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pfmc-assessments / sa4ss

Generate a stock assessment document from Stock Synthesis output
https://pfmc-assessments.github.io/sa4ss/
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.bib file: automated creation of .bib files for top journals #57

Closed kellijohnson-NOAA closed 3 years ago

kellijohnson-NOAA commented 3 years ago

Problem

It is a lot of work to make .bib files by hand or through software such as Endnote, Zotero and Mendeley. I mention these particular software platforms because I know they are being used by people using sa4ss. These resulting bib files are often fraught with errors. Manual creation of the files takes hundreds of hours and can still be full of errors. Nelson Beebe suggests that the only way to make .bib files without errors is to treat it like a fish ageing experiment, where every entry is created by two independent individuals and the results are checked for consistency. Inconsistencies are looked at by both individuals along with the source that was used to create that entry such that inconsistencies can be reconciled. This will never happen for us, so we have to find some other solution.

Proposal

Nelson Beebe from the Math Department of the University of Utah has an extensive bibliography collection and method to create it. He has offered to create full bibliographies using is freely available software for up to 10 journals. All we need is a list and the associated publisher. I would like to send him this list before 🎃 2021. This issue will track ideas regarding what journals are important. Using the bib files out of this effort will not be required, but they will be available :smile:.

I think a decent start might be from Trevor Branch's Top 100 cited articles in fisheries list that lead to the publication in Fisheries Research titled What makes some fisheries references highly cited?. Some of these are pretty obscure journals though that we probably are not going to be using going forward into the future.

For clarity, his workflow creates a single .bib file per journal with EVERY publication from that journal that they have online. This file would be available to us and the rest of the world on the University of Utah Math Department website and be updated as new issues are published. Bib keys would be consistent through time. So in theory, we could all be using the same .bib files for these journals. If the process works well for sa4ss, then we could add more journals as time allows. I think we could set up a GitHub workflow to automate the process, though this would take quite a bit of work and the resulting files still need some editing of proper nouns for capitalization see :cucumber: section.

For sure candidates

This list will be completed as people propose and vote on journals.

Add proposed journals in individual comments so that we can use 👍 as votes. I repeat, one journal per comment and feel free to add as many comments as you want. You can even 👍 your own comment.

:cucumber:

k-doering-NOAA commented 3 years ago

Canadian Journal of Fisheries and Aquatic Sciences

kellijohnson-NOAA commented 3 years ago

Journal of Fish Biology

kellijohnson-NOAA commented 3 years ago

Ecological Modelling

kellijohnson-NOAA commented 3 years ago

Reviews in Fish Biology and Fisheries

kellijohnson-NOAA commented 3 years ago

Natural Resource Modeling

kellijohnson-NOAA commented 3 years ago

Transactions of the American Fisheries Society

kellijohnson-NOAA commented 3 years ago

Journal of Mathematical Biology

kellijohnson-NOAA commented 3 years ago

Fish and Fisheries

kellijohnson-NOAA commented 3 years ago

Final 10 journals are as follows:

  1. Fisheries Research
  2. ICES Journal of Marine Science
  3. Canadian Journal of Fisheries and Aquatic Sciences
  4. Fish and Fisheries
  5. Journal of Fish Biology
  6. Ecological Modelling
  7. Reviews in Fish Biology and Fisheries
  8. Natural Resource Modeling
  9. Frontiers in Marine Science
  10. Marine Policy
kellijohnson-NOAA commented 3 years ago

Early feedback from Nelson suggests that ICES uses Oxford publishing, a publisher that stops downloads from text-based tools, i.e., lyns, wget, and curl. So it might not be possible to get this journal. Elsevier and Wiley are easy 🥇 .