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TSRI, 400-S helplib@scripps.edu

858-784-8705

Reference Manager 12 Training Guide

Welcome Presenter Angela Murrell Outreach and Instruction Librarian Kresge Library amurrell@scripps.edu 858-784-9785 Download site http://www.scripps.edu/library/software/refman/ Must be TSRI Faculty, Post Doc, Student, or Staff Use your TSRI email account (Without the @scripps.edu part) to sign in Reference Manager Training Guide Page

A. Getting Started .............................................................................................2 B. Searching PubMed w/in Ref. Man...............................................................4 C. Automatically Importing Records

1. Web of Science ................................................................................6 D. Manually Importing Records

1. PubMed............................................................................................7 2. Manual Import into Reference Manager step ..................................8 3. SciFinder Scholar.............................................................................9

E. Working with Reference Manager 1. Adding PDFs .................................................................................10 2. Adding URLs.................................................................................10 3. Searching the database...................................................................10 4. Edit terms in the Term Manager ....................................................12

F. Generating a Reference List.......................................................................13 G. CWYW ......................................................................................................14

Questions Please feel free to ask questions throughout the workshop. If you have questions that occur to you after the workshop, or that you wish to discuss individually, please feel free to contact me at any time.

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A. Getting Started 1. Download the program from the Library website.

Open Reference Manager and go to Help > Updates to check for updates.

2. Add a shortcut to Reference Manager to the desktop • Go to Start > Programs > ReferenceManager 12 > right click on “Reference

Manager 12” • Select Send to then Desktop (Create shortcut)

3. Add Reference Manager to the Quick launch bar • Go to Start > Programs > ReferenceManager 12 > “Reference Manager 12” • Drag the file to the Quick Launch bar.

4. Create a new Database

• Open Reference Manager • Go to File > New Database… • Name the database. • Choose the location to save it to from the Look in: pull down list. • Click New.

• New databases open in “Read-Write Exclusive”. You can check the Access rights by going to File > Properties.

• When opening an existing database, you can choose Access rights as: Read-Write Share Read-Only Share Read-Write Exclusive – Default – must be in this mode to edit term lists or copy

periodical lists. However, no one else can open the database while you have it open in read-Write Exclusive.

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5. To set the current database to Read-Write Share (so others can use a shared library) • Close the database. • Then go to File > Open Database… • Select “Read-Write Share” for Access rights: at the bottom.

• Then select the database and click Open.

6. Setting SFX as the OpenURL tool • Go to Tools> Options … Click on Internet search tab • Check the box next to Enable OpenURL. • Delete current text in OpenURL Path: box. • Type in: http://sfxhosted.exlibrisgroup.com/scripps/. • Click Apply. • Click OK.

7. Copy a Periodical list to the Term Manager

• The database must be open in “Read-Write Exclusive” access mode. • Activate the term manager , go to Tools > Term Manager > Activate or F5 • Click on the “periodicals” tab. • Go to Tools > Term Manager > Copy Periodicals… • Select the list from “Copy from:” pull down menu (choose Chemical or Medical)

• Click OK

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B. Searching PubMed from within Reference Manager

• Go to Tools > Internet Search • A search window will open.

• Be sure PubMed is selected from the pull down menu. • Select a field to search. • Type in your search term(s) • To add additional terms use a “Connector” (AND, OR, NOT) • Choose the second field. • Type in term(s) • Click the Binoculars.

• The search will then display a number of records retrieved. • Click OK. •

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• The records will display in a separate TAB in the “Reference List” window. • Mark or highlight records you wish to keep. • Right click in the lower frame of the Reference Window. • Select Copy Between Databases..

• Select which references to copy (Highlighted, Marked, Unmarked, All) • Select the destination database. • Click Copy.

• Close the Search Tab by clicking on the “search” tab. • Right Click on the lower part of the “Reference List” window. • Select Close Search Database… (fist choice in the drop down menu)

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C. Automatically Importing Records Some databases support direct exporting of citations into Reference Manager.

1. Importing from Web of Science

• First perform your search in ISI Web of Science. • Mark the records you wish to save. • Scroll to the bottom.

• Select the records to export. Select “Full record”. • Click the button Save to EndNote, RefMan, ProCite button.

If you use Internet Explorer: • Choose the database to save citations to. • Click OPEN.

If you use Firefox:

• You will see this screen first:

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D. Manually Importing Records Some Databases do not. This is the procedure to import records from these databases in the form of .txt files. First select and download the references using the instructions specific for the database. 1. Importing from PubMed (Manual Import)

• First perform your search in PubMed. • Next, Mark the citation(s) you wish to Export to RefMan. • Click on Send to: and select “File”. • For Format choose “MEDLINE” • Click Create File.

• When the File Download window appears:

o Click Save o If prompted, select the drive/folder you want your file saved in. o In the File name: box type the name of the file (or use the default

pubmed_result.txt). o For Save as: select the “Text file (.txt)” for the type.

• Click Save. • Go to Reference Manager and use the Manual Import

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2. Manual Import into Reference Manager step (Uses .txt file downloaded from PubMed or SciFinder)

• To import citations that have been saved in text format, go to File >Import Text File… • A box will appear:

o In Database: use the pull down list to choose name of Database you want your citations to go in.

o For Filter: use the button to select the filter for the database the records are from.

o Text File: use the button to select the file that you saved the records as, should be a “.txt” file type.

• Click Import. • A status of your imported results will appear. • Click OK. • Click Close.

Import Options: Use these Import Filters for the following databases: Database Format of Records Import Type Import Filter

PubMed MEDLINE Manual PubMed.cap SciFinder Scholar Tagged .txt Manual RIS.cap

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3. Importing citations from SciFinder Web (Manual Import)

• Search SciFinder as usual. • Once you have selected the citations you wish to import, click Export

• Choose the “Citation export format (*.ris) • Name the file. • Click Export.

• Go to Reference Manager and use the Manual Import (see item D 2 above). • Use the “RIS” filter.

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E. Working with Reference Manager 1. Add links to files and pdf’s

• Highlight the record, • Click in the field you wish to add the link to. • Go to References > Link to … or CTRl-k • Locate the pdf or file • Click Open.

2. Adding URL’s • Highlight the record, • Type or copy paste the URL into the Related links field.

3. Searching the database

• Open the Reference Manager database • Go to Reference > Search References • From the drop down menu choose the database to search. • Select a Field from the drop down menu • Type in a search term. If the field is indexed, a list of possible terms will appear.

• Double-Click on your choice. • Close the box by clicking “X”. • You may add additional fields and terms in the rows below. Repeat the steps above. • They can be connected using Boolean terms using the “Connector” drop down menu.

o “AND” requires both search parameters to be in the record.

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o “OR” will find records were either parameter is met.

• Click on the binoculars to perform the search. • Results display on the right in the Results column. (ie. 5 for Author McCowen, B.; 3 that

also include the word “whistle’ in the title.) • Click on the result number to view records.

• To manipulate or close the “retrieved” window, Right-Click on the reference list. • Choose Close Retrieved Reference List to close the window.

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4. Edit terms in the Term Manager • If Term Manager is not open, activate it (Tools > Term Manager > Activate) • Click on the “Terms” tab in the Term Manager. • To change a term, highlight the term. • Then go to Tools >Term Manager > Global Edit

• In the Global Edit window you will see the term listed in SOURCE. Type your correction in DESTINATION box. (To close the Keywords box it click x in corner.)

• Click Replace. This will change all occurrences of the term. Editing Journal names is a little trickier. If the correct abbreviation exists, but is listed as a full journal title, you will have to perform a Global Edit to change the abbreviation into the full journal name. Then you can click on the full journal name and type in the correct abbreviation in the field on the right.

5. Copy Field: Use this to add a note or change a field to a list of selected records. • First mark the records to change. • Then, in one record, type in the correct information in the selected field. • Next go to Edit >Copy Field… a window will pop up.

• Select the Reference List (default is the current one) and select “Marked references.” • Then choose to Overwrite or Append to the existing field. • Click Copy. Pop ups will appear asking to perform change on each record. • Click Yes to All, or go through each record question individually.

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F. Generating a reference list

• In Reference Manager, open the database you wish to work with. • Go to Tools >Bibliography >Generate from Reference List… • In the General tab choose

o References to include: “All references in List” or “Marked References” o Destination: “File” will allow you to send it to word processing software. o Output style: click on the button with 3 dots (…) next to the output style box.

This will open a window and also you to browse for the style, or type in a few letters and a drop down list will appear.

o Choose your style and click Open. o Optional Fields: select or deselect any fields.

• In the Bibliography tab the format should be set based on the style you choose. However you can change the title, the prefix or suffix separators, etc.

• In the Page tab you can choose margins and page numbering.

• When done click OK. • Save as box appears.

o Select location of file. o File name: choose a name. o Save as type: use the pull

down menu to select Microsoft Word or WordPerfect.

• Click Save. • Then open the file in the Microsoft

Word or WordPerfect and do any touchups

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G. Cite While You Write This is a feature of Reference Manager that allows you to automatically insert and format

citations into a MS Word or Word Perfect document. This is the tool bar for Reference Manager in Word 2003.

You can also access the features from Tools > Reference Manager 12 > This is the Reference Manager ribbon in Word 2007

1. Adding citations in MS Word a. Insert Citation

2003 – Go to Tools > Reference Manager 12 > Insert Citations… or click or 2007 – click on the top of the Insert Citation button. • Type in a word in the title, year, and/or author name. • Highlight the reference of interest. • Click Insert.

b. Insert Marked Reference(s)

• Go to Reference Manager 12. • Mark (Check) the reference to add. (Hold down CTRL to select more then 1.) 2003 – Go to Tools > Reference Manager 12 > Insert Selected Citation(s) or click

2007 – Select the Bottom of the Insert Citation button, and choose Insert select citations

2. Choosing a reference style 2007 – Choose the style from the pull down menu or click the arrow in the corner for the Generate Bibliography window. 2003 – Go to Tools > Reference Manager 12 > Generate Bibliography…

• Under the Bibliography tab • Select the format from the pull down menu next to Output Style:. • Select the font and size, indentation and reference numbering.

• Under the Fields tab select any optional fields. • Click OK.

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3. Unformat Citations • To return to the {Author, year id/#} format and still be linked to Reference Manager

2003 – Go to Tools > Reference Manager 12 > Unformat Citations 2007 – Pull down the “Convert Citations and Bibliography menu,

choose Convert to unformatted citations

4. Remove Field Codes • To convert a formatted document to a finished, Word document no longer linked to

Reference Manager • This will create a copy or the document that can no longer be affected by Reference

Manager. The original document is still linked to Reference Manager. 2003 – Go to Tools > Reference Manager 12 > Remove Field Codes 2007 – Pull down the Convert Citations and Bibliography

Choose Convert to plain text

5. Go to Reference Manager 12 • Go to Tools > Reference Manager 12 > Go to Reference Manager • If Reference Manager is open, this will toggle you to Reference Manager.

6. Editing citations in MS Word In order to edit citations in a Word document, you must use the Edit Citations feature,

or the change will disappear the next time you use Format Bibliography. • Click on the citation you wish to edit.

2003 – Go to Tools > Reference Manager 12 > Edit Citation(s) 2007 - Click Edit Citations

• Makes changes to the highlighted citation. • To add another reference to this citation, click Insert… • Click OK when done.