[org-ref.git] / org-ref.org

#+TITLE: The org-ref manual
#+AUTHOR: John Kitchin
#+DATE: 2015-03-15 Sun

* Introduction to org-ref
Org-ref is an addon library for org-mode cite:Dominik201408 that provides rich support for citations, and cross-references in org-mode. org-ref is especially suitable for org-mode documents destined for LaTeX export.

The basic idea of org-ref is that it defines 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 interfaces with helm-bibtex to facilitate citation entry.

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.

org-ref is [[id:32B558A3-7B48-4581-982B-082017B0AEE8][customizable]].

** Basic usage of org-ref

*** Sources of bibtex entries

*** Bibliography links
org-ref provides a bibliography link to specify which bibtex files to use in the document. You should use the full filename with extension, and separate filenames by commas. This link is clickable; clicking on a filename will open the file. Also, if your cursor is on a filename, you will see a minibuffer message about whether the file exists or not.

There is also a bibliographystyle link that specifies the style. This link does nothing but export to \bibliographystyle{link-string}.

If you use biblatex, then you use an addbibresource link. biblatex support is not very well tested by me, because we do not use it.

*** Citations
    :PROPERTIES:
    :CUSTOM_ID: citations
    :END:
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  reftex-default-bibliography.

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, select the reference(s) you want in the helm-bibtex buffer and press enter. The citation will be inserted automatically into your org-file. If the cursor is on a citation key, you should see a message in the minibuffer that summarizes which citation it refers to. If you click on a key, you should see a helm selection buffer 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 [[id:32B558A3-7B48-4581-982B-082017B0AEE8][customizable]], and set to "cite". If you want another type of citation type, then type C-u before pressing enter in the helm-bibtex selection buffer. You will be prompted for the type of citation you actually want.

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.

If you want to /replace/ an existing key in a citation, put the cursor on the key, run the insert citation command, and type C-u C-u before pressing enter in the helm-bibtex selection buffer. The key will be replaced. Of course, you can just delete it yourself, and add a new key.

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 run the command org-ref-sort-citation-link which will sort the keys by year, oldest to newest.

org-ref has basic support for pre/post text in citations. We have very little need for this in scientific publishing; we write pre text before the citation, and post text after it. However, you can get pre/post text by using a description in a cite link, with pre/post text separated by ::. For example, [[cite:Dominik201408][See page 20::, for example]].

You may want to bind a hydra menu to a key-binding or key-chord. For example:

#+BEGIN_SRC emacs-lisp
(key-chord-define-global "kk" 'org-ref-cite-hydra/body)
#+END_SRC

This will allow you to quickly press kk while on a cite link to access functions that can act on the link.

*** label links
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.

Or you can put a label link into a caption like this.
#+caption: Another simple table. label:tab-ydata
| y |
| 4 |
| 5 |

org-ref can help you insert unique labels with the command elisp:org-ref-helm-insert-label-link. This will show you the existing labels, and insert your new label as a link.

label links are "functional" if you put your cursor on the link, you will get a message in the minibuffer showing you the number of occurrences of that label in the buffer. That number should be one!

*** ref links
A ref link refers to a label of some sort. For example, you can refer to a table name, e.g. Table ref:table-1.

#+tblname: table-1
#+caption: A simple table.
| x |
| 1 |
| 2 |

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

#+label: table-3
#+caption: A simple table.
| x |
| 1 |
| 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-helm-insert-ref-link.

ref links are functional. If you put the cursor on a ref link, you will get a little message in the minibuffer with some context of the corresponding label. If you click on the ref link, the cursor will jump to the label.

A brief note about references to a section. This only works if you put a label in the org-mode headline. Otherwise, you must use a CUSTOM_ID and a CUSTOM_ID link.

**** Miscellaneous ref links
org-ref provides a pageref, nameref and eqref link.

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


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

Then you can refer to Eq. eqref:eq:1 in your documents.

** org-ref customization of helm-bibtex
org-ref adds a few new features to helm-bibtex. First, we add keywords as a searchable field. Second, org-ref modifies the helm-bibtex search buffer to include the keywords. Since keywords now can have a central role in searching, we add some functionality to add keywords from the helm-bibtex buffer as a new action.

We change the order of the actions in helm-bibtex to suit our work flow, and add some new actions. We define a format function for org-mode that is compatible with the usage defined in section [[#citations]]. Finally, we add some new fallback options for additional scientific search engines.

** Some basic org-ref utilities
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 helm buffer.

org-ref-clean-bibtex-entry will sort the fields of a bibtex entry, clean it, and give it a bibtex key.

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

** LaTeX export
All org-ref links are designed to export to the corresponding LaTeX commands.

** Other exports
There is some basic support for HTML and ascii export. Not all bibtex entry types are supported, but basic support exists for articles and books.

* Other libraries in org-ref
These are mostly functions for adding to bibtex files, or for operating on bibtex files.

** doi-utils
This library adds two extremely useful tools for getting bibtex entries and pdf files of journal manuscripts. Add this to your emacs setup:
#+BEGIN_SRC emacs-lisp
(require 'doi-utils)
#+END_SRC

The 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.

** isbn
#+BEGIN_SRC emacs-lisp
(require 'isbn)
#+END_SRC

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

- isbn-to-bibtex

** pubmed
#+BEGIN_SRC emacs-lisp
(require 'pubmed)
#+END_SRC

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.

pmcid:PMC3498956

pmid:23162369

nihmsid:NIHMS395714

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

- pubmed-insert-bibtex-from-pmid

** arxiv
#+BEGIN_SRC emacs-lisp
(require 'arxiv)
#+END_SRC

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:

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

** sci-id
#+BEGIN_SRC emacs-lisp
(require 'sci-id)
#+END_SRC

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

** jmax-bibtex
These are functions I use often in bibtex files.

- jmax-bibtex-generate-longtitles
- jmax-bibtex-generate-shorttitles
- jmax-stringify-journal-name :: replace a journal name with a string in
     `jmax-bibtex-journal-abbreviations'
- jmax-set-journal-string :: in a bibtex entry run this to replace the journal
     with a string
- jmax-title-case-article :: title case the title in an article
- jmax-sentence-case-article :: sentence case the title in an article.

- jmax-replace-nonascii :: replace nonascii characters in a bibtex
     entry. Replacements are in `jmax-nonascii-latex-replacements'.

- jmax-title-case-article
- jmax-sentence-case-article

- jmax-bibtex-next-entry :: bound to M-n
- jmax-bibtex-previous-entry :: bound to M-p

- Functions to act on a bibtex entry or file
  - jmax-bibtex-hydra/body :: gives a hydra menu to a lot of useful functions.
  - jmax-bibtex-new-entry/body :: gives a hydra menu to add new bibtex entries.
  - jmax-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.
You can do that like this before you require jmax-bibtex:

#+BEGIN_SRC emacs-lisp
(setq jmax-bibtex-hydra-key-binding "\C-cj")
#+END_SRC

Or this if you like key-chords:

#+BEGIN_SRC emacs-lisp
(key-chord-define-global "jj" 'jmax-bibtex-hydra/body)
#+END_SRC

* Appendix
** Customizing org-ref
   :PROPERTIES:
   :ID:       32B558A3-7B48-4581-982B-082017B0AEE8
   :END:
You will probably want to customize a few variables before using org-ref extensively. One way to do this is through the Emacs customization interface: [[elisp:(customize-group "org-ref")]].

Here is my minimal setup:
#+BEGIN_SRC emacs-lisp
(setq reftex-default-bibliography '("~/Dropbox/bibliography/references.bib"))

(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/")
#+END_SRC



* References
# <<bibliography link>>
bibliography:org-ref.bib