The org-ref manual (version 3)

@@latex:\maketitle@@ @@latex:\tableofcontents@@

Introduction to org-ref

Org-ref is a library for org-mode cite:&Dominik201408 that provides rich support for citations, labels and cross-references in org-mode. org-ref is especially suitable for org-mode documents destined for LaTeX export and scientific publication. org-ref is also extremely useful for research documents and notes. org-ref bundles several other libraries that provide functions to create and modify bibtex entries from a variety of sources, but most notably from a DOI.

The basic idea of org-ref is that it defines a convenient interface to insert citations from a reference database (e.g. from a bibtex file(s)), cross-references to targets in the document, and a set of functional org-mode links for citations, cross-references and labels that export properly to LaTeX, and that provide clickable functionality to the user. org-ref uses bibtex-completion for the candidates you can use for citations.

org-ref provides a fairly large number of utilities for finding bad citations, extracting bibtex entries from citations in an org-file, and functions for interacting with bibtex entries. We find these utilities indispensable in scientific writing.

org-ref has been in development since sometime in 2013. It was written to aid in the preparation of scientific manuscripts. These are the first dozen scientific articles we wrote with it:

cite:hallenbeck-2013-effec
cite:mehta-2014-ident-poten
cite:xu-2014-relat-elect
cite:xu-2014-probin-cover
cite:miller-2014-simul-temper
cite:curnan-2014-effec-concen
cite:boes-2015-estim-bulk
cite:xu-2015-linear-respon
cite:xu-2015-relat-between
cite:boes-2016-neural-networ
cite:boes-2017-neural-networ
cite:xu-2017-first-princ

Be sure to check out the supporting information files for each of these. The org source for the supporting information is usually embedded in the supporting information. You may also find these two perspective articles cite:kitchin-2015-examp,kitchin-2015-data-surfac-scien interesting, as well as this article on data sharing cite:kitchin-2016-autom-data we wrote.

Biblatex users should read section ref:sec-biblatex-users.

If you want to export this document to another format like PDF or HTML, see section ref:sec-other-forms.

2021 version 2 vs version 3

A new citation syntax was recently (2021) integrated into org-mode. Initially I thought this would make at least the citation part of org-ref obsolete. I no longer think that is the case though. One of the goals of org-ref is to provide complete coverage of natbib/biblatex citation commands, with syntax that is close to what you would write in LaTeX, and that is close to what you would read in the LaTeX documentation. The new org-mode citation syntax does not do that. It uses a very different notion of citation and bibliography style syntax. I still think there is significant value to new writers, as well as more experienced writers who are very familiar with LaTeX to use the org-ref approach.

An early criticism of org-ref was its limited capability to support prenote/postnote syntax, especially for multiple citations. It turns out to be reasonably straightforward to support this, and version 3 does fully support the same syntax as the org-mode citation syntax, and it supports common prefix/suffix text, as well as local prefix/suffix text on each citation reference. I have intentionally chosen to use & as the prefix for bibtex keys in org-ref, so that it is explicitly different than the one org-cite uses (@) to reduce confusion about which syntax you are using.

citep:See; in &kitchin-2015-examp page 12; in &kitchin-2015-data-surfac-scien figure 6; for examples

You can use both version 2 and version 3 syntax in the same document (although you should not mix them in the same citation). Here are the same citations from above in version 3 syntax.

cite:&hallenbeck-2013-effec
cite:&mehta-2014-ident-poten
cite:&xu-2014-relat-elect
cite:&xu-2014-probin-cover
cite:&miller-2014-simul-temper
cite:&curnan-2014-effec-concen
cite:&boes-2015-estim-bulk
cite:&xu-2015-linear-respon
cite:&xu-2015-relat-between
cite:&boes-2016-neural-networ
cite:&boes-2017-neural-networ
cite:&xu-2017-first-princ

You should not mix org-ref links and org-cite citations. They are treated separately and you are not likely to get what you want.

Another criticism was that non-LaTeX exports were usually not that good because org-ref either implemented a minimal formatting engine, and because my early effort at developing a citeproc in org-ref fizzled out. Now, there is citeproc-el, and org-ref supports that for export.

The new citation syntax does not cover labels and cross-references, which are essential in our scientific writing. org-ref continues to support this. We anticipate a long life for org-ref.

Should you use org-ref? If your main export target is LaTeX, and you want cross-references, then probably so.

If you have no need for cross-references (either you don’t use them, or vanilla org syntax is adequate), or if you don’t like using ivy, and don’t want to roll your own citation inserter, then you may not need org-ref.

At this time, I have not integrated the org-cite capability I wrote in https://github.com/jkitchin/org-ref-cite into org-ref. I have not decided if that is a good or bad idea to do.

known issues with org-ref and org-citations

You should not try to define a cite/*: (i.e. do not define a link type that starts with cite/) link. org-cite will probably think it is an org-citation.

Basic configuration <<basic-configuration>>

You have to setup bibtex-completion variables if you want default bibliographies, notes, pdfs, and other features. You should also set the bibtex-autokey-* variables for generating bibtex keys if you use doi-utils.

Here is the setup I use.

(use-package ivy-bibtex
  :init
  (setq bibtex-completion-bibliography '("~/Dropbox/emacs/bibliography/references.bib"
					 "~/Dropbox/emacs/bibliography/dei.bib"
					 "~/Dropbox/emacs/bibliography/master.bib"
					 "~/Dropbox/emacs/bibliography/archive.bib")
	bibtex-completion-library-path '("~/Dropbox/emacs/bibliography/bibtex-pdfs/")
	bibtex-completion-notes-path "~/Dropbox/emacs/bibliography/notes/"
	bibtex-completion-notes-template-multiple-files "* ${author-or-editor}, ${title}, ${journal}, (${year}) :${=type=}: \n\nSee [[cite:&${=key=}]]\n"

	bibtex-completion-additional-search-fields '(keywords)
	bibtex-completion-display-formats
	'((article       . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${journal:40}")
	  (inbook        . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} Chapter ${chapter:32}")
	  (incollection  . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
	  (inproceedings . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
	  (t             . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*}"))
	bibtex-completion-pdf-open-function
	(lambda (fpath)
	  (call-process "open" nil 0 nil fpath))))

(use-package org-ref
  :ensure nil
  :load-path (lambda () (expand-file-name "org-ref" scimax-dir))
  :init
  (add-to-list 'load-path
	       (expand-file-name "org-ref" scimax-dir))
  (require 'bibtex)
  (setq bibtex-autokey-year-length 4
	bibtex-autokey-name-year-separator "-"
	bibtex-autokey-year-title-separator "-"
	bibtex-autokey-titleword-separator "-"
	bibtex-autokey-titlewords 2
	bibtex-autokey-titlewords-stretch 1
	bibtex-autokey-titleword-length 5)
  (define-key bibtex-mode-map (kbd "H-b") 'org-ref-bibtex-hydra/body)
  (define-key org-mode-map (kbd "C-c ]") 'org-ref-insert-link)
  (define-key org-mode-map (kbd "s-[") 'org-ref-insert-link-hydra/body)
  (require 'org-ref-ivy)
  (require 'org-ref-arxiv)
  (require 'org-ref-scopus)
  (require 'org-ref-wos))


(use-package org-ref-ivy
  :ensure nil
  :load-path (lambda () (expand-file-name "org-ref" scimax-dir))
  :init (setq org-ref-insert-link-function 'org-ref-insert-link-hydra/body
	      org-ref-insert-cite-function 'org-ref-cite-insert-ivy
	      org-ref-insert-label-function 'org-ref-insert-label-link
	      org-ref-insert-ref-function 'org-ref-insert-ref-link
	      org-ref-cite-onclick-function (lambda (_) (org-ref-citation-hydra/body))))

Basic usage of org-ref

Bibliography links

index:bibliography index:bibliographystyle

org-ref provides a bibliography link to specify which bibtex files to use in the document.

A comma separated list of relative or absolute paths
A comma separated list of files found in your BIBINPUTS environment variable

This link is clickable; clicking on a filename will open the file. On export, the bibliography will appear at the position where the link is defined. Usually this link goes near the end of your document, e.g. like here.

There is also a nobibliography link, which is useful for specifying a bibliography file, but not listing a bibliography in the exported document.

There is also a bibliographystyle link that specifies the style. This link does nothing but export to a LaTeX command. For LaTeX export a bibliography and bibliographystyle link is required if you use bibtex. If you use biblatex see ref:sec-biblatex-users.

These links support completion, so you can type C-c C-l, choose one of them, and it will help you complete the link.

Citations <<citations>>

index:cite

org-ref uses the bibliography link to determine which bibtex files to get citations from, and falls back to the bibtex files defined in the variable bibtex-completion-bibliography if no bibliography link is found. Note that you must include a bibliography link in your document if you are exporting your document to pdf; bibtex-completion-bibliography is not used by the LaTeX exporter.

For simple citation needs, org-ref is simple to use. At the point you want to insert a citation, you select the “Org -> org-ref -> Insert citation” menu (or use the key-binding you chose for inserting org-ref links), select the reference(s) you want in the completion buffer and press enter. The citation will be inserted automatically into your org-file. You “select” an entry by using the arrow keys (or C-n and C-p) to move up and down to the entry you want. You can also narrow the selection by typing a pattern to match, e.g. author name, title words, year, BibTeX key and entry types. If you want to match any other field, you need to add it to the variable bibtex-completion-additional-search-fields.

If the cursor is on a citation key, you should see a tooltip that summarizes which citation it refers to. If you click on a key, you should get a hydra menu with some actions to choose, including opening the bibtex entry, opening/getting a pdf for the entry, searching the entry in Web of Science, etc…

The default citation type is customizable (org-ref-default-citation-link), and set to “cite”.

See http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf for the cite commands supported in bibtex index:natbib, and http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf for the commands supported in biblatex. index:biblatex.

If the cursor is on a citation, or at the end of the citation, and you add another citation, it will be appended to the current citation.

index:cite!shift Finally, if you do not like the order of the keys in a citation, you can put your cursor on a key and use shift-arrows (left or right) to move the key around. Alternatively, you can use shift-up or you can run the command org-ref-sort-citation-link which will sort the keys by year, oldest to newest.

Alternatively, there is a keymap defined on cite links. By default this map is defined in the variable org-ref-cite-keymap.

There are navigation bindings that work on a cite link.

C-left	Jump to previous key
C-right	Jump to next key
S-left	move key to the left
S-right	move key to the right

You can also sort a cite link with multiple keys by year.

S-up	sort keys by ascending year

Pre/post text support

org-ref has two versions of syntax. In version 2 there is very limited support for pre/post text in citations. You can get pre/post text by using a description in a cite link, with pre/post text separated by ::. For example, See page 20::, for example. I do not recommend you use this anymore.

version 3 is much more capable, similar to the new org-cite syntax. The general syntax is:

Common prefix; prenote 1 &key1 postnote1; prenote n &keyn postnote n; Common suffix

The tradeoff is you have to prefix the keys with &, separate them by semicolons, and the links have to be bracketed if you put spaces in the notes. The previous citation in version 3 looks like citep:See page 20 &Dominik201408, for example as “local” pre/postnotes, or citep:See page 20 ;&Dominik201408;, for example, as “common” or “global” pre/post notes. You can do this with multiple keys too: citep:See &Dominik201408 pg. 2;and &kitchin-2015-examp for examples. Note in this example, the internal prefix on the second reference is ignored, because the cite command does not support it; use biblatex with a multicite if you need that in your citations. There are still a few caveats. Natbib only supports a single set of pre/post notes; some citation styles with biblatex support the full syntax. Not all cite types in LaTeX support pre/post text (e.g. cite, citenum do not support them), so be careful when you use them.

labels

index:label

LaTeX uses labels to define places you can refer to. These can be labels in the captions of figures and tables, or labels in sections. We illustrate some uses here. You can use label links, but it is preferred to use name keywords or other native org label mechanisms.

Here is a way to use a label link:

y

4

5

This is the preferred way to label a table.

y

4

5

org-ref can help you insert unique labels with the command org-ref-insert-label-link. This will show you the existing labels, and insert your new label as a link. There is no default key-binding for this.

ref links <<ref-links>>

index:ref

A ref link refers to a label of some sort. You can use the label in a name keyword, a LaTeX label, a CUSTOM_ID property, a label link (ref:sec-label-link), or a radio target.

For example, you can refer to a table name, e.g. Table ref:table-1. You have to provide the context before the ref link, e.g. Table, Figure, Equation, Section, and so on.

x

1

2

Or you can refer to an org-mode label as in Table ref:table-3.

Note: You may need to set org-latex-prefer-user-labels to t if you refer to things by their “name” for the export to use the name you create.

(setq org-latex-prefer-user-labels t)

y
3
2

You can also refer to an org-ref label link as in Table ref:tab-ydata.

To help you insert ref links, use the “Org -> org-ref -> Insert ref” menu, or run the command = org-ref-insert-ref-link=.

ref links are functional. If you put the cursor on a ref link, you will see a tooltip with some context of the corresponding label. If you click on the ref link, you will get a hydra to jump to it or change the ref type.

You can make a ref link to a section with a CUSTOM_ID. For this to work, you should set org-latex-prefer-user-labels to t.

Also note that “#+tblname:” and “#+label:” are deprecated in org-mode now, and “#+name:” is preferred.

Miscellaneous ref links label:sec-misc

index:ref!pageref index:ref!nameref index:ref!eqref

org-ref also provides these links:

pageref: The page a label is on
nameref: The name of a section a label is in
eqref: Puts the equation number in parentheses
autoref: A command from hyperref that automatically prefixes the reference number. (requires hyperref)
cref & Cref: cleveref – Intelligent cross-referencing
crefrange & Crefrange: cleveref – Intelligent cross-referencing

Note for eqref, you must use a LaTeX label like this:

\begin{equation} \label{eq:1} e^x = 4 \end{equation}

or a named equation like this:

\begin{equation} e^x = 4 \end{equation}

Then you can refer to Eq. eqref:eq:1 or ref:eq-in-name in your documents.

Autoref works like this: autoref:table-3, autoref:sec-misc.

The crefranges require two labels to define the range: Crefrange:table-1,table-3 and crefrange:table-1,table-3

These links do not have much meaning outside of LaTeX.

Some other links

index:list of tables index:list of figures

org-ref provides clickable links for a [[list-of-tables:]] and [[list-of-figures:]]. These links don’t need a path, so you have to put them in brackets. These export as listoftables and listoffigures LaTeX commands, and they are clickable links that open a mini table of contents with links to the tables and figures in the buffer. There are also interactive commands for this: elisp:org-ref-list-of-tables and elisp:org-ref-list-of-figures.

Some basic org-ref utilities

index:bibtex!clean entry

The command org-ref does a lot for you automatically. It will check the buffer for errors, e.g. multiply-defined labels, bad citations or ref links, and provide easy access to a few commands through a side-window buffer.

org-ref-clean-bibtex-entry will sort the fields of a bibtex entry, clean it, and give it a bibtex key. By default, this function does a lot of cleaning:

adds a comma if needed in the first line of the entry
makes sure the DOI field is an actual DOI, and not a URL
fixes bad year entries
fixes empty pages
escapes ampersand and percentage signs
generate a key according to your setup
runs your hook functions
sorts the fields in the entry
checks the entry for non-ascii characters
converts article title to title case (note: see below to convert titles in other entry types)

This function has a hook org-ref-clean-bibtex-entry-hook, which you can add functions to of your own. Each function must work on a bibtex entry at point. (Note: the default behavior can be changed by removing the relevant functions from the initial value of org-ref-clean-bibtex-entry-hook.)

Here are the functions run on cleaning:

org-ref-clean-bibtex-entry-hook

org-ref-bibtex-format-url-if-doi

orcb-key-comma

org-ref-replace-nonascii

orcb-&

orcb-%

org-ref-title-case-article

orcb-clean-year

orcb-key

orcb-clean-doi

orcb-clean-pages

orcb-check-journal

org-ref-sort-bibtex-entry

orcb-fix-spacing

You can add your own function to the hook like this.

(add-hook 'org-ref-clean-bibtex-entry-hook 'org-ref-replace-nonascii)

org-ref-extract-bibtex-entries will create a bibtex file from the citations in the current buffer.

LaTeX export

index:export!LaTeX

All org-ref links are designed to export to the corresponding LaTeX commands for citations, labels, refs and the bibliography/bibliography style. Once you have the LaTeX file, you have to build it, using the appropriate latex and bibtex commands. You can have org-mode do this for you with a setup like:

(setq org-latex-pdf-process
      '("pdflatex -interaction nonstopmode -output-directory %o %f"
	"bibtex %b"
	"pdflatex -interaction nonstopmode -output-directory %o %f"
	"pdflatex -interaction nonstopmode -output-directory %o %f"))

I have also had success with this setup:

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

BibTeX users

To have your citations compiled by BibTex, you must include a bibliography link. You will also need to include a bibliographystyle link, unless you are using a LaTeX style that includes that for you.

Note that some citation types may require additional LaTeX packages to be included in your export settings.

Here are the natbib types (these will export in LaTeX with the unsrtnat style). These will export differently in author-year styles.

Here are some examples of the pre/post note syntax for each natbib type. Not all of these make sense. For example the plain cite command does not take pre/post notes, even with natbib. If you use these a lot, you should use citet/citep. Not all of the commands take pre/post notes, e.g. citenum.

[[citet:See &kitchin-2015-examp page 2]]: citet:See &kitchin-2015-examp page 2
[[citet*:See &kitchin-2015-examp page 2]]: citet*:See &kitchin-2015-examp page 2
[[citep:See &kitchin-2015-examp page 2]]: citep:See &kitchin-2015-examp page 2
[[citep*:See &kitchin-2015-examp page 2]]: citep*:See &kitchin-2015-examp page 2
[[citealt:See &kitchin-2015-examp page 2]]: citealt:See &kitchin-2015-examp page 2
[[citealt*:See &kitchin-2015-examp page 2]]: citealt*:See &kitchin-2015-examp page 2
[[citealp:See &kitchin-2015-examp page 2]]: citealp:See &kitchin-2015-examp page 2
[[citealp*:See &kitchin-2015-examp page 2]]: citealp*:See &kitchin-2015-examp page 2
[[citenum:&kitchin-2015-examp]]: citenum:&kitchin-2015-examp
[[citetext:See &kitchin-2015-examp page 2]]: citetext:See &kitchin-2015-examp page 2
[[citeauthor:See &kitchin-2015-examp page 2]]: citeauthor:See &kitchin-2015-examp page 2
[[citeauthor*:See &kitchin-2015-examp page 2]]: citeauthor*:See &kitchin-2015-examp page 2
[[citeyear:See &kitchin-2015-examp page 2]]: citeyear:See &kitchin-2015-examp page 2
[[citeyearpar:See &kitchin-2015-examp page 2]]: citeyearpar:See &kitchin-2015-examp page 2
[[Citet:See &kitchin-2015-examp page 2]]: Citet:See &kitchin-2015-examp page 2
[[Citet*:See &kitchin-2015-examp page 2]]: Citet*:See &kitchin-2015-examp page 2
[[Citep:See &kitchin-2015-examp page 2]]: Citep:See &kitchin-2015-examp page 2
[[Citep*:See &kitchin-2015-examp page 2]]: Citep*:See &kitchin-2015-examp page 2
[[Citealt:See &kitchin-2015-examp page 2]]: Citealt:See &kitchin-2015-examp page 2
[[Citealt*:See &kitchin-2015-examp page 2]]: Citealt*:See &kitchin-2015-examp page 2
[[Citealp:See &kitchin-2015-examp page 2]]: Citealp:See &kitchin-2015-examp page 2
[[Citealp*:See &kitchin-2015-examp page 2]]: Citealp*:See &kitchin-2015-examp page 2
[[Citeauthor:See &kitchin-2015-examp page 2]]: Citeauthor:See &kitchin-2015-examp page 2
[[Citeauthor*:See &kitchin-2015-examp page 2]]: Citeauthor*:See &kitchin-2015-examp page 2

biblatex users <<sec-biblatex-users>>

In the latex header you specify the style and bibliography file using addbibresource. Here is an example:

#+latex_header: \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear, hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true] {biblatex}
#+latex_header: \addbibresource{tests/test-1.bib}

Sometimes it is necessary to tell bibtex what dialect you are using to support the different bibtex entries that are possible in biblatex. You can do it like this globally.

(setq bibtex-dialect 'biblatex)

Or like this in a bibtex file:

% -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-

Make sure you invoke biblatex in the org-latex-pdf-process. Here is one way to do it.

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

Finally, where you want the bibliography put this empty link:

[[printbibliography:]]

The regular biblatex cite links support common pre/post notes, and multiple keys. These are:

org-ref-biblatex-types

Cite

parencite

Parencite

footcite

footcitetext

textcite

Textcite

smartcite

Smartcite

cite*

parencite*

supercite

autocite

Autocite

autocite*

Autocite*

Citeauthor*

citetitle

citetitle*

citedate

citedate*

citeurl

fullcite

footfullcite

notecite

Notecite

pnotecite

Pnotecite

fnotecite

The multitype links support common pre/postnotes, and individual pre/post notes. These are the multicite commands:

org-ref-biblatex-multitypes

cites

Cites

parencites

Parencites

footcites

footcitetexts

smartcites

Smartcites

textcites

Textcites

supercites

autocites

Autocites

Here is a full example. This only exports correctly in biblatex or with CSL, so I include it as an example here.

[[cites:See; in &kitchin-2015-examp page 1;in &kitchin-2015-data-surfac-scien page 2;and in &kitchin-2016-autom-data page 3; for examples]]

Other exports

index:export!html index:export!ascii index:export!latex index:export!markdown index:export!odt

All other exports are handled by citeproc now. This is done by preprocessing in a dedicated exporter called org-ref. There is a new entry in the export menu

C-c C-e r h	html
C-c C-e r m	md
C-c C-e r a	ascii
C-c C-c r o	odt
C-c C-e r l	latex
C-c C-c r O	org buffer

org-ref-export

org-ref now supports the use of citeproc-el to export citations to non-LaTeX backends. See section sec-other-forms for more details. You can also use ./org-ref-natbib-bbl-citeproc.el

org-refproc

org-ref also supports exporting cross-references to other formats using ./org-ref-refproc.el. This library also works by pre-processing a copy of the buffer to convert org-ref cross-reference links to org-syntax before exporting to the target backend. This even support cleveref style links with automatic prefixing and sorting. Compression of the references is not yet supported.

See ./examples/refproc.org for a pretty comprehensive set of examples.

Other libraries in org-ref

These are mostly functions for adding entries to bibtex files, modifying entries or for operating on bibtex files. Some new org-mode links are defined.

doi-utils

index:doi

This library adds two extremely useful tools for getting bibtex entries and pdf files of journal manuscripts. Add this to your emacs setup:

(require 'doi-utils)

This provides two important commands:

doi-utils-add-bibtex-entry-from-doi

This will prompt you for a DOI, and a bibtex file, and then try to get the bibtex entry, and pdf of the article.

doi-utils-add-entry-from-crossref-query

This will prompt you for a query string, which is usually the title of an article, or a free-form text citation of an article. Then you will get a helm buffer of matching items, which you can choose from to insert a new bibtex entry into a bibtex file.

This library also redefines the org-mode doi link. Now, when you click on this link you will get a menu of options, e.g. to open a bibtex entry or a pdf if you have it, or to search the doi in some scientific search engines. Try it out doi:10.1021/jp511426q.

Bibtex key format

The key is formatted according to the settings of bibtex-autokey-* variables. I use these settings. Look at the documentation of them to see how to get the format you want. The function (bibtex-generate-autokey) does this.

The settings I use are:

(setq bibtex-autokey-year-length 4
	bibtex-autokey-name-year-separator "-"
	bibtex-autokey-year-title-separator "-"
	bibtex-autokey-titleword-separator "-"
	bibtex-autokey-titlewords 2
	bibtex-autokey-titlewords-stretch 1
	bibtex-autokey-titleword-length 5)

Troubleshooting doi-utils

Occasionally weird things happen with a DOI. The first thing you should check is if the json data for the DOI can be retrieved. You can do that at the command line, or in a sh block like this:

curl -LH "Accept: application/citeproc+json" "http://doi.org/10.1021/jp511426q"

If you do not get json data, doi-utils will not be able to generate the bibtex entry.

Not all PDFs can be retrieved. doi-utils uses a set of functions to attempt this. Here is the list.

doi-utils-pdf-url-functions

aps-pdf-url

science-pdf-url

nature-pdf-url

wiley-pdf-url

springer-chapter-pdf-url

springer-pdf-url

acs-pdf-url-1

acs-pdf-url-2

acs-pdf-url-3

iop-pdf-url

jstor-pdf-url

aip-pdf-url

science-direct-pdf-url

linkinghub-elsevier-pdf-url

tandfonline-pdf-url

ecs-pdf-url

ecst-pdf-url

rsc-pdf-url

pnas-pdf-url

copernicus-pdf-url

sage-pdf-url

jneurosci-pdf-url

ieee-pdf-url

ieee2-pdf-url

ieee3-pdf-url

acm-pdf-url

osa-pdf-url

asme-biomechanical-pdf-url

siam-pdf-url

agu-pdf-url

plos-pdf-url

generic-full-pdf-url

You can check if a url for the PDF can be found like this. If you get a url, you can probably download a pdf.

(doi-utils-get-pdf-url "10.1021/jp511426q")

https://pubs.acs.org/doi/pdf/10.1021/jp511426q

org-ref-bibtex

These are functions I use often in bibtex files.

Generate new bibtex files with adapted journal names

The variable org-ref-bibtex-journal-abbreviations contains a mapping of a short string to a full journal title, and an abbreviated journal title. We can use these to create new versions of a bibtex file with full or abbreviated journal titles. You can add new strings like this:

(add-to-list 'org-ref-bibtex-journal-abbreviations
  '("JIR" "Journal of Irreproducible Research" "J. Irrep. Res."))

org-ref-bibtex-generate-longtitles: Generate a bib file with long titles as defined in `org-ref-bibtex-journal-abbreviations’
org-ref-bibtex-generate-shorttitles: Generate a bib file with short titles as defined in `org-ref-bibtex-journal-abbreviations’

Modifying bibtex entries

org-ref-stringify-journal-name: replace a journal name with a string in `org-ref-bibtex-journal-abbreviations’
org-ref-set-journal-string: in a bibtex entry run this to replace the journal with a string selected interactively.
org-ref-title-case-article: title case the title in an article entry.
org-ref-title-case: title case the title for entries listed in `org-ref-title-case-types’.
org-ref-sentence-case-article: sentence case the title in an article entry.
org-ref-replace-nonascii: replace nonascii characters in a bibtex entry. Replacements are in `org-ref-nonascii-latex-replacements’. This function is a hook function in org-ref-clean-bibtex-entry.

The non-ascii characters are looked up in a list of cons cells. You can add your own non-ascii replacements like this. Note backslashes must be escaped doubly, so one \ is \\\\ in the cons cell.

(add-to-list 'org-ref-nonascii-latex-replacements
  '("æ" . "{\\\\ae}"))

These functions are compatible with bibtex-map-entries, so it is possible to conveniently apply them to all the entries in a file like this:

(bibtex-map-entries 'org-ref-title-case-article)

Bibtex entry navigation

org-ref-bibtex-next-entry: bound to M-n
org-ref-bibtex-previous-entry: bound to M-p

Hydra menus for bibtex entries and files

Functions to act on a bibtex entry or file

org-ref-bibtex-hydra/body
gives a hydra menu to a lot of useful functions like opening the pdf, or the entry in a browser, or searching in a variety of scientific search engines.

org-ref-bibtex-new-entry/body
gives a hydra menu to add new bibtex entries.

org-ref-bibtex-file/body
gives a hydra menu of actions for the bibtex file.

You will want to bind the hydra menus to a key. You only need to bind the first one, as the second and third can be accessed from the first hydra.

Formatted bibtex entry citations

If you click on a citation link, there should be a menu option to copy a formatted citation, which will copy the citation string to the clipboard. This is a lightly formatted version using bibtex-completion.

If you are on a bibtex entry, the `org-ref-bibtex-hydra/body’ has an option to copy a formatted citation for the entry your cursor is in.

org-ref-wos

This is a small utility for Web of Science/Knowledge (WOK) (http://apps.webofknowledge.com).

(require 'org-ref-wos)

wos: Convenience function to open WOK in a browser.
wos-search: Search WOK with the selected text or word at point

There is also a new org-mode link that opens a search: wos-search:alloy and segregation

org-ref-scopus

This is a small utility to interact with Scopus (http://www.scopus.com). Scopus is search engine for scientific literature. It is owned by Elsevier. You must have a license to use it (usually provided by your research institution).

(require 'org-ref-scopus)

Interactive functions:

scopus: Convenience function to open Scopus in a browser.
scopus-basic-search: Prompts for a query and opens it in a browser.
scopus-advanced-search: Prompts for an advanced query and opens it in a browser.

Some new links: Open a basic search in Scopus: scopus-search:alloy Au segregation

Open an advanced search in Scopus: scopus-advanced-search:au-id(7004212771). See http://www.scopus.com/search/form.url?display=advanced&clear=t for details on the codes and syntax, and http://help.elsevier.com/app/answers/detail/a_id/2347/p/8150/incidents.c$portal_account_name/26389.

A functional link to a document in Scopus by its “EID”: eid:2-s2.0-72649092395. Clicking on this link will open a hydra menu to open the document in Scopus, find different kinds of related documents by keywords, authors or references, and to open a page in Scopus of citing documents.

There is also a scopusid link for authors that will open their author page in Scopus: scopusid:7004212771

org-ref-isbn

index:isbn

(require 'org-ref-isbn)

This library provides some functions to get bibtex entries for books from their ISBN.

isbn-to-bibtex
isbn-to-bibtex-lead

It also provides some variables for customizing the bibtex entry.

org-ref-isbn-clean-bibtex-entry-hook
org-ref-isbn-exclude-fields
org-ref-isbn-field-name-replacements

org-ref-pubmed

index:pubmed

PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. This library provides some functions to initiate searches of PubMed from Emacs, and to link to PubMed content.

(require 'org-ref-pubmed)

This library provides a number of new org-mode links to PubMed entries. See http://www.ncbi.nlm.nih.gov/pmc/about/public-access-info/#p3 for details of these identifiers. These links open the page in PubMed for the identifier.

pmcid:PMC3498956

pmid:23162369

nihmsid:NIHMS395714

Also, you can retrieve a bibtex entry for a PMID with

pubmed-insert-bibtex-from-pmid

There are some utility functions that may be helpful.

pubmed: Open PubMed in a browser
pubmed-advanced: Open PubMed at advanced search page.
pubmed-simple-search: Prompts you for a simple query and opens it in PubMed.

There is a new org-mode link to PubMed searches: pubmed-search:alloy segregation

org-ref-arxiv

index:arxiv

This library provides an org-mode link to http://arxiv.org entries: arxiv:cond-mat/0410285, and a function to get a bibtex entry and pdfs for arxiv entries:

(require 'org-ref-arxiv)

arxiv-add-bibtex-entry
arxiv-get-pdf

org-ref-sci-id

index:orcid index:researcher id

(require 'org-ref-sci-id)

This package just defines two new org-mode links for http://www.orcid.org, and http://www.researcherid.com. Here are two examples:

orcid:0000-0003-2625-9232

researcherid:A-2363-2010

x2bib

index:bibtex!conversion

(require 'x2bib)

If you find you need to convert some bibliographies in some format into bibtex, this library is a starting point. This code is mostly wrappers around the command line utilities at http://sourceforge.net/p/bibutils/home/Bibutils. I thankfully have not had to use this often, but it is here when I need it again.

ris2bib: Convert an RIS file to a bibtex file.
medxml2bib: Convert PubMed XML to bibtex.
clean-entries: Map over a converted bibtex file and “clean it”.

org-ref-latex

This provides some org-ref like capabilities in LaTeX files, e.g. the links are clickable with tooltips.

org-ref-pdf

org-ref-pdf allows Emacs to get bibliography information from pdf files that contain a DOI. You must have pdftotext installed where Emacs can find it. This library is known to not work on Windows very well.

org-ref-url-utils

Allows you to drag-n-drop a webpage from a browser onto a bibtex file to add a bibtex entry (as long as it is from a recognized publisher that org-ref knows about). This library does not work well on Windows.

Appendix

Other things org-ref supports

org-completion

index:completion index:link!completion

Most org-ref links support org-mode completion. You can type C-c C-l to insert a link. You will get completion of the link type, type some characters and press tab. When you select the type, press tab to see the completion options. This works for the following link types:

bibliography
bibliographystyle
all cite types
ref

Indexes

index:index

org-ref provides links to support making an index in LaTeX. (http://en.wikibooks.org/wiki/LaTeX/Indexing).

index: creates an index entry.
printindex: Generates a temporary index of clickable entries. Exports to the LaTeX command.

You will need to use the makeidx package, and use this in the LaTeX header.

#+LATEX_HEADER: \usepackage{makeidx}
#+LATEX_HEADER: \makeindex

You will have to incorporate running makeindex into your PDF build command.

This is not supported in anything but LaTeX export.

Glossaries and acronyms

index:glossary

org-ref provides some support for glossary and acronym definitions.

gls: a reference to a term
glspl: plural reference to a term
Gsl: capitalized reference to a term
Glspl: capitalized plural reference to a term
gslink: Link to alternative text in the link description.
glssymbol: The symbol term
glsdesc: The description of the term
ac: a reference to an acronym
Ac: capitalized reference to an acronym
acp: a plural reference to an acronym
Acp: capitalized plural reference to an acronym
acrshort: Short version of the acronym
acrfull: The full definition of the acronym
acrlong: The full definition of the acronym with (abbrv).

There are two useful commands:

org-ref-add-glossary-entry: Add a new entry to the file
org-ref-add-acronym-entry: Add a new acronym to the file

Here is an example of glossary link for an acronym and an actual TLA. Each link has a tool tip on it that shows up when you hover the mouse over it. These links will export as the LaTeX commands need by the glossaries package.

You will need to incorporate running the command makeglossaries into your PDF build command. You also need use the glossaries LaTeX package.

Here is a minimal working example of an org file that makes a glossary.

#+latex_header: \usepackage{glossaries}
#+latex_header: \makeglossaries

#+latex_header_extra: \newglossaryentry{computer}{name=computer,description={A machine}}
#+latex_header_extra: \newacronym{tla}{TLA}{Three letter acronym}

A gls:computer is good for computing. Gls:computer is capitalized. We can also use a bunch of glspl:computer to make a cluster. Glspl:computer are the wave of the future. Don't forget what a ac:tla is.

\printglossaries

This is not supported in anything but LaTeX export.

If you have a lot of glossary entries and you want to have them in an external file, you can put them in a tex file, and then include them in the org file like this. Here the glossary entries are saved in a file in the same directory as glossary.tex. This should still work with the tooltips.

#+latex_header: \loadglsentries[main]{glossary}

Finally, you can define the glossary entries in org tables like this. They will be deleted before a LaTeX export.

#+title: Test
#+latex_header: \usepackage{glossaries}
#+latex_header: \makeglossaries


# This will not show in your export. It must be named glossary
#+name: glossary
| label | name  | description   |
|-------+-------+---------------|
| tree  | Tree  | A woody plant |
| shrub | Shrub | A woody bush  |

Checkout how a gls:tree differs from a gls:shrub.


#+name: acronyms
| Key  | Short | Long                           |
|------+-------+--------------------------------|
| mimo |       | multiple-input multiple output |
| qos  | QoS   | quality-of-service             |
| bb   | BB    | branch and bound               |


First ac:bb. Second ac:bb. First ac:qos. Second ac:qos.

# This is where your glossary and acronym entries will be put.
#+latex: \printglossaries

\glsaddall \printglossaries

Index

This is a functional link that will open a buffer of clickable index entries:

@@latex:\renewcommand{\indexname}{}@@ printindex:

References

<<bibliographystyle link>> bibliographystyle:unsrtnat

<<bibliography link>> bibliography:org-ref.bib

a	to ascii and open
h	to html and open
l	to latex and open	all cite links and bibliography are exported to latex
o	to OpenOffice and open
O	to org buffer	only goes to a buffer so you don’t overwrite the current buffer
e	to email

Files

org-ref.org

Latest commit

History

org-ref.org

File metadata and controls

The org-ref manual (version 3)

Introduction to org-ref

2021 version 2 vs version 3

known issues with org-ref and org-citations

Basic configuration <<basic-configuration>>

Basic usage of org-ref

Bibliography links

Citations <<citations>>

Pre/post text support

labels

ref links <<ref-links>>

Miscellaneous ref links label:sec-misc

Some other links

Some basic org-ref utilities

LaTeX export

BibTeX users

biblatex users <<sec-biblatex-users>>

Other exports

org-ref-export

org-refproc

Other libraries in org-ref

doi-utils

Bibtex key format

Troubleshooting doi-utils

org-ref-bibtex

Generate new bibtex files with adapted journal names

Modifying bibtex entries

Bibtex entry navigation

Hydra menus for bibtex entries and files

Formatted bibtex entry citations

org-ref-wos

org-ref-scopus

org-ref-isbn

org-ref-pubmed

org-ref-arxiv

org-ref-sci-id

x2bib

org-ref-latex

org-ref-pdf

org-ref-url-utils

Appendix

Other things org-ref supports

org-completion

Indexes

Glossaries and acronyms

Other forms of this document <<sec-other-forms>>

Build notes

PDF

Best practices for other formats

Other formats using CSL

Other formats without using CSL

Index

References