Brief guide to using Reference Manager

Introduction

Contents

Reference Manager is a software package that will help you to collect and manage citation information and to generate formatted bibliographies in a range of styles (there are hundreds of styles packaged with the software, including classic styles like Harvard & Vancouver). The software is available for Windows only; it can be downloaded onto UCL computers, or can be purchased (with an educational discount) for home-use (see more details). The Reference Manager website offers advice about the compatabililty of different version of Word with Reference Manager (www.refman.com/rmword2k7.asp).

This guide will enable you to create a Reference Manager database and to use the basic facilities of the software. The guide is based on Reference Manager version 12. If you would like further help or to arrange a training session, please do not hesitate to contact us (library@ion.ucl.ac.uk, IoN extension 4144). Also see the Frequently Asked Questions section at the end of this page.

UCL also offers an alternative bibliographic management tool - Endnote (which offers a Mac version). The two products are very similar; Reference Manager is sometimes favoured by research groups wishing to collaborate on a database. More information about Endnote is available in our Endnote guide.

Getting started: creating a new database

  • Open the Reference Manager software
  • Choose "New Database" from the File menu
  • The dialogue box allows you to enter a name for the database and choose where to save it; simply type your chosen file name and click "New"
  • Note: this creates 2 files, one with an ".rmd" extension and one with an ".rmx" extension. You need both of these files to use the database so please don't be tempted delete either of them.

Setting up your database

  • The database will have been created using Reference Manager's default settings but you can amend these settings if you wish.
  • To amend the Reference List display choose "Reference List Display" from the Tools menu, e.g. to include a column displaying the publication year or the periodical name.
  • To change the importing settings so that duplicate records are not imported, choose "Options" from the Tools menu, click the Import tab and move the radio button from 'Import' to 'Do not import'.

  • To import an index of journal names and abbreviations (it is recommended that you do this before you start to build your database), follow these steps:

    • choose "Term Manager" from the "Tools" menu and click "Activate" (make sure that the "Periodicals" tab is selected, located on the left)
    • choose "Term Manager" from the "Tools" menu again and click "Copy periodicals"
    • from the drop-down menu choose "Medical" and click OK

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Add references to your database

There are 3 ways to add references to your database. You can simply type in the data manually, you can perform an Internet search from within Reference Manager, or you can import a set of results as a text file (e.g. from PubMed or Web of Science). Each method is described below. Note: Reference Manager can look for duplicates in your database so that you do not have the same reference listed twice.  Go to the Tools menu, choose Batch Operations and choose "Duplicate search...".

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Add references manually

  • From the References menu, select "New" and a blank reference form is opened.
  • From the drop-down menu next to "Reference Type", select the relevant publication type for the new reference you are entering (e.g. Journal, Book Chapter, etc.)
  • Enter information into each field as appropriate, using the tab key to move to the next field
  • Some fields are marked with an asterisk to indicate that they are mandatory. If you forget to complete a mandatory field, Reference Manager will not let you save the reference.

Copying references from bibliographic databases to Reference Manager

    • Web of Science
    • PubMed
    • OvidSP (includes Medline)
    • NHS Search 2.0 (includes Medline

The procedure will change depending on which database you are importing references from. Some databases have a helpful built-in export option while other databases may require you to save the references into a text file and then import it into Reference Manager later. Below are 4 examples of key databases, but please ask if you need help importing from another source. The 4 exmaples are:

  • Importing references into Reference Manager from Web of Science

    • Login into Web of Science, via the Web of Knowledge, at http://wos.mimas.ac.uk (you will need to use your UCL Athens username and password if you are working off-site).
    • Do a search as usual and mark the references you would like to add to your Reference Manager database.
    • There are buttons at the top & the bottom of the screen to "Save to “Endnote, RefMan, ProCite”. After selecting this option the export application should launch automatically. If it doesn't, click the “Export” button.
    • When prompted, choose which Reference Manager database you want to use and click "Open"; the references are automatically sent to this database and an "Imported" tab is created displaying the items you have just imported.

  • Importing references into Reference Manager from PubMed

    • Go to PubMed and run a search as usual, marking the references you want to import (you might want to add selected items to the Clipboard first).
    • To save your selected items to a file, use the “Send to” drop-down menu on the right, choose "File" and then select "MEDLINE" instead of "Summary" format from the drop-down menu. This allows you to save the references as a text file with the default filename pubmed-result.txt
    • Go back to Reference Manager and select "Import text file" from the File menu (Note: if you are using version 10 this option is found in the References menu).

    • A dialog box will appear and you need to check the options before importing:

      • database: make sure you are importing the references to the correct database
      • filter: locate the correct filter by clicking the browse button (the button with 3 small dots on it). The software includes filters for many databases, E.g. the Pubmed filter is the one to choose if your results are coming from PubMed. Please contact the Library for help if you cannot find the filter you require or if the filter does not seem to work.
      • text file: select the text file you want to import by clicking the browse button
    • Click the Import button
    • When the import is complete you will get a confirmation message and the references will have been added to your database and can also be viewed in the tab marked "Imported"
    • Remember to check the quality of the data you have imported and check for duplicates.

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  • Importing references into Reference Manager from OvidSP (includes Medline)

    • Open Medline OvidSP via the databases page and run a search as usual and mark the references you would like to add to your Reference Manager database.
    • At the top of the results list click the Export button. From the resulting dialog box, choose Reference Manager from the "Export to:" menu, choose which fields you want to export and then click Export Citation(s). When prompted, click Open, and then choose your Reference Manager database to import the references. An "Imported" tab is created displaying the items you have just imported.

  • Importing references into Reference Manager from the NHS databases (including Medline) [please note that this service is available to NHS staff only, see the Databases page for further details.]

    • Go to the National Library for Health website (www.library.nhs.uk). Login with your NHS Athens account and under Resources select Books, Journals and Healthcare databases. Then select “Healthcare databases Advanced Search”.
    • Select “Medline” and click on “Next”. Run a search as normal and mark the articles that you want. At the bottom of the page under “Output format” select “RIS”. Choose a display format and click on “Export Results”.
    •  When prompted, choose your Reference Manager database and click "Open", the references are automatically sent to this database and an "Imported" tab is created displaying the items you have just imported

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Search PubMed, Web of Science and library catalogues from within Reference Manager

You can import references from some Internet resources directly from within Reference Manager - for example PubMed, Web of Science or, using a system called z39.50, some library catalogues. The references you find using Reference Manager’s Internet search are placed in a temporary database from which you can copy items into your own database.

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Searching PubMed & Web of Science from Reference Manager

  • From the References menu, choose "Search References" and then click the box marked "Internet Search".
  • Select either "PubMed" or "Web of Science" from the Internet search drop down list. [Tip: remember that your searching will need to conform to PubMed or WoS standards - e.g. for PubMed do not use a comma between the author's surname and the initials]

The search screen will look like this:

Retrieval

  • When you have retrieved some records, they will be displayed in a tab (at the bottom of the screen) marked Search1, Search2, etc. These can then be copied into your database as follows:

    • From the "References" menu, select "Copy between databases"
    • Choose to copy from the search (e.g. Search1) and to copy to your database (both need to be open at the same time.

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Searching library catalogues of the world (z39.50 sites)

  • Note: this option allows you to search for book information. It allows you to search for authors and titles only, not the contents of the books - i.e. not book chapters.
  • From the References menu select "Search References" and tick the "Internet search" box.
  • Select "Z39.50 sites" from the drop-down list
  • Start the Internet search by selecting the "Start Retrieval" tool button (binocular icon)
  • The "Z39.50 Hosts and Databases" window appears for you to choose libraries to search.
  • Check the box preceding the name of the database. Click OK.
  • Results are displayed in a temporary database which you can save. Alternatively you can drag selected items into your test database
  • Note: Access to Z39.50 sites can vary depending on a number of conditions. Sometimes the databases may be inaccessible while being updated. Often networks restrict access to certain communication ports that may be used by various databases. Lastly, some databases require a paid subscription and will prompt for a username and password

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Search your database

You can search within your own Reference Manager database to locate specific references for editing, or for printing bibliographies. You can create a 'search strategy', a description of the criteria you would like Reference Manager to use when searching for references in one or multiple open databases. You can search limit the search to specific fields if you need to. If you create a search strategy that you want to use again, it can be saved.

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Create & save a search strategy

  • In the References menu choose "Search References".
  • Place your cursor in the first column labelled "Field" and select the name of the field you would like to search from the drop-down menu.
  • In the "Parameter" column; type in the word you want to search for
  • You can build up a search on the rows below. Select AND, OR or NOT from the first column (AND will find the records that contain both parameters; OR will find the records that contain either or both parameters; NOT will find the records that contain only the first parameter).
  • Click on the binocular icon to run the search.
  • To save the strategy, click the "Strategy Files" icon (binoculars with a disk).
  • The "Retrieval Strategy" dialog box appears.
  • Click the "Save" button and give the search strategy a name and click OK
  • Select the Strategy Files once more to confirm your search is saved for future use. 
  • You can return to this screen, highlight one of your saved strategies and select "Load".
  • Click on "Close" to return to the Retrieval window.

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Create a bibliography

One of the most powerful features of Reference Manager is its ability to automatically create bibliographies using a range of output styles. There are two methods of creating a bibliography: manually create a static bibliography from within Reference Manager; use the "Cite While You Write" feature to create a bibliography dynamically as you compose a document in Word (see below).

  • To manually create a static bibliography: first search your database for the references you require
  • Go to Tools and then Bibliography.
  • From the Bibliography menu select "Generate from reference list"
  • Choose to send the bibliography directly to the printer or to a file
  • Select the output style you wish to use
  • If you choose to save to a file you should use the dialog box to give the file a name and say where you want to save it then click "OK"
Bibliography Setup


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Cite While You Write

When the Reference Manager software is installed into a computer, a toolbar is automatically added to Word. If the toolbar does not appear when you open Word, you can activate it from the View menu by selecting "Toolbars" and then selecting the Reference Manager toolbar from the list.

The Reference Manager toolbar will allow you to search your Reference Manager database directly from your Word document, to insert citations, and to build up the bibliography at the end of your document. To add citations into the body of your Word document you should make sure that your Reference Manager database is open.

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Inserting citations

  • In your Word document, begin to type your document and, when you reach a point where you want to cite a particular article, click the Insert Citation button on the Reference Manager toolbar (the first icon on the left)
  • A search box appears where you can search for an author or keyword to find the reference you want to cite - NB: the search is referring to the contents of your Reference Manager database & so it is important that the reference is already contained within that database. (You may need to specify which Reference Manager database to use by using the drop-down list of the Look In box).
  • When you have identified the reference you want, click the Insert button to insert a 'place-holder' in the appropriate place within your Word document.
  • This causes two pieces of formatting - [1] the in-text citation is added & formatted and [2] the citation is added to the reference list at the bottom of your document.
  • If you wish to cite a batch of references, in the same place in your Word document, first mark the items you want within your Reference Manager database and then return to your Word document & select "Insert Marked References" from the toolbar.

Formatting the bibliography

  • As you enter citations, a bibliography (or a list of references) is automatically generated at the bottom of the Word document. At the same time the in-text citations are formatted.
  • You can change the style & formatting by selecting a different Output Style. The output style determines the format of the in-text citations, as well as the format of the bibliography at the end of the document.
  • To change the output style (or if you want to 'refresh' the formatting), click Generate Bibliography or Update Citations & Bibliography icon (the name of the icon depends on which version of Word you are using) on the Reference Manager toolbar.
  • If you do not see the Output Style you want in the list, contact the lbirary for help.

Frequently Asked Questions

  • Using DOIs. Sometimes an article has been published online but does not yet have volume/page numbers. Where this is the case, it is good practice to use a DOI (Digital Object Identifier) in their place. A DOI is guaranteed to never change and so will allow you to create a permanent link. You can usually find the DOI on the article's webpage and it will look something like this: doi:10.1000/jfake.12.341. To link to this DOI you would simply remove the prefix 'doi:' and add the web address http://dx.doi.org/. So the complete link for this example would be: http://dx.doi.org/10.1000/jfake.12.341

  • Amended output style: Harvard. Students have commented on two aspects of the Harvard output style which they are not happy with so - we have provided an amended style to 'fix' this. Please note that this output style is not an 'official' release, just a local solution. To use the file, first save it to your PC by right-clicking the following link & choosing 'Save As' - amended Harvard. Then you can select it when generating your bibliographies. So, what does this amended style do?

    • Where an article is cited in your text more than once, the standard Harvard output style lists it as e.g. (Brown et al. 2011) the first time it is cited; but for subsequent mentions of the same article, all the authors are listed, e.g. (Brown, Jones, Smith & Martin 2005). In the amended output style only the first author is listed each time.
    • where an article is available online-only additional text can be added to the 'Availability' field to say, e.g. "Available at: http://www.awebsite.com/ [accessed 7 December 2008]" but this text does not appear in the bibliography when using the standard Harvard output style. This field has been incorporated into the amended Harvard output style and so the text will now appear in the bibliography.

  • Web Publisher feature

    • This feature is not currently supported by the ION Library or the ION Computing Unit. The Web Publisher feature allows you to publish databases on an intranet or the internet and you may choose to offer them as read-only or with read/write access. You will need to talk to your network administrator before activating this feature, especially if you operate within a firewall.

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Getting further help

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