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doi2cite

README.md

pandoc-doi2cite

This pandoc lua filiter helps users to insert references in a document with using DOI(Digital Object Identifier) tags. With this filter, user s do not need to make bibtex file by themselves. Instead, the filter automatically generate bib file from the DOI tags, and convert the DOI tags into citation keys available by --citeproc.

What the filter do are as follows:

  1. Search citations with DOI tags in the document
  2. Search corresponding bibtex data from __from_DOI.bib file
  3. If not found, get bibtex data of the DOI from http://api.crossref.org
  4. Add reference data to __from_DOI.bib file
  5. Check duplications of reference keys
  6. Replace DOI tags to the correspoinding citation keys

Prerequisites

  • Pandoc version 2.0 or newer
  • This filter does not need any external dependencies
  • This filter should be executed before pandoc-crossref or --citeproc

DOI tags

Following DOI tags can be used:

The first one (@https://doi.org/) may be the most useful because it is same as the accessible URL.

YAML header

The file name of the auto-generated bibliography file MUST be __from_DOI.bib, but the place of the file can be changed (e.g. './refs/__from_DOI.bib' or 'refs\\__from_DOI.bib' for Windows). Yo u can designate the filepath in the document yaml header. The yaml key is bibliography, which is also used by --citeproc.

Example

example1.md:

---
bibliography:
  - 'my_refs.bib'
  - '__from_DOI.bib'
---

# Introduction
The Laemmli system is one of the most widely used gel systems for the 
separation of proteins.[@LAEMMLI_1970] By the way, Einstein is genius.
[@https://doi.org/10.1002/andp.19053220607; @doi.org/10.1002/andp.1905
3220806; @doi:10.1002/andp.19053221004]

Example command 1 (.md -> .md)

pandoc --lua-filter=doi2cite.lua --wrap=preserve \
-s example1.md -o expected1.md

Example command 2 (.md -> .pdf with ACS style):

pandoc --lua-filter=doi2cite.lua --filter=pandoc-crossref --citeproc \
--csl=sample1.csl -s example1.md -o expected1.pdf

Example result expected1