Importing files into EndNote

Transcription

1 Importing files into EndNote There are various ways in which you can add citations to your EndNote database. The most labour intensive is to type or cut and paste the information from another source. In this document we will focus on the process of importing files that have been downloaded from a searching database (eg. Cochrane, PubMed, Embase). Irrespective of the actual database searched, we recommend downloading files that contain abstracts (which we need for the list of citations) as well as keywords to facilitate subsequent searching. A. Standard steps for importing There are some standard steps for importing files into EndNote: Choose (and open) the EndNote library into which you want the citations inserted Select Import from the File menu Find (and select) the file to import Choose the appropriate import option Choose your preference for the handling of duplicate citations Choose preference for text translation Click the import button Check that files have been imported View the imported files to ensure the fields are appropriately filled (Copy desired citations into separate target library) Close library when finished A number of these steps may need some additional explanation, these are listed below. Choose EndNote Library The EndNote library into which you want the citations inserted, will depend on your working plan. You may already have a large database (library) into which you wish to insert all your references. As there is no undo option after importing, it is far easier to import the citations within the file into a new library first. Here checks can be made, and if need be files deleted without concern, and when you are happy the appropriate citations can be copied/dragged/imported to your chosen destination library. (Note: although there is no undo feature, the imported citations are by themselves in an open window, and can be selected and deleted without affecting the rest of your library.) Find (and select) the file to import The files that have been downloaded should be in the default location for your files downloaded from the Internet. If you have the option of choosing the target folder, for ease of organization you may wish to choose to save (or move after saving) to a specific working folder. Use the top half of the box to navigate around your computer to find the appropriate file. C2010Importing.doc Page 1 of 20 P Morley 1 Mar 2008

2 Choose the appropriate import option There are a number of import options available. The major ones are importing from another EndNote library, and from a saved text file. We need to choose Import from the file menu: Selecting Import brings up the next window, showing pop-up menus for Import options, Duplicate and Text translation : The clicking on the import options bar brings up the Import Dialog Box, which will look something like this: C2010Importing.doc Page 2 of 20 P Morley 1 Mar 2008

3 The most relevant filter for our purposes are: EndNote Library Used to import references from one EndNote library into another. If the library you are importing from is closed or locked, all references are imported. If you the library you are importing from is open, with read/write access, the showing references are imported. ISI-CE Used to import text files downloaded from the Web of Science and other Thomson Scientific sources. Other import filters EndNote includes hundreds of import filters configured to import data from a variety of online databases. When you import a file, you may not see the import filter that you need in this list. Choose Other Filters from the Import Options list to find the filter that matches the source of the data you want to import. Import filters that you have recently used or chosen as your favourites will be listed in the Import Options list in the Import dialog. The filter with a tick is the filter that is currently selected. Note: if there are problems with importing/translation, there may be a more recent version of the import filter available on the EndNote website. (A more detailed description of the other import options is contained in Appendix 1 : EndNote s Import options). Choose your preference for the handling of duplicate citations Duplicate citations are citations that are deemed to be identical with ones already in the library you are importing into. By default, a reference is considered a duplicate when the Author, Year, Title, and Reference Type match a reference already in the library. The dialog box shows the three options: C2010Importing.doc Page 3 of 20 P Morley 1 Mar 2008

4 The three options available are: Import All = Imports the references, including duplicates. Discard Duplicates = Imports the references, except duplicates. Import into Duplicates Library = Duplicate references are imported into a library called File-Dupl.enl, where File is the name of the library into which you are importing. The common practice is to choose import into duplicates library as default, as it is another check on the process of importing. If you wish to see the current preferences for the selection of duplicates, or would like to change these preferences, you need to access the EndNote Preferences menu: Then select Duplicates, which reveals the terms used to compare fields: C2010Importing.doc Page 4 of 20 P Morley 1 Mar 2008

5 Choose preference for text translation Various options are available. The default is to leave the Text Translation option set to No Translation. (see Appendix 2 : Text import options and displaying special characters for EndNote for further details if required) Click the import button Straightforward! Check that files have been imported If you have imported into an empty library, a window will be generated with the successfully imported files: In this case 77 imported files makes up the entire library. If you are importing into an existing library, you should see a dialog box summarising your success: C2010Importing.doc Page 5 of 20 P Morley 1 Mar 2008

6 In this case there should also be a new window representing the 855 imported references: There should also be a window representing the new duplicate library file: If no files have been imported, you have either selected the wrong file to import, or the import preferences chosen have not matched the type of file you have selected. In this case you should open the file you wish to import, and check that it is in an appropriate format. The formats of the downloaded files are all slightly different (hence the large number of filters available for import). The generic format includes a list of identifiers (eg. 2 capital letters) which are used to separate the pieces of information in the file. An example of the sort of file expected is shown below (an Embase download): See appendix 3 for further details (Appendix 3 : EndNote Recommended Download Format & Import Option for various Information Providers). C2010Importing.doc Page 6 of 20 P Morley 1 Mar 2008

7 View the imported files to ensure the fields are appropriately filled A quick look at the import window should tell you if author, year and title (depending on your display preferences in EndNote) have come across appropriately: Two additional quick checks are also reasonable. Firstly check the preview pane at the bottom of the window. If it says Show preview (as below), click on the arrow to show the selected reference: When a reference is selected it should now show in the Preview Pane : The format in which this reference is presented depends on the Output Style selected: C2010Importing.doc Page 7 of 20 P Morley 1 Mar 2008

8 In the above example, the chosen output style is Vancouver, but another could be selected, or edited if preferred. The other way to check the quality of the imported data in more detail is to open a single citation (by double-clicking) and scrolling down through the fields to ensure that the required information (eg. abstract, keywords etc) has been imported appropriately. Copy desired citations into separate target library Once the importing process is complete, you may wish to either import the new library into an existing one, or you may wish to copy (and paste) citations, or drag selected citations to the target library. B. Importing citations from files saved from other databases 1. PubMed (Medline) Saving your search results from PubMed (to be imported into EndNote) As discussed in the document C2010Searching.doc, the results of your searches can be downloaded in a format that is recognised by EndNote. In general, the instructions are summarised below, in Appendix 3, as well as on the PubMed website: _and_ ing_#pubmedhelp.exporting_citations_ In general you select the citations, display them as Medline, and send them to a file: C2010Importing.doc Page 8 of 20 P Morley 1 Mar 2008

9 If no articles are selected, Pubmed will export them all. Be patient! Before attempting to export a file of citations, make sure that the web page is fully loaded, and that the display type is correct (ie. Medline: starting with PMID- then number) as shown below: This file will be saved as a text file with a name such as pubmed_result-16.txt. Importing to EndNote from PubMed Once you have opened your choice of destination (an endnote file) you can then import the selected file using the appropriate import option (in this case the import file = PubMed (NML).enf ): C2010Importing.doc Page 9 of 20 P Morley 1 Mar 2008

10 2. Cochrane database Exporting results from Cochrane databases After your search is complete, you need to export your selected citations (see C2010Searching.doc). If we want to export all the studies, click on Export All Results button (at either top or bottom of display): The alternative is to select those that you wish to save, and click on Export Selected Citations (at the bottom of the display): From either approach the resulting screen is as follows: You should select Abstract and citation, and the computer format that you wish (eg. PC or MAC), and click Go. The result is a text file (eg. cit-abs-plain txt) that can be imported into Endnote: C2010Importing.doc Page 10 of 20 P Morley 1 Mar 2008

11 Importing documents into EndNote After downloading the text file from the Cochrane database as above, this can be imported into EndNote. After choosing your appropriate destination Endnote library, choose File: Import. Find/select the file you wish to import, then choose the appropriate import filter from Other filters : Cochrane Library (Wiley).enf : Next click on the Import button. The citations should be then imported into the Endnote file that you have chosen. If there are problems with the importation, or the details within the fields, you should check that you have the most up-to-date version of that import filter. The Cochrane Reviews import easily using the filter referred to above. Downloaded files containing Trials can be caught up with this filter, as the default type of publication in the standard Cochrane filter is an electronic article (like a cochrane review) rather than a journal article, and the volume number is not given a code. A minor modification can be made, or one prepared previously ( Cochrane Library (Wiley)C2010.enf ) and can be provided. 3. Embase (using OVID) Importing downloaded files from Embase into EndNote After selecting the references you wish to download, click Results Manager. Choose the following options: Fields: Complete Reference C2010Importing.doc Page 11 of 20 P Morley 1 Mar 2008

12 Citation Format: Reprint/Medlars (or Direct Export, if available) Click the or Save button. Save the file as plain text (*.txt). Direct Export option The direct export option results in a saved ovidweb.cgi file which when opened will prompt you for an endnote library to open (to import citations into). The appropriate Ovid filter will be selected automatically when using Direct Export option. If you are using Ovid's multiple database searching, you must select the Direct Export citation format. Reprint/Medlars option The Reprint/Medlars format prompts you to choose a preferred save option: The result is a named text document (eg. cites-1.txt ) which can be imported using the standard filter: If you are using Ovid for Windows: Select the Options button from within the "Save Documents" dialog box. From the list of options, choose the Output Format, then click OK. On the screen that then appears, choose Reprint Format. C2010Importing.doc Page 12 of 20 P Morley 1 Mar 2008

13 Appendix 1 : EndNote s Import options (The following has been modified from the relevant EndNote help screen). EndNote Library Used to import references from one EndNote library into another. If the library you are importing from is closed or locked, all references are imported. If you the library you are importing from is open, with read/write access, the showing references are imported. EndNote Import Used to import text files that have been exported from EndNote. Refer/BibIX Used to import text files exported from the Refer or BibIX programs. Tab-Delimited Used to import text files in which the fields within a single reference are separated by tabs. Reference Manager (RIS) Used to import text files exported from Reference Manager, Reference Update, Reference Web Poster, or any other source that uses the RIS format. ISI-CE Used to import text files downloaded from the Web of Science and other Thomson Scientific sources. EndNote Generated XML Used to import file exported in EndNote XML format. Other (import) filters EndNote includes hundreds of import filters configured to import data from a variety of online databases. Most likely, the first time you import a file, you will not see the import filter that you need in this list. Choose Other Filters from the Import Options list to find the filter that matches the source of the data you want to import. Import filters that you have recently used or chosen as your favorites will be listed in the Import Options list in the Import dialog. The filter with a tick is the filter that is currently selected. Note: if there are problems with importing/translation, there may be a more recent version of the import filter available on the EndNote website, Use Connection File EndNote provides the option of using a connection file as an import filter. This is useful if you need to import the Connect.log file generated by using EndNote s Connect command to search a remote database. The Connect.log file should include all of the references from your previous session. See The Log File for more information. C2010Importing.doc Page 13 of 20 P Morley 1 Mar 2008

14 Appendix 2 : Text import options and displaying special characters for EndNote (The following has been pasted from the EndNote help file). To allow for the appropriate import of Unicode characters, save TextEdit files as "Western (Mac OS Roman)," and Microsoft Word files as "Unicode Text (UTF-8)." If the appropriate option does not appear on the Save dialog, you can first select it under Preferences. When you are copying text from the Web, or viewing an HTML document exported from EndNote, set encoding to Unicode (UTF-8). To do this in Internet Explorer, go to the View menu and choose Encoding. If the encoding information in the import file is not recognized, no records will be imported into EndNote. If the encoding is recognized, but is incorrect for translation from the source program, Unicode characters will be corrupted during the Import operation. Displaying Unicode Characters in EndNote EndNote uses Unicode to encode special characters, so that data can be easily translated between platforms, programs, and languages. If characters do not appear as they should in EndNote, you may need to change your display font. Some fonts do not include certain characters (you may see boxes rather than text). From the EndNote menu, choose Preferences and click the Display Fonts option. We recommend using a Unicode font as the display font, to display the majority of Unicode characters. C2010Importing.doc Page 14 of 20 P Morley 1 Mar 2008

15 Appendix 3 : EndNote Recommended Download Format & Import Option for various Information Providers (These have been abstracted from the relevant EndNote help file). AARP AgeLine There is no method for downloading data from this database. Instead, save the results screen as a plain text file with your web browser s Save command. The resulting text file contains tags that are preceded by 18 spaces. Import Option: Ageline (AARP) filter ACM Digital Library (Association for Computing Machinery) Users with subscription access to this web site can save multiple records to a BINDER. Once saved, you can export the records in an EndNote format. Non-subscribers can download one record at a time: 1. Create a search. 2. Click on an article. 3. Scroll half-way down the page and select DISPLAY EndNote. Limitations: Since only plain text files can be imported into EndNote, you cannot import images, graphics, etc. Before importing, you may need to edit the file to insert a comma after corporate author names. Otherwise, EndNote will not be able to distinguish corporate authors from personal authors. Import Option: EndNote Import CSA (formerly Cambridge Scientific Abstracts) From the CSA search results screen, click Save/Print/ . On the Save/ Print/ screen, select: Record Format: Full Record Save File Format: PCMac Click Save. Your Web browser asks where to save the file. If your Web browser lets you save in different file formats, make sure you save as a Text Only (*.txt) file. Import Option: Various filters for CSA databases are provided in the EndNote Filters folder. CAS SciFinder Save references in the Tagged Format (*.txt). Import Option: SciFinder (CAS) filter C2010Importing.doc Page 15 of 20 P Morley 1 Mar 2008

16 Current Contents on Diskette (CCOD) - Mac Save references in the EndNote format. Import Option: EndNote Import Current Contents on Diskette (CCOD) - Windows Save references in the EndNote format. Import Option: EndNote Import DIALOG Set your communication software's option to capture text. Use Dialog's Format 5 with "tag" appended to the TYPE command -- type "s1/5/1-20 tag". You must download data in Format 5. If Format 5 is not available, try the full format, which is sometimes the same as Format 5. For questions concerning Dialog s many formats, please contact Dialog's tech support. Import Option: Various DIALOG filters are provided in the EndNote Filters folder. DIMDI Use the DLOAD command with report D1 (e.g. DLOAD REPORT=D1). Import Option: Various DIMDI filters are provided in the EndNote Filters folder. EBSCOhost After adding your selected references to your folder, click View Folder or Folder has items to see its contents. If you choose to or save the references, uncheck the boxes to include HTML and PDF; also make sure that Standard Field Format is checked and set to Detailed Citation and Abstract. If you choose not to save to disk, you must also check the Bibliographic Manager tab, then choose Citations in a format that can be uploaded to bibliographic management software or Citations in Direct Export format. Import Option: Various EBSCO filters are provided in the EndNote Filters folder. EDINA Use the Name format, where data is tagged with words such as Author rather than AU. Because there are so many different formats used for source data, you may need to manually edit source data after importing. EndNote cannot parse author names that are not clearly delimited, such as "S Hughes B Reynolds S A Bell & C Gardner. You will need to manually edit author names. Import Option: Various EDINA filters are available in the EndNote Filters folder. Emerald Display the marked list, click display for download (ASCII), and then save as a plain text file. The filter provided works for these Emerald databases: C2010Importing.doc Page 16 of 20 P Morley 1 Mar 2008

17 Emerald Management Reviews at Computer Abstracts International Database at International Civil Engineering Abstracts at Computer & Communications Security Abstracts at Current Awareness Abstracts at Limitations: Page numbers are separated by a hyphen with spaces on either side of it. You will need to manually remove the spaces after importing. Import Option: Emerald filter InfoTrac (Gale) From the Delivery panel at the bottom of the marked list window, restrict the contents to citation; do not choose full article. Limitations: Records often have extraneous information in the title field, which must be removed manually after importing. Import Option: InfoTrac (GALE) filter INIST 1. Click the Enregistrer button. 2. Select the records you wish to download. 3. Under Quels champs? choose "Tous les champs." 4. Under Incluez choose "Numéro de notice et nom de la base de données" and "Libellés abrégés." 3. Click the Sauvegarde de notices button Import Option: Various INIST filters are provided in the EndNote Filters folder. INNOPAC Save references in the EndNote format. Import Option: EndNote Import ISI CD (Citation Indexes) From the File menu, choose Save Records. In the Save Records dialog, choose the NLM Medline format from the Export Format menu. Import Option: Citation Indexes (ISI) filter Knowledge Finder Place document in the Save file, and select the document. Choose Export Selected Documents from the File menu. Import Option: Various Knowledge Finder filters are provided in the EndNote Filters folder. C2010Importing.doc Page 17 of 20 P Morley 1 Mar 2008

18 Medscape After selecting the desired records and adding them to your clipboard, click the Save or Clipboard link. Save or your clipboard in PC or Mac MEDLARS format as a plain text (*.txt) file. Import Option: MEDLINE (Medscape) filter NERAC Save your file as plain text (*.txt). Import Option: NERAC OCLC FirstSearch Mark those references to be saved and click Export. At the next page, choose EndNote and then click Export. EndNote will prompt you to select the corresponding filter. Import Option: Various OCLC filters are provided in the EndNote Filters folder. Ovid After selecting the references you wish to download, click Results Manager. Choose the following options: Fields: Complete Reference Citation Format: Reprint/Medlars (or Direct Export, if available) Click the or Save button. Save the file as plain text (*.txt). Import Option: The appropriate Ovid filter will be selected automatically when using Direct Export option. If you are using Ovid's multiple database searching, you must select the Direct Export citation format. Ovid for Windows Select the Options button from within the "Save Documents" dialog box. From the list of options, choose the Output Format, then click OK. On the next screen, choose Reprint Format. Import Option: Various Ovid filters are provided in the EndNote Filters folder. ProQuest 1. Select the desired references and then click the My Research Summary tab. 2. Click the Documents and Bibliography tab. 3. Choose Export, then either Export directly to ProCite, EndNote or Reference Manager, or Download in a format compatible with ProCite, EndNote, Reference Manager and RefWorks. If you choose the former, make sure your data is displayed in a tagged format before saving as a text file. Import Option: ProQuest filter PsycINFO at After marking the records you wish to download, choose Full PsycINFO Record then click the Display Marked Records button. Select the text, then copy and C2010Importing.doc Page 18 of 20 P Morley 1 Mar 2008

19 paste it into a text editor, saving the file it as plain text (*.txt). Import Option: Use the PsycINFO (APA) filter. PubMed 1. From the drop-down list next to "Display," choose MEDLINE. 2. From the "Send to" list, choose File and save the file as a plain text file (*.txt). You can check current download instructions for NLM PubMed at any time at Import Option: PubMed (NLM) filter Reference Update Select Reference Listings from the Output menu, and choose the following options: Device: ASCII File - No Printer codes (be sure to enter the path and file name for the output file.) Output Format: Medline Click Print to create the output file. Import Option: Reference Update (ISI) filter SilverPlatter WebSPIRS Once you've obtained your search results, click Save. Select the following Save Records options: Which fields?: All fields Include: Record number and database name Field labels: Short labels. Click the Save Records button. Use your Web browser to save the page as "Text Only" (do not save in HTML format). Import Option: Various SilverPlatter filters are provided in the EndNote Filters folder. STN Set your communication software s options to capture text to a file. Type the command Display All. Import Option: Various STN filters are provided in the EndNote Filters folder. UnCover (Ingenta) Using your software, save references ed to you as a "Plain Text" or "Text Only" file. Import Option: UnCover (INGENTA) VHL (Virtual Health Library) 1. After selecting the desired references, scroll to the bottom of the page and click Your collection (or Su selleccíon ). C2010Importing.doc Page 19 of 20 P Morley 1 Mar 2008

20 2. Cancel the print dialog, and then save the screen as a plain text file. Import Option: Various VHL filters are provided in the EndNote Filters folder. Web of Science Display your marked references. Then, look under Output Records and select the option to output Full Records. Next, click Export to Reference Software to have the references exported directly to EndNote. (See Direct Export Formats.) You may also choose Save to File to save the references to a text file and import them into EndNote. Import Option: ISI-CE Wilson Select the following options Destination: Choose or save. Include: Record numbers and full-text links (optional). Format: Choose text. Import Option: WilsonWeb C2010Importing.doc Page 20 of 20 P Morley 1 Mar 2008