Italicize biological entities in title en masse

under-review
reference-management

#1

Is there a way to italicize biological taxonomies in the title en masse across the library? I am writing a microbe-rich paper and all the paper titles have been imported into Paperpile without italics. It’s a massive pain to have to open 90 references and put in an HTML italic tag around all organism names.

If this is not possible at present, would you please consider introducing en masse editing for the Paperpile library? Thanks so much!


#2

No there is no way to do this in bulk. The main issue is that most formats like RIS don’t support italics so if you export from other programs this information gets lost. Also PubMed does not contain the information. I think we handle BibTeX import correctly already and we want to improve our Zotero migration to include markup information.


#3

I wonder if, before importing into Paperpile you could add some plaintext markup to the words that need to be italicized? I sometimes do this with Markdown syntax, like _so_ or *like this*. Several scripts exist to convert Markdown syntax back to rich text. (It seems these forums support Markdown!)


#4

I tried this roundabout way that didn’t lead anywhere:

  1. downloaded the BibTeX,
  2. used perl to enclose all organism names in html italic tags and
  3. re-uploaded to Paperpile in the hopes that
  4. duplicate merging would somehow retain the italic tags.

However, duplicate merging just lost the italic tags again. Perhaps an option to tell the duplicate merging process to retain the italics tag might be a solution for this? Thoughts?


#5

We don’t recommend this workflow.

The duplicate merging just adds a layer of complexity where things can go wrong. Also with the merging you would lose the connection between Paperpile and your Google Doc as the merging creates a new item from the two old ones. Your Google Doc will still work fine but it will use the old copy to format your citations.

Also Paperpile does not even allow you to upload a BibTeX file when it detects that more than 90% of the items are already in your database.

I tried to think of another workaround but I’m afraid I also can’t come up with one.


#6

Five years later, still interested in this topic. Any updates? I’ve been using the “< i >” method, but find it buggy and not consistent.