • Mining scholarly full text data or metadata for when terms arise. Here's a good example from the rentrez README

@emhart emhart added the Planning label Aug 8, 2014

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sckott commented Aug 8, 2014

From François Michonneau -

...identify parts of the tree of life that are studied but not resolved. In other words, are there species/genera/families that are regularly included in ecological/physiological studies but that are not represented in genbank/treebase? The challenge here would be to identify the species names from the full text of the articles but I can imagine that by querying taxonomic databases with taxize it might not be impossible...

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njahn82 commented Aug 17, 2014

Another possible use case for fulltext could be to load tables and supplementary material in tabular form into R.

An example with rebi that fetches Europe PubMed Central

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sckott commented Aug 17, 2014

thanks @njahn82 That's a great idea to support easy import of tabular data. Although advanced uses could do themselves, we should make it easy to extract the tabular data.

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sckott commented Nov 22, 2014

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sckott commented Oct 13, 2015

Another possible use case for fulltext could be to load tables and supplementary material in tabular form into R.

taken care of (i think) in ft_get_si() now

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dwinter commented Oct 23, 2015

Hi @sckott , thought you might like to see a use case "in the wild". Using ft_get_si() in a reproducible workflow/example for rotl that we hope to reference in an MS about that package:

https://github.com/ropensci/rotl/blob/meta_analyses_eg/vignettes/meta-analysis.Rmd

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sckott commented Oct 23, 2015

@dwinter awesome! Thanks. Any thoughts on how it could be better

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dwinter commented Oct 23, 2015

Thanks to you and @willpearse for creating it -- a really helpful addition.

The only tiny snag I hit was the readxl::read_excel guesses file type by name (and you can't specify the format argument, and the lower-level functions for each type aren't exported) . I don't know if it's possible, but if the file-path-like object returned by ft_get_si could maintain the extension that might be helpful. (Though the work-around of specifying the save.name is no great problem)

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willpearse commented Oct 23, 2015

Thanks - this is useful to know, and I'll fix this in the next update. Great to know this is actually being used in the wild :D

We've discussed something similar to this ( #69 ), which I've written (but not merged) a solution to, so it should appear very soon. Thanks again!!!

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sckott commented Oct 24, 2015

Thanks for the feedback @dwinter

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sckott commented Dec 2, 2015

closing, open issues for individual use cases

@sckott sckott closed this Dec 2, 2015

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