Citation Management
With
Mathematica's citation management features, you can annotate and add references to research papers written using
Mathematica. These features work in conjunction with the standard BibTeX format for reference data as well as with EndNote, a powerful system from Thomson Reuters that allows you to perform online research as well as automatically format citations for thousands of different journals.
Citation Management Using EndNote
EndNote, a powerful, industry-standard research tool, is one way the citation management features of
Mathematica can be used to allow you to research, cite, and annotate a notebook. In order to manage citations in
Mathematica with EndNote, the EndNote software must be installed and running.
Create Reference Databases for Use When Writing Papers
EndNote is a research tool from Thomson Reuters. With EndNote, you can build a database of references, both manually by entering data yourself, and also automatically by searching various online libraries. EndNote Link for
Mathematica interfaces with EndNote and allows you to insert references from your EndNote database into a
Mathematica notebook you are writing.
Manage Formatting References According to Various Publication Standards
One of the most powerful features of EndNote is that it also contains a large database of bibliographical and citation styles for over 3000 different publications. Each publication has its own standards for formatting bibliographies. By using EndNote Link for
Mathematica, you can prepare a notebook for submission to one publication and then easily reformat the citations and bibliographies for submission to another.
EndNote Link and Plugin Interface
EndNote interfaces to
Mathematica via
Mathematica's EndNote Link plugin. This is an additional piece of software from Wolfram Research that is installed in the EndNote plugins directory on your computer when
Mathematica is installed. The plugin serves as the link between EndNote and
Mathematica. If EndNote is running, the bibliographical reference menu items in the submenu become active.
Performing Research with EndNote
This is not a tutorial on how to use EndNote. For that you should refer to the documentation that comes with EndNote. For now, you will just use it in a very basic way, to search for online references.
Search the online PubMed database for all articles with the name "Sherlock" in the author list. Click on
PubMed in the
Online Search category. Enter
in the field on the
Search tab next to the first
Author Contains, and press
Enter.
Here EndNote finds 1406 records in the PubMed database.
Press
Enter to bring them all into the local database.
Bringing References into Mathematica
Now start
Mathematica if it is not already running. Here, for the purpose of illustration, is a dummy paper.
Inside
Mathematica, place the selection in the place where you would like to insert a citation and select .
The
Mathematica Insert Citation dialog will come up with all the references in your EndNote database.
Mathematica caches copies of all these references, so this dialog will come up faster after the first launch.
This shows the different components of the
Insert Citation dialog.
Filtering and Sorting Citations
The
Insert Citation dialog displays all the current references you have in your database. However, sometimes you may want to narrow down your collection to display only references with given keywords. For this you can use the filtering features of the
Insert Citation dialog. Entering a search term in the input field at the top of the dialog and then clicking
Find will display only those references that contain the term. It will also highlight the term in the list of references. Here, only the references containing the term "bile" are being displayed.
You can also sort the entries by author, year, and title.
Inserting and Deleting Citations
Inserting Single Citations
The citation management features in
Mathematica are only supported inside of text cells. To insert a citation, make sure the insertion point is inside of a text cell, select the reference from the list, and click
Insert in the dialog. The citation will appear in the text and a bibliography end note will appear at the end of the notebook.
The style of the citation and bibliography entry is determined by the currently selected citation style. The default style is numbered, but you can select from over 3000 predefined styles (when using EndNote). For example, here is what the same citation in the
Physical Review B style looks like.
Automatic Citation Numbering
If you are using a citation style that involves sequential numbers, they will be automatically recomputed whenever you insert a new citation. If you insert a citation between two existing citations, it will be renumbered when
Mathematica recomputes all the citation numbers in sequence. Citations will
not be recomputed if you delete text containing citations. To readjust the citation numbering in this case, select and from the menu.
Inserting Multiple Citations
The
Insert Citation dialog allows you to select more than one reference at a time by holding down the
Ctrl key for each additional reference selected. When two or more references are selected, they are automatically grouped together, according to the grouping conventions of the currently selected citation style. In addition, if you insert a citation immediately adjacent to an existing citation, they will also be grouped according to the style's grouping rules.
Refreshing Reference Library
While you are editing a notebook with
Mathematica, you may wish to go back to EndNote or another data source and do more research, possibly changing your database of references. When you return to
Mathematica, any new references will not appear in the
Insert Citation dialog until you click the
Refresh button
at the upper-right corner of the dialog. When you click
Refresh,
Mathematica's internal cache of references will be cleared and then rebuilt.
Changing Citation Styles
To change the citation style for the entire notebook to that of a different journal or publication, choose from the menu. The
Citation Styles dialog will come up populated by all the different citation styles that EndNote (or BibTeXLink) supports.
To set a new citation style, choose the publication from the drop-down menu and click
OK. The citations and bibliographical entries will be reformatted to correspond to the new publication.
Note that EndNote by default supports a subset of all available styles. This smaller subset is more useful and improves performance with this dialog. If you would like to install all styles, it is an option during the installation of EndNote. If you do install the full set of styles, the
Citation Styles dialog will take a few seconds to come up while the drop-down list is fully populated.
Mathematica caches this list, so that subsequent launches of the dialog will be faster.
Citation Management for BibTeX References
Selecting a BibTeX File as the Data Source
In the data source drop-down menu at the bottom of the
Insert Citation dialog, choose BibTeX. A dialog will come up asking for you to choose the .bib file to be used for your reference database. Choose the .bib file and
Mathematica will load the database. Once
Mathematica loads the database, the references will appear in the
Insert Citation dialog and you can insert them as in the above examples.
You can use references from several different BibTeX files. If your reference is not in the currently loaded set of BibTeX references,
Mathematica will also search any repository specified by the
environment variable when rebuilding a bibliography.
Note:
Mathematica does not, at present, support mixing BibTeX citations with EndNote citations in the same notebook.
Advanced Topic: Using Journal Styles with BibTeX References
Mathematica supports only a small number of predefined journal styles for BibTeX citations and bibliographies. However, you can modify these styles and add new ones that are customized to your research.
In the under is the list of templates that are used to customize citations and bibliographies. Each template is defined by a string, which names the template followed by two additional strings that contain cell definitions for the citation and bibliography cells, respectively. Each cell template contains tags of the form $TAGNAME$, which correspond to the tags in a BibTeX entry.
For example, here is a sample BibTeX entry.
@Misc{elliptic,
author = {Wolfram, Stephen},
title = {Solving the Quintic with {M}athematica},
howpublished = {http://library.wolfram.com/examples/quintic/},
year = 1999
}
Here is the string from BibTeXTemplates, which defines how a bibliographical cell would appear.
Cell[TextData[{" $REFNUM$. $AUTHOR$, ",
StyleBox["$TITLE$", FontSlant->"Italic"],
" $YEAR$. ",
"$HOWPUBLISHED$"}],
"$CELLSTYLE$",
Editable->False,
TaggingRules->{ReferenceData -> ""}]
Here is how the bibliography cell is then formatted when it gets inserted into the notebook.
1. Wolfram, Stephen,
Solving the Quintic with Mathematica 1999. http://library.wolfram.com/examples/quintic/
The additional special tags, $REFNUM$ and $CELLSTYLE$, should not be deleted and are filled in by
Mathematica's citation formatting machinery when the template is processed into a cell and inserted into the notebook.
Cell definitions with tags that do not correspond to BibTeX entries are not replaced, but are left in their $TAGNAME$ form. You can use this feature to resolve discrepancies between the bibliography format and the fields in the BibTeX entries.
Inserting and Editing Notes
Inserting Notes
In addition to being used with EndNote or BibTeX,
Mathematica also supports inserting raw notes into text cells that do not correspond to entries in a bibliographical database. For this mode of operation, EndNote or BibTeXLink does not need to be running or even installed. To insert a note, choose from the menu. The
Insert Note dialog will appear.
The input field in this dialog will accept any standard
Mathematica input, including text, graphics, and typeset equations. Click
Insert and a citation will be inserted at the current text-insertion point. A note entry, similar to a bibliographical entry, will be inserted at the end of the notebook.
Editing Notes
To edit a note, select the note citation and select from the menu. The
Insert Note dialog will reappear and allow you to modify the content of the note.
Clicking
Insert will update the notebook to reflect the new contents of the note.
