PubMode -- An interface to PubMed for Emacs
===========================================

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.


0. Licence
==========

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.

1. Requirements
===============

Currently the mode only runs with GNU Emacs 22.x.  


2. Installation
===============

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.

3. Usage
========

Below you find a detailed documentation of all functions. Before you
read it, I suggest to simply give it a try and run "M-x pub-med". 


3.1. Invocation
===============

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.

3.2. The selection window
=========================

3.2.1. Navigation
-----------------

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] 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 if
switch to page the first time.

To perform a new PubMed search press [p]. To search related articles
to the current item press [r].

3.2.2. Modes of view
--------------------

There are three detail levels to view the entries:

 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 [1] [2] and [3]. If you just
want to toggle the detail-level for the current item, use [d].

3.2.3. Marking entries
----------------------

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].

3.2.4. Exit the selection buffer
--------------------------------

[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.



3.3. Importing citations as plain text
======================================

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.


3.4. Importing citations for use with BibTeX/LaTeX
==================================================

3.4.1 Setting the BibTeX 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.

3.4.2 Importing BibTeX entries
------------------------------

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...


3.4.2 Inserting LaTeX citations
-------------------------------

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.


4. Viewing full text articles in external browser
=================================================

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.


5. Keyboard commands
====================

  [Up]/[Down]    Select previous/next item in the list.
 [Left]/[Right]   Switch to previous/next page.

     [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.
     [p]         New PubMed query.
     [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])



6. Customization
================

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".


pub-autos-save
--------------

If non-nil, the BibTeX-file is saved automatically
upon exit of the PubMed results window. By default this option is set
to true.

pub-key-template 
----------------

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 lowercase), 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 lowercase), 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.

pub-limit
---------

Number of items shown on one page. Default is 15.

pub-bibtex-file 
---------------

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.

pub-bibtex-abstract 
-------------------

If non-nil abstracts are included as field in the BibTeX entries created. 


pub-double-brace 
----------------

Enclose title in BibTex entry in double braces or not. Hide Rest 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
preserving 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.

pub-default-detail
------------------

Set your default detail level 1,2 or 3 of the PubMode selection window.

   1: brief view with only the first Author and the reference without title.
   2: Summary with full reference and all authors. 
   3: Summary with abstract 

By default this value is initialized to 2.

pub-line-width
--------------

Line width of the text in the PubMode selection window. Lines longer
than that value are broken. Default value is 65.


7. Contact
==========

Stefan Washietl <[email protected]>

See www.tbi.univie.ac.at/~wash/PubMode for updates and News.

Feel free to contact me with comments/bug-fixes/feature-request etc.