org-ref: citations, cross-references, indexes, glossaries and bibtex utilities for org-mode

Introduction to org-ref on YouTube.

Screenshots

Here are some annotated images of basic insertion of citations in org-mode.

The links in org-ref are functional. They do things when your cursor is on them, or you click on them, and sometimes when the mouse hovers over them.

Here is an example of a menu of actions you get when you click on a cite link.

org-ref can analyze your org-file and tell you about it, for example if there are bad citations, multiply defined labels, bad reference links, missing bibliography files, etc… You can select each one and it will jump to the location to help you fix it.

Installation

Package installation via Melpa

org-ref has been added to Melpa. This is the recommended way to install org-ref as it will also install all the dependencies.

(add-to-list 'package-archives
	     '("melpa" . "http://melpa.org/packages/") t)
(when (< emacs-major-version 24)
  ;; For compatibility
  (add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/")))
(package-initialize)

Then, you should be able to do M-x package-list-packages, find org-ref and install it.

Installation via github

Make sure all the dependencies are installed. Then clone this repo, add it to your load-path.

git clone https://github.com/jkitchin/org-ref.git

Add this to your .emacs file

(require 'org-ref)

Configuration

You should set these variables. Here is an example of how mine are set in an init.el file.

(setq reftex-default-bibliography '("~/Dropbox/bibliography/references.bib"))

;; see org-ref for use of these variables
(setq org-ref-bibliography-notes "~/Dropbox/bibliography/notes.org"
      org-ref-default-bibliography '("~/Dropbox/bibliography/references.bib")
      org-ref-pdf-directory "~/Dropbox/bibliography/bibtex-pdfs/")

You may want to set some convenient keys for working in your bibtex file. These commands operate on the citation key at point.

If you use bibtex-completion frontends such as `helm-bibtex` or `ivy-bibtex` as the citation key completion method you should set these variables too, to the same path as the equivalent `bibtex-completion` variables.

(setq bibtex-completion-bibliography "~/Dropbox/bibliography/references.bib"
      bibtex-completion-library-path "~/Dropbox/bibliography/bibtex-pdfs"
      bibtex-completion-notes-path "~/Dropbox/bibliography/bibtex-notes")

;; open pdf with system pdf viewer (works on mac)
(setq bibtex-completion-pdf-open-function
  (lambda (fpath)
    (start-process "open" "*open*" "open" fpath)))

;; alternative
;; (setq bibtex-completion-pdf-open-function 'org-open-file)

There are alternative citation key completion methods.

org-ref-helm-cite: An alternative to helm-bibtex
org-ref-ivy-cite: Uses ivy for key completion
org-ref-reftex: Uses reftex and org-mode for completion (no longer developed)

If you plan to build PDF files via LaTeX you need to make sure that org-latex-pdf-process is set to process the bibliography (using bibtex or biblatex). Here is one example of how to do that (see ./org-ref.org::*LaTeX export for other alternatives).

(setq org-latex-pdf-process (list "latexmk -shell-escape -bibtex -f -pdf %f"))

Finally, add this to your init.el files.

(require 'org-ref)

Go forth and citate.

Some other useful libraries in org-ref

Note many of these have been renamed with an org-ref prefix.

doi-utils: Download bibtex entries and PDFs from doi and crossref queries.
org-ref-pdf: Add drag-n-drop PDF to create bibtex entries
org-ref-url-utils: Add drag-n-drop urls to create bibtex entries
org-ref-bibtex: Utility functions for bibtex
org-ref-latex: org-ref-like features in LaTeX.
org-ref-arxiv: arxiv links, add bibtex entries from arxiv.org.
org-ref-pubmed: pubmed links, add bibtex entries from PMID.
org-ref-isbn: Add bibtex entries from a book ISBN
org-ref-wos: WebOfKnowledge links and queries
org-ref-scopus: Scopus links and queries
x2bib: Convert bibliography formats to and from bibtex
nist-webbook: Links to NIST Webbook resources

Manual

For more information, see the org-ref manual, or preferably use M-x org-ref-help in emacs.

Errors and issues

Please report errors here: issues.

Contributors

I would like to thank the contributors to org-ref, and everyone who has filed an issue, or asked about org-ref on the org-mode Mailing list.

zaeph/org-ref