PubMode is an Emacs interface to the PubMed library of biomedical literature. Its purpose is to give streamlined access to PubMed citations during the creation of documents without any distractions like web-browsers, import-scripts, or external bibliography applications. In particular, the mode is designed to work with BibTeX and LaTeX fully automatizing the process of creating BibTeX entries and inserting citations.
PubMode is free software and licenced under GNU Genaral Public License version 3.
See file COPYING for details. See file NCBI-DISCLAIMER for copyright and disclaimers for PubMed data.
Currently the mode only runs with GNU Emacs 22.x and up.
Add the 3 lines to .emacs and everything should be ready for use
(add-to-list 'load-path "~/some/directory/PubMode-0.1/lisp") (autoload 'pub-med "pub" "PubMed Interface for Emacs" t) (global-set-key (kbd "C-c p") 'pub-med)
If you want (or must) access the internet through a proxy-server you have to tell Emacs to do so. Run "M-x customize-variable" on the variable "url-proxy-services". In the customization menu, put in the address of your http-proxy and save the settings.
See file INSTALL for more detailed installation instructions.
Below you find a detailed documentation of all functions. Before you read it, I suggest you simply give it a try and run "M-x pub-med".
Call the command "M-x pub-med" and you will be prompted for your search term. Input your search term as you would do it on the NCBI web-site.
See www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html for details.
Depending on your internet connection and the availability of the NCBI web-site, the resuts will appear after a few moments. Your current window will be split and you will be presented a list of articles in a buffer called PubMed Results.
Use the arrow keys [Up] and [Down] or the keys [p] and [n] to scroll through the list of articles. By default only 15 articles are shown per site. Using the [right] and [left] arrow keys you can switch between pages. Note that each page is downloaded separately so there can be some delay the first time you switch to a page.
To perform a new PubMed search press [s]. To search articles related to the current item press [r].
There are four detail levels to view the entries:
0: Very brief view with just the DOI URI 1: Brief view with only the first author and the reference without title. 2: Summary with full reference and all authors. 3: Summary with full reference and all authors and abstract.
You can switch between the views using [0], [1], [2], and [3]. If you just want to toggle the detail-level for the current item, use [d].
By default all commands described in the next sections work on the currently selected items. If you want to apply a command to multiple items you can mark items using the space-bar [ ]. For un-marking, also use the space-bar. To mark all items on the current page, use [a]. You can unmark all items using [d].
[q] closes the PubMed Results buffer and also the split window that was opened. Also hitting [ENTER] closes the buffer. However, depending on the mode (text or BibTeX, see below) it will apply the default action to the currently selected item.
When writing documentation, presentations, referee-reports, web-sites etc. it is often necessary to include references as plain text.
For this purpose you can hit [t]. This will paste the currently active item or all marked items to the buffer where you initiated your PubMed search from. Alternatively, using [w] you can copy the text to the clipboard (more precisely the Emacs "kill-ring"). You can then insert ("yank") the text wherever you want using the command "C-y".
The format of the imported citation is the same as you see it in the selection window. You can change the detail level as described in section 3.2.2.
By default, the [ENTER] key has the same effect as [t] and pastes the current item or marked items. However, it immediately exists afterwards. Note, that the behaviour of the [ENTER] key is different when you are editing a LaTeX file.
PubMod can convert citations to BibTeX format ready for use with LaTeX/BibTeX. For the most common scenarios, PubMode will find the correct BibTeX file for adding references automatically: If you are editing a BibTeX file, the current file will be the target file. If you are editing a LaTeX file with a \bibliography statement pointing to a BibTeX file, this file will be used.
In any other situation, you can set the BibTeX file manually by pressing [f]. You will be asked automatically, if no file is specified and you try to import references.
The currently active BibTeX file is shown in the mode-line of the PubMed results buffer in brackets.
You can also set a BibTeX file (e.g. your central reference database) that is always used by default. You can set the variable pub-bibtex-file in the customization menu (see section 5. Customization ). If this variable is set, no attempts will be made to choose the file automatically and you will not be asked for a file name. You can temporarily change this variable for the session using the [f] command.
Once a BibTeX file has been specified, PubMed compares the search results with the entries in the file on the basis of the PubMed identifier (PMID). If there is already an entry with the same PMID the item will be marked by "*" in the list.
Hitting the [b] key converts the currently active item or all marked items to BibTeX format and appends it to the specified BibTeX file.
They BibTeX key is automatically generated. The default format of the key is Name:Year (eg. Smith:2008) but can be customized individually (see section 5. Customization).
If there is already an entry with the same key you will be asked what to do: Hitting [s] skips the item and does nothing. [r] replaces the existing item with the new item. [a] adds the new item to the file with a modified key, eg. Smith:2008a, Smith:2008b...
If you have imported an item to the BibTeX file (indicated by "*") you can easily insert a LaTeX citation by pressing [c]. This inserts a \citation command at the current position of the buffer where you have initiatied your PubMed search. If you have marked several items, they will combined in one \citation statement.
If you have started your PubMed search from a file endig in *.tex. The default behaviour of the [ENTER] key is a combination of [b]+[c]+[q], i.e. it imports the current item/marked items, inserts a corresponding \cite statement and exits the buffer.
PubMode allows to view biblographic details of articles as well as the abstract. If you want to view the full-text of the article, press [o]. This opens an external browser showing the full-text link as provided by the PubMed LinkOut system. If no full-text is available for an article, this command redirects you to the PubMed entry on the NCBI web-site. You can set your default browser and its behaviour (new window, new tab etc) by customizing several variables in the browse-url group.
[Up]/[Down] and [n/p] Select previous/next item in the list. [Left]/[Right] Switch to previous/next page.
[0] very brief DOI view' [1]brief view'
[2] summary view' [3]abstract view'
[d] Toggle detail level of current item.
[Space] Mark/un-mark current item. [a]/[u] Mark/un-mark all items on the current page.
[t] Import current item/marked items as text.
[b] Import current item/marked items to BibTeX file.
[c] Insert citation for current item/marked items. Item
has to be imported before it can be cited.
[w] Copy current item/selected items to the kill-ring
(clipboard') for yanking (pasting') into another
buffer.
[s] New PubMed query search.
[r] Search related articles for current item.
[f] Choose BibTex file.
[o] Open full-text (if available) in external browser.
[h] Show this help screen. [q] Exit the PubMed selection window. [ENTER] Import and cite item/selected items and exit ([b]+[c]+[q])
There are a few customization variables available. You can either set them manually in your .emacs or by using the standard customization interface. You can run "M-x customize-group" and choose the group "pub".
If non-nil, the BibTeX-file is saved automatically upon exit of the PubMed results window. By default this option is set to true.
Define the pattern of the BibTeX key.
You can access the following special fields:
%N Last name of first author (first letter uppercase), eg. Smith
@N Last name of first author (all uppercase), eg. SMITH
%J Journal abbreviation (first letters uppercase), eg. J_Mol_Biol
@J Journal abbreviation (all uppercase), eg. J_MOL_BIOL
%P PubMed ID, eg. 12621444
%Y Year (four digits), eg. 2008 %y Year (two digits), eg. 08
The length of the author field can be limited by appending the number of characters to the N, eg. @N3 would give SMI instead of SMITH.
The default key is %N:%Y, which gives keys of the form Smith:2008.
Number of items shown on one page. Default is 15.
Default destination file for imported BibTeX entries.
If this variable is empty, the BibTeX file is determined as follows: The current file is used if PubMode is called from a BibTeX file itself. If a \bibliography LaTeX command can be found this file is used. If none of both applies, the user is asked to set a destination manually.
If non-nil abstracts are included as field in the BibTeX entries created.
Enclose title in BibTex entry in double braces or not. If this is option is non-nil, the title field in the BibTeX entry will be enclosed in an additional set of curly brackets {}. This makes BibTeX preserve upper and lowercase. In general you should let the style decide which letters to print upper or lowercase, which, however, may require manually insertion of braces to fix words like DNA or IGF-2.
Set your default detail level 0, 1, 2 or 3 of the PubMode selection window.
0: very brief view with only the DOI URI. 1: brief view with only the first Author and the reference without title. 2: summary with year and all authors (journal name is omitted). 3: summary with abstract.
By default this value is initialized to 2.
Line width of the text in the PubMode selection window. Lines longer than that value are broken. Default value is 65.
Original author: Stefan Washietl wash@tbi.univie.ac.at
Feel free to contact me with comments/bug-fixes/feature-request etc.
For this fork of the project, GitHub issues would work best: https://github.com/jshoyer/pubmode/issues