3.1 Reference management software

Outline Reference Managing Software Overview and comparisons Reference Manager 11 EndNote X1 and EndNote Web ProCite (RefWorks) Other tools Zotero – a research tool Web 2.0: Connotea and CiteULike Exporting references from bibliographic databases

Reference Managing Software

Overview and comparisons

Reference Manager 11

EndNote X1 and EndNote Web

ProCite

(RefWorks)

Other tools

Zotero – a research tool

Web 2.0: Connotea and CiteULike

Exporting references from bibliographic databases

In the good old days... ... we used index cards!

Reference management software Reference Management Software (RMS) or bibliographic management software enables you to: Search or download, store and organize your references (not only articles!) include abstracts, keywords and notes with the references produce lists of references (and bibliographies) for yourself or others automatically insert citations of references and create a bibliography as you write a document ( Cite While You Write ) Depending on the software you can opt for a desktop version, an network version or an online version of the software.

Reference Management Software (RMS) or bibliographic management software enables you to:

Search or download, store and organize your references (not only articles!)

include abstracts, keywords and notes with the references

produce lists of references (and bibliographies) for yourself or others

automatically insert citations of references and create a bibliography as you write a document ( Cite While You Write )

Depending on the software you can opt for a desktop version, an network version or an online version of the software.

References? You may want to refer to : Books Chapters of books Journal articles Conference papers Manuscripts Personal communications E-mails Web sites Pictures Data Spreadsheets etc

You may want to refer to :

Books

Chapters of books

Journal articles

Conference papers

Manuscripts

Personal communications

E-mails

Web sites

Pictures

Data

Spreadsheets

etc

Pros and cons  easy to use – Windows (or Mac) type interface convenient - automatic downloading of references flexible - many reference types and output styles accurate - you can keep track of publications used in your research  requires time to learn (courses at KULEUVEN for Endnote and Reference Manager ) some output styles may not be available or suitable not all online resources allow automatic downloading



easy to use – Windows (or Mac) type interface

convenient - automatic downloading of references

flexible - many reference types and output styles

accurate - you can keep track of publications used in your research



requires time to learn (courses at KULEUVEN for Endnote and Reference Manager )

some output styles may not be available or suitable

not all online resources allow automatic downloading

Important features in RMS Database import = from major bibliographic databases or publishers Database connectivity = direct search from within your RMS Database management = organize and group your references Database output = in different output styles for exchange Cite While You Write = inserting references into your document Bibliographic styles = generating your bibliographies in a format style you need ( e.g Vancouver, NLM,... )

Database import = from major bibliographic databases or publishers

Database connectivity = direct search from within your RMS

Database management = organize and group your references

Database output = in different output styles for exchange

Cite While You Write = inserting references into your document

Bibliographic styles = generating your bibliographies in a format style you need ( e.g Vancouver, NLM,... )

Cite While You Write Plug-in in MS Word Reference Manager Cite While You Write Plug-in in MS Word Endnote Web Examples of the Cite While You Write feature

Workflow Create a database by Direct search and/or Importing references from bibliographic databases Inserting references into document Cite while you write Generate your own bibliography

Create a database by

Direct search and/or

Importing references from bibliographic databases

Inserting references into document

Cite while you write

Generate your own bibliography

Comparison of software Thomson Scientific offers a portfolio of bibliographic software, like Reference Manager , EndNote and ProCite . There are a lot of websites which compare the different software products: Thomson ( http :// www.isiresearchsoft.com/ ) compares Reference Manager, Endnote and ProCite Wikipedia offers a comprehensive list of all features in: Comparison of Reference Management Software

Thomson Scientific offers a portfolio of bibliographic software, like Reference Manager , EndNote and ProCite .

There are a lot of websites which compare the different software products:

Thomson ( http :// www.isiresearchsoft.com/ ) compares Reference Manager, Endnote and ProCite

Wikipedia offers a comprehensive list of all features in: Comparison of Reference Management Software

Choosing the right software: tips and tricks Check out the possibilities of the trial versions of the software AND have look at their websites Pay attention to: Bibliographic output styles (your favourite journals) Database connectivity (which?, search features) Import filters (Can you import references from PubMed, ISI Web of Science, other databases?) Do you prefer desktop software or online tools? Extra features available like Cite While You Write Does the K.U.Leuven has a Campus Licence? Are there courses? Look on the internet and the websites of vendors for video’s (webcasting, screencasting) and tutorials

Check out the possibilities of the trial versions of the software AND have look at their websites Pay attention to:

Bibliographic output styles (your favourite journals)

Database connectivity (which?, search features)

Import filters (Can you import references from PubMed, ISI Web of Science, other databases?)

Do you prefer desktop software or online tools?

Extra features available like Cite While You Write

Does the K.U.Leuven has a Campus Licence? Are there courses?

Look on the internet and the websites of vendors for video’s (webcasting, screencasting) and tutorials

1. Reference Manager 11 Database connectivity (PubMed, Web of Science, Aleph, and many others) Import filter for PubMed and ISI: available Cite While You Write functionality (MS Word, WordPerfect) Many bibliographic style formats, especially for biomedical researchers Allows you to publish your reference database on the internet or an intranet Windows only Campus licence at KULEUVEN (individual or network) + courses at KULEUVEN ( link o r RSS feed ) http://www.referencemanager.com/

Database connectivity (PubMed, Web of Science, Aleph, and many others)

Import filter for PubMed and ISI: available

Cite While You Write functionality (MS Word, WordPerfect)

Many bibliographic style formats, especially for biomedical researchers

Allows you to publish your reference database on the internet or an intranet

Windows only

Campus licence at KULEUVEN (individual or network) + courses at KULEUVEN ( link o r RSS feed )

http://www.referencemanager.com/

2. EndNote X1 EndNote X1 is desktop software, similar to Reference Manager Import filter for PubMed and ISI: available Pro: allows you also to store images and objects According to ISI the most popular citation manager No Campus licence at KULEUVEN though there are courses at KULEUVEN ( link or RSS feed ) http://www.endnote.com/

EndNote X1 is desktop software, similar to Reference Manager

Import filter for PubMed and ISI: available

Pro: allows you also to store images and objects

According to ISI the most popular citation manager

No Campus licence at KULEUVEN though there are courses at KULEUVEN ( link or RSS feed )

http://www.endnote.com/

3. EndNote Web Endnote Web is the free online and web-based version of EndNote = no installation needed Complementary to EndNote X1 You need to create an account via Web of Knowledge Database connectivity, but not only Thomson databases! (also PubMed, ScienceDirect, …) Easy to use, basic functions Store up to 10,000 references in your account (limited) Thousands of publication styles Cite While You Write plug-in requires download and install (MS Word) Just give it a try, it’s free!

Endnote Web is the free online and web-based version of EndNote = no installation needed

Complementary to EndNote X1

You need to create an account via Web of Knowledge

Database connectivity, but not only Thomson databases! (also PubMed, ScienceDirect, …)

Easy to use, basic functions

Store up to 10,000 references in your account (limited)

Thousands of publication styles

Cite While You Write plug-in requires download and install (MS Word)

Just give it a try, it’s free!

Once you have an account... First register in WoK

Homepage of My EndNote Web http://myendnoteweb.com/

Searching in PubMed with EndNote Web

Procite Results from PubMed. Create a Group for your references, e.g. Common cold

Creating a Group of references

Create your bibliography in a specific bibliographic style Saved as RTF for MS Word

You can import files from bibliographic databases, eg. PubMed

A result of importing references from PubMed

EndNote X1 vs. EndNote Web

4. ProCite Features comparable with Reference Manager and EndNote Import filter PubMed and ISI: yes is preferred by many humanities researchers and librarians Only for Windows platform provides flexibility to group references and creates subject bibliographies No open URL compliance No Campus licence, no courses at KULeuven http://www.procite.com/

Features comparable with Reference Manager and EndNote

Import filter PubMed and ISI: yes

is preferred by many humanities researchers and librarians

Only for Windows platform

provides flexibility to group references and creates subject bibliographies

No open URL compliance

No Campus licence, no courses at KULeuven

http://www.procite.com/

6a. Zotero (research tool) is a browser extension (add on) for Firefox and Flock only Automatic capture of citation information from web pages e.g. PubMed, Web of Science (partially), ScienceDirect, Nature… Storage of PDF, files, images, links, and whole web pages Formatted citation export Free and open source Integration with Microsoft Word, Open Office and WordPress http://www.zotero.org/

is a browser extension (add on) for Firefox and Flock only

Automatic capture of citation information from web pages e.g. PubMed, Web of Science (partially), ScienceDirect, Nature…

Storage of PDF, files, images, links, and whole web pages

Formatted citation export

Free and open source

Integration with Microsoft Word, Open Office and WordPress

http://www.zotero.org/

After a PubMed Search, just click on the yellow folder icon in the address bar and you will get a pop-up Make a selection of references you want to import into Zotero

6b. Other reference tools (web2.0) In the scientific community too web 2.0 tools are often used for sharing information with friends or colleagues tagging documents or files (keywords) connecting to people and networking social bookmarking

In the scientific community too web 2.0 tools are often used for

sharing information with friends or colleagues

tagging documents or files (keywords)

connecting to people and networking

social bookmarking

An example of web 2.0 tools in scientific information BiomedCentral offers social bookmarking buttons to several websites on each abstract

Connotea Connotea is a free online reference management service for scientists, researchers and clinicians. Launched in December 2004, by Nature Publishing Group. It is a social bookmarking tool, similar to CiteULike and del.icio.us , where users can save links to their favourite websites focus on academic resources (e.g. scientific websites, journal articles, etc.) will automatically collect metadata for an article or page being bookmarked http://www.connotea.org/

Connotea is a free online reference management service for scientists, researchers and clinicians.

Launched in December 2004, by Nature Publishing Group.

It is a social bookmarking tool, similar to CiteULike and del.icio.us , where users can save links to their favourite websites

focus on academic resources (e.g. scientific websites, journal articles, etc.)

will automatically collect metadata for an article or page being bookmarked

http://www.connotea.org/

Copy bookmarks from others in Connotea or get them from a website.

Describe your bookmark and annotate it

Export your references from Connotea

CiteULike CiteULike is a social bookmarking service for academics for sharing websites, journal articles and other resources Free and open source Web-based share, store, organize academic papers you are reading surf web and add papers to your personal library extracts the citation details (metadata) automatically www.citeulike.org But: no reference output function

CiteULike is a social bookmarking service for academics for sharing websites, journal articles and other resources

Free and open source

Web-based

share, store, organize academic papers you are reading

surf web and add papers to your personal library

extracts the citation details (metadata) automatically

www.citeulike.org

But: no reference output function

Homepage CiteULike with bookmarks from all users.

Exporting your references from a database When to execute an export of references from a bibliographic database? when there is no database connectivity to a specific bibliographic database When you want to execute complicated searches or setup an extensive search strategy 3 examples: PubMed, Web of Science and Embase

When to execute an export of references from a bibliographic database?

when there is no database connectivity to a specific bibliographic database

When you want to execute complicated searches or setup an extensive search strategy

3 examples: PubMed, Web of Science and Embase

Exporting citations from PubMed In your search results, use the citation check boxes to select citations. To export all the citations do not select any citations. From the Display menu, select MEDLINE . From the Send to menu, select File (for download). Import this file to your reference management program (works with Reference Manager, EndNote and ProCite).

In your search results, use the citation check boxes to select citations. To export all the citations do not select any citations.

From the Display menu, select MEDLINE .

From the Send to menu, select File (for download).

Import this file to your reference management program (works with Reference Manager, EndNote and ProCite).

Choose the MEDLINE display (of all or of your selected references)

Other citation tools The references in MEDLINE format

Choose File in the ‘ Send to’ dropdown menu

Download your file ( Save to Disk ). Open your Reference Managing Software and import the file. Note: Make sure your pop-up blocker allows downloading the file.

Exporting citations from Web of Science Execute a Search in Web of Science Above each Results page you will see following buttons More options are available at the bottom of every Results page

Execute a Search in Web of Science

Above each Results page you will see following buttons

More options are available at the bottom of every Results page

Scroll down to the bottom of your results list in Web of Science. Step 1: Select the records for output Step 2: Abstract needed? Step 3: Choose one of the options, e.g. Save to EndNote Web , Save to other reference software or choose another output format (e.g .

Exporting citations from Embase.com Select you references and click on ‘Export’

Pick your export format from the dropdown menu Note: Check out your Pop-up blocker!