How to download records from PubMed to EndNote:

Using a Filter—Using a Connection File—Creating Links to Full-text Articles

Using a Filter

After you have performed your search on PubMed and marked the records which you wish to download, use the Display option to select MEDLINE.

Your records will now be displayed in the Medline format. Click on the down arrow next to the Send To button. Choose File from the display options.



When prompted, Save the file. By default, PubMed will save the file as a text document, which is the correct format for import to EndNote.

The file of records should now be stored on your computer and can be imported into an EndNote library. When importing the records, use the filter which you can download from our filters page.

Using a Connection File

You can search PubMed from within EndNote and import references directly to your library. To do this, use the Connect function. Select the connection file called PubMed. Or you can download a slightly modified uq_pubmed connection file from our connection files page.

Unlike most other connection files, the PubMed connection file can be used on any computer which has the EndNote software and an Internet connection.

Creating Links to Full-text Articles

Note:

• Linking to the full text of journal articles will only work if the article is available free on the web, or if you are using a computer on campus, with a university IP address.
• If you are working off campus, you will need to search the titles of the journals in the Library catalogue to connect to full text of subscription journals.
• Another option, both on campus and off campus, is to use the OpenURL function in EndNote.
• Yet another option, which currently only works on campus, is to use the Find Full Text function, which was introduced in EndNote X2.

If you use the connection file, the downloaded references will include links back to PubMed in the URL field. You can then use the links in PubMed to connect to the full text of the articles.

If you use the filter, the downloaded references will not include links. There are two options for manipulating these references so that they will include links:

• Create a link back to PubMed
• Create a link to the journal website using the Digital Object Identifier (DOI)

Create a Link back to PubMed

If you have used the filter to download references from PubMed, the PubMed ID number will be imported into the Accession Number field in your EndNote references. You can get EndNote to move this into the URL field, and then convert it into a link back to PubMed.

After importing the references, select the references in your EndNote library, and then click on References on the top menu bar, and select Change and Move Fields.

When the dialogue box opens, click on the Move Fields tab. In the box labelled From, select the Accession Number field. In the box labelled To, select the URL field. Then check the option Replace Entire Field. Click on the OK button.

Now that the PubMed ID number is in the URL field of your references, you have to add a string of text before it to create a link back to the PubMed record. As before, select the references in your EndNote library, and use the References>Change and Move Fields command.

When the dialog box opens, you will see the Change Fields tab. In the box labelled In, select the URL field. Then select the option Insert before field's text. Then type in the box http://www.ncbi.nlm.nih.gov/pubmed/ and uncheck the box labelled Include a space after the new text. Click on the Go button.

You should now find that your references contain a link back to PubMed in the URL field.

Create a link to the journal website using the Digital Object Identifier (DOI)

The references will include the Digital Object Identifier (DOI) if it is present in the PubMed record. In some cases, you can convert the DOI into a link to the full-text of the article on the publisher's website.

Beware: Some journal editors are now requiring that authors include the DOI in their bibliographic citations. If you need to insert the DOI in references, do not follow the procedure given below for creating links to full text articles. This procedure modifies the DOI to create a URL.

Our Pubmed filter and connection file (see above) have been edited to import the DOI into the appropriate field. In versions 8 to X of EndNote, that field is called Electronic Resource Number. In EndNote X1 the field was renamed to DOI.

Note that this procedure only applies to EndNote 8 and later versions. EndNote 7 and earlier versions have no field specifically for the DOI. In EndNote 7 it would be possible to modify a filter or connection file to import the DOI into a designated field which is not otherwise being used, e.g. Call Number.

Select the references in your EndNote library and click on References on the menu bar. Select Change and Move Fields.

When the dialog box opens, the Change Fields tab is selected by default.

On this tab, go to the In box and select the DOI or Electronic Resource Number field. The name of this field depends on the version of EndNote which you are using.

Then check the option Insert before field's text and type in the window: http://dx.doi.org/

At the bottom, uncheck the option Include a space after the new text. The screen should look like this:



Click on the OK button, and EndNote will insert the text before the DOI in the appropriate field of each reference.

All references with a DOI should now have a link. Some references downloaded from PubMed do not have a DOI, and these will just have the inserted text in the DOI or Electronic Resource Number field. In such cases, you cannot link to the full text.