Exporting data from reference management software

Transcription

1 Exporting data from reference management software Step 1: Finding the correct tagged text file Step 2: Saving the tagged text file Output Style in the right place Step 3: Using the style file to export your records from ProCite, and EndNote. Getting your records out of ProCite How to edit the ProCite Output style Troubleshooting in ProCite Getting your records out of EndNote How to edit EndNote Output Style Getting your records out of Reference Manager How to edit the Reference Manager Output Style When you migrate to the CRS, you ll use the Import Register function. However, there will be times that you will simply want to import records easily into the CRS from ProCite, EndNote or Reference Manager. In order for this process to be as smooth as possible, you should export your records in a particular tagged text output style. We have created three basic Output Styles, one for each of the main bibliographic software applications used by TSCs: ProCite, and EndNote. (An Output Style and guidance notes for Reference Manager will be available in the near future). We ve called these files: Tagged_text_Procite_for_CRS Tagged_text_EndNote_for_CRS Tagged_text_Reference_Manager_for_CRS This documentation takes you through the process step by step on how to use these generic tagged text files and how you can tailor those files should you wish to do so (for example, how to add more fields to the core fields given in the generic filters/styles). Step 1: Finding the correct tagged text file If you do not already have a suitable tagged text Output Style file, you can find the ones we have created on the TSC Portal under the CRS Portal's "Downloads, Filters & Software Updates" tab. Step 2: Saving the tagged text file Output Style in the right place You ll need to save the Style file on your local drive (usually your c-drive) in the Styles folder of your bibliographic software. Here s the pathway: 1

2 For EndNote: c-drive > Program files > EndNote > Styles For ProCite: c-drive > Program files > ProCite > Styles For Reference Manager: c-drive > Program files > Reference Manager > Styles Tip: Once you have saved the file in this folder you may need to restart your computer for the bibliographic software to recognise the new style file you have just saved. Step 3: Using the style file to export your records from ProCite, and EndNote The following fields are common to both Output styles: : Author (AU), Title (TI), Original language title if not English (OT), Source (SO), Year (YR), Volume (VL), Number (NO), Pages (PG), Abstract (AB), Study design (DE). We know that not everyone puts the same sort of data in the same fields so this guide includes information on how to edit the Style files so that they work the way you want them to. Each application has a slightly different way of outputting records, so we ll take each in turn starting with ProCite. ProCite Getting your records out of ProCite: 1. Mark the records you want to go into the CRS using the check boxes on the left hand side: 2. Go to File > Print Bibliography: 2

3 3. This will launch the Print output screen where you will then be able to view the Output Style pick list: Select the newly saved Output style: Tagged_text_PROCITE_for_CRS Tip: It may be that the Output Style does not show up in the list. To locate it another way, just click on the little which will allow you to browse the Program files on your c-drive. Go to the Styles file from here and click on the Output Style you need. 4. In ProCite, the default output is to not include the Abstract even if your Output Style includes a mapping to the Abstract field (field 43 in ProCite). To make sure Abstracts are outputted: once you have selected the correct Output Style, click on the Configure button just to the right on the Output Style pick list. This will launch the Configure Bibliography dialogue box. From this box, select the Fields tab and check the Show Abstract box (the Show Notes box will already be checked; you can leave that checked) and then click OK: 3

4 5. You ll be able to view the document before saving it and it s a good idea to take a look at a few records to see whether they look right to you (i.e. do they have the right information in the right fields and is it presented correctly). A record in tagged text format using the recommended Output Style will look like this (plus or minus fields depending on whether edits have been made to the style or not more detail on how to edit the style files are shown below): You can see that the core fields are shown and %%%% is used to separate records. 6. Save the file by clicking Save and select Text Only from the Save as Type pick list. This generic Output Style takes what it finds in fields 01 Author/s (mapped to AU in CRS), 04 Title (TI), 05 Original title if not in English (TO), 10 Source (SO), 20 Year (YR), 22 Volume (VL), 24 Number (NO), 25 Pages (PG), 39 Study design (DE), 43 Abstract (AB). If some of these fields are empty, that s fine; it doesn t try to export them. This is what it thinks are in those fields: How to edit the ProCite Output Style You can edit the Output Style to add new fields to the export file or remove existing fields. Add a field to be exported: Method 1: A permanent solution to adding fields for export is to edit the Output Style file itself, or to create a copy of the existing one and edit the copy. This is recommended if you think you will always or often wish to export fields not exported in the generic styles. (In the example below the Keywords filed is being added to the Output Style file) 1. Locate the file on the c-drive in Program files > ProCite > Styles 4

5 2. Double click on the.pos file It will look like this when it opens: 3. Click on the Bibliography tab which will show the current fields exported, and in the Definition panel, add in the field/s you want: Field 45 has been added. KW is the field tag used by the CRS for the Keywords field. It needs a colon after it as the delimiter and the number of the field followed by the name of the field used by ProCite. 4. Click the little disk icon to save your changes, or click Save As from the File menu to save your changes but retain the original Style file (you ll need to give it a new name) 5. Export a set of records using the newly modified file, to check that the new field/s now appear in the tagged text file 5

6 Method 2: Specific fields can be selected to output at the Print Bibliography stage using the Configure Bibliography dialogue box. 1. As before, mark the records for export 2. Go to File > Print Bibliography 3. Select the correct Output Style from the pick list (or by browsing the Styles folder on the c-drive) 4. Click Configure and from the Configure Bibliography dialogue box select the Fields tab: 5: Click on the Select Fields button. This will bring up the list of fields from which you select the new fields to be exported (in this example it s Field 42), and then click OK: 6

7 Tip: your field selections will be remembered for the duration of the session in ProCite so you shouldn t need to re-select the additional field/s should you wish to export other records. Once you close ProCite however, the additional selection will be forgotten and you ll need to do the steps above to add any new fields for export. How to remove a field from export 1. Locate the tagged text file on the c-drive in Program files > ProCite > Styles 2. Double-click to open the.pos file 3. Click on the Bibliography tab 4. Find the field/s you wish to remove from the list in Definition panel 5. Delete the field and click Save (or File > Save As if you would rather save an alternative copy of the Style file i.e. with the required field/s removed) Troubleshooting in ProCite Getting records out of ProCite in a format that will enable a smooth import into the CRS should be fairly straightforward using the tagged text Output Style file. There is however one potential problem; sometimes records in ProCite contain breaks that cause the output mappings to falter. A key example of when this might happen is for Abstracts that have been spilt in sections whereby each part of an abstract begins on a new line with a sub heading followed by a colon (which is the same delimiter used in the Output Style file). The way to prevent fields getting split up on export is to perform a simple data integrity check which will identify and remove breaks in the text of a record. 1. In your ProCite file, mark the records for export 2. Go to Database > Edit Marked Records > Global Find/Replace 3. In the Global Find/Replace panel, Select All (which will highlight all the fields) and enter ^p (you must use the carat ^ sign) in the Find Text box and just place your cursor in the Replace With box. Click OK 7

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9 4. Repeat step 3 above for ^t and for ^l (lower case L) This should clean your records of any breaks that could potentially cause content to split incorrectly across fields. EndNote Getting your records out of EndNote: 1. Select the record you wish to export from your EndNote file. In the example below there are three records selected for export: 2. At the top of the screen there is a Bibliographic Output Style pick list. Select the EndNote Output Style that you saved earlier on your c-drive, in this case Tagged Text Submission EndNote: 9

10 3. Go to File and then select Export. This will open the Save dialogue box where you can select how and where to save your tagged text file. Make sure to save it as a Text File (.*txt): 5. If you open your saved tagged text file, it should look something like this: This generic Output Style takes what it finds in fields Author (AU), Title (TI), Original language title if not English (OT), Source (SO), Year (YR), Volume (VL), Number (NO), Pages (PG), Abstract (AB), Study design (DE). If some of these fields are empty, that s fine; it doesn t try to export them. How to edit the EndNote Output Style You may want to edit the EndNote output style. How to add a field to be exported: 1. In EndNote, select the records for export and select the Output Style you wish to edit. In this case, it would be the generic Style file: Tagged_text_EndNote_for_CRS. 10

11 2. Click on the Edit drop-down menu at the top of the screen 3. Scroll down to Output Styles to find Tagged_text_EndNote_for_CRS: 4. Open the Output Style file which will look like this: 5. Click on Templates from the left hand side menu. This will open the panel which lists the fields that the Output Style currently exports: 11

12 6. Type in the field/s you want added following the syntax used: You need to copy the syntax of the other field entries: Field tag followed by colon followed by name of field as used in the EndNote workform with at the end. For example: KW: Keywords 7. Save the changes. The default is to save the edits as a new Style file which will then be available from the Output Style pick list along with the original one. How to remove a field from export 1. In EndNote, select the Output Style you wish to edit from the Output Style pick list near the top of the screen: 2. Then from the menu bar across the top, select Edit > Output Style > Edit tagged_text_endnote_for_crs as outlined above 3. When the Output Style file is open, click on Templates from the left hand navigation bar as outlined above: 4. From the bibliography panel, simply delete the field/s you no longer wish to be there. When you then go to close the Style file, you will be prompted to save your changes. Reference Manager Getting your records out of Reference Manager: 1. Mark the records you want to import into the CRS using the check boxes on the left hand side: 12

13 2. Ensure that the correct Output Style is selected. Go to File > Print. This will launch the Bibliography Setup screen. From the References to include, select Marked references in list. From Destination, select File, and from Output Style, select the tagged text Reference Manager style that is compatible with the CRS. Then Click OK. 3. Name the file and to choose a destination for saving it. Once done, double click on the file you have saved and it should look like this: 13

14 This is now in a suitable format to enable smooth import into the CRS. This generic Output Style takes what it finds in the Author/s field (mapped to AU in CRS), Title (TI), Original title if not in English (TO), Source (SO), Year (YR), Volume (VL), Number (NO), Pages (PG), Study design (DE), Abstract (AB). If some of these fields are empty, that s fine; it doesn t try to export them. How to edit the Reference Manager Output Style You may wish to edit the Reference Manager Output Style. How to add a field to be exported: 1. From the Reference Manager menu bar, select Tools and then Bibliography and Open Output Style. 2. Navigate to the Output Style you wish to edit then click Open. The Output Style selected is previewed here 3. When open the Output Style appears like this: 14

15 4. Go to File > Save As from the main Reference Manager toolbar, and give the Style you are about to edit, a new name: 4. To add or remove fields, click on the Bibliography tab: 15

16 5. In the Definition for <Generic> panel you can type to add fields following the same syntax as for existing fields, or delete a line to delete the mapping to a field on export. 16