Update reference list prior to manuscript submission

[rando2]

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Since we have been writing this since March 20th, a lot of papers that we read as preprints have probably been published subsequently! Prior to submission, we should track down the peer-reviewed versions of these.

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David Nicholson, who has been super helpful about providing technical suggestions for this project, has developed an approach to match preprints from bioRxiv with their published versions. This code uses the bioRxiv API to look up the DOI of the published version based on the preprint DOI.

I think perhaps what we'd want to do is pull a list of preprints we cite that have published versions so that we can double-check whether their conclusions have remained the same and then provide a list of DOIs to a python script that will replace them in the text?

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We could just auto-replace, or leave the references to the preprints.

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I would love to make sure this sounds reasonable to @cgreene and @agitter.

[agitter]

If we have a mapping from bioRxiv DOIs to journal DOIs, we may be able to use Manubot's aliases to update to the journal DOI without changing how we cite the paper in the text. That is, we would leave the bioRxiv DOIs in the text instead of having to write a script to replace them. I haven't done that before and would need to confirm it works and that it maintains the cross-references to the Mount Sinai reviews in Appendix A.

I do think we would need to double-check the conclusions before updating DOIs. That could take a while because we cite so many preprints. We could decide to save this for after the initial submission if you want to submit some of the papers soon.

[rando2]

See #791 for a possible quick, temporary work-around to this! @cgreene agreed that we may just want to submit with the reference list as-is.