Reference management for LaTeX users

Reference management for LaTeX users : a toolbox

Recommended software

JabRef is the reference management software recommended by the Library for people writing papers in LaTeX. It runs on Linux, Mac OS X and Windows and integrates well with LaTeX editors such as Kile, WinEdt, Emacs, etc.

BibDesk is a good alternative for people working under Mac OS X, as it integrates somewhat better in the workflow.

Import references

Attention: automatic import saves time by removing the need to copy-paste references into your reference management software but you still need to review each imported reference to ensure that there were no errors or lost information during the import.

Last update: April 2009. This page is currently under revision.

JabRef

 BibDesk

ISI Web of Knowledge

  
  1. Select the records to export
  2. Click on the Save to EndNote button
  3. Save as file
  4. From within JabRef, use the File->Import (ctrl-I) function
  5. Set Files of Type to ISI
  6. Check the imported references, then OK
  1. Select the records to export
  2. Click on the Save to EndNote button
  3. Save as file and open with BibDesk
  4. Check the imported references
  5. Drag and drop the references from the imported file into your database

or

  1. Use the inline search box for ISI from within BibDesk: Searches -> Web of Science SCI
  2. Check for quality, then click the Import button on relevant results

Warning: the inline search box does not query all databases.

EngineeringVillage

  
  1. Select the records to export
  2. Click on the Download button
  3. Select the BibTeX format
  4. Save as file and open with JabRef
  5. Check the imported references
  6. Copy the downloaded records into your database (ctrl-C, ctrl-V)
  1. Select the records to export
  2. Click on the Download button
  3. Select the BibTeX format
  4. Save as file and open with BibDesk
  5. Check the imported references
  6. Drag and drop the references from the imported file into your database

Scopus

  
  1. Select the records to export
  2. Click on the Output button
  3. Select Export format: RIS format
  4. Select Output: Abstract format
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to RIS
  8. Check the imported references, then OK
  1. Select the records to export
  2. Click on the Output button
  3. Select Export format: RIS format
  4. Select Output: Abstract format
  5. Save as file and open with BibDesk
  6. Check the imported references
  7. Drag and drop the references from the imported file into your database

PubMed (Medline)

  
  1. Select the records to export
  2. Select Display: XML in the drop-down menu
  3. Select File in the rightmost drop-down menu
  4. Save as file
  5. From within JabRef, use the File->Import (ctrl-I) function
  6. Set Files of Type to Medline
  7. Check the imported references, then OK

or

  1. Use the inline search box for Medline from within JabRef: Web Search -> Search Medline (F5).
  2. Select the records to export, check for quality, then OK

Warning: the inline search box does not query all databases.
  1. Select the records to export
  2. Select Display: MEDLINE in the drop-down menu
  3. Select File in the rightmost drop-down menu
  4. Save as file and open with BibDesk
  5. Check the imported references
  6. Drag and drop the references from the imported file into your database

or

  1. Use the inline search box for PubMed/Medline from within BibDesk: Searches -> PubMed
  2. Check for quality, then click the Import button on relevant results

Warning: the inline search box does not query all databases.

Ovid

  
  1. Select the records to export
  2. Select Fields: Complete Reference
  3. Select Result Format: Ovid
  4. Click the Save button
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to Ovid
  8. Check the imported references, then OK

Not available :-(

Use JabRef to convert the references to BibTeX until a better solution is found.

CSA Illumina

  
  1. Select the records to export
  2. Click Save, Print, Email
  3. Click the Save button
  4. Save as file
  5. From within JabRef, use the File->Import (ctrl-I) function
  6. Set Files of Type to CSA
  7. Check the imported references, then OK

Not available :-(

Use JabRef to convert the references to BibTeX until a better solution is found.

Infoscience

  
  1. Select the records to export
  2. Select Export: BibTeX on the right-hand side
  3. Save as file and open with JabRef
  4. Check the imported references
  5. Copy the downloaded records into your database (ctrl-C, ctrl-V)
  1. Select the records to export
  2. Select Export: BibTeX on the right-hand side
  3. Save as file and open with BibDesk
  4. Check the imported references
  5. Drag and drop the references from the imported file into your database

NEBIS

  
  1. Select the records to export
  2. Click Mail/Save
  3. Select Predefined Format: EndNote, RefMan, ProCite, etc.
  4. Leave the other fields blank
  5. Save as file
  6. From within JabRef, use the File->Import (ctrl-I) function
  7. Set Files of Type to RIS
  8. Check the imported references, then OK

Reference import not available yet :-( Use JabRef to convert the references to BibTeX until a better solution is found.

or

You can set up an inline search box using the Z39.50 protocol. To do this

  1. Choose Searches -> New Search Group...
  2. Select Type: Z39.50
  3. Select Server: Other and fill up the following information

A note on inline search functionnalities

For many databases, you can search directly from within the reference management software (inline search)

Warning: this should not be used for extensive litterature research, since inline search typically does not query all available databases.

Always do your litterature research on the web, and export relevant results in your reference management software. Inline search tools should only be used to retrieve known references.

Cite while you write (CWYW)

Windows: Set up CWYW using WinEdt and JabRef

A button  push selection to WinEdt (ctrl-L) is available on the JabRef toolbar (also works with other editors, such as LyX, Kile, Emacs, etc.)

Linux: Set up CWYW using JabRef

In order for this to work, you have to set up a LyX pipe (even if you don't use the LyX editor). On your home directory, create a .lyx folder, and an empty file called lyxpipe in it. Then, configure both JabRef and Kile to use this file as the LyX pipe. In JabRef, go to Options -> Preferences -> External programs and set the Path to LyX pipe field.

When all is set, use the same procedure as under Windows (see above).

Mac OS X: Set up CWYW using JabRef

In JabRef, select the references you want to cite, then choose Edit -> Copy \cite{BibTeX key} (⌘-K). Paste it (⌘-V) in your editor (e.g. TexShop).

Mac OS X: Set up CWYW using BibDesk

In BibDesk, select the references you want to cite, then choose Edit -> Copy (⌘-C). Paste it (⌘-V) in your editor (e.g. TexShop). To specify what should be copied when hitting ⌘-C (\cite string, whole reference etc.), go to BibDesk -> Preferences -> Citation and choose Default format: TeX cite command.

Resources

 

All our best wishes for a successful thesis ! -- The Library team

Comic by Jorge Cham