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Setting up PubMed LinkOut tool for Alma

PubMed offer two options for setting up openURL linking and we selected the LinkOut Local tool rather than the Outside Tool, as the Outside tool requires a link to an ILL form that is automatically populated when the Alma resolver cannot find the article in Primo. We decided not to use this functionality as not all UWA patrons can use ILL. Instead LinkOut Local sets up PubMed like Google Scholar, in that the Find It@UWA button only appears when it matches our holdings.

These were the steps involved in setting up openURL linking:

  1. Contacted as per instructions on with the request to set up LinkOut and our registration details.


  1. They responded with a request to submit our Resource File ( and the Identity File ( Manually creating the XML identity file is easy enough, but Alma will not produce the Resource file unless the Publishing to PubMed profile is set up. If I had access to a test FTP site it would have been possible to set up a dummy publishing profile to force Alma to generate the Resource file, but I don’t, so I had to create the XML Resource file manually.


  1. I ran an Extended Export from Alma of all the PubMed Central portfolios we have activated. For the XML file NCBI requires the holdings to be listed in the format: “1234-5678” [is] AND 1994:2010 [dp] From the Excel export, I copied and pasted the list of ISSNs, Global From Year, and Global To Year dates into a separate Excel sheet. I then used concatenate to generate the XML string.


  1. The XML list of holdings were then pasted into the XML Resource file template in Notepad++. I found though that when I validated the file ( there were a lot of duplications in Alma as well as holdings with no ISSN, which PubMed won’t accept. I had to manually clean up the file both in Notepad++ and in Alma for future publishing. NCBI advised that you could also not have open holdings, they advise entering year 3000 as the coverage end year. So I added this to any open coverage in the Excel sheet.


  1. NCBI replied with our registration details including the Provider ID, NameAbbr and University Name, which I was requested to add into the XML files and resend them to NCBI.


  1. NCBI then set up our FTP account, as well our Library Submission Utility account. I could now proceed to setting up the Alma Publishing profile.


  1. Before the publishing profile is set up, it’s important to define Augmentation so the link resolver works with PubMed:
    Navigate to: Administration > General Configuration > Configuration Menu
    – Click: Integration Profiles
    – Click: Add Integration Profile << If it is already set up, “Edit” it >>
    – Integration Type is: Resolver Augmentation
    – Change the “Pubmed Definitions” section to: Active


  1. The FTP definition is set up in General Configuration > External Systems > S/FTP definitions.


  1. The publishing profile is then set up in Resource Configuration > Publishing Profiles > Publish electronic records to PubMed:
    1. We scheduled the job weekly, but manually ran the job the first time.


    1. You need to manually add the Identity file to the FTP server, as Alma will not load this. I also ran the Alma generated file against the file validator, and it came back with no errors.


    1. Once completed, notify NCBI that the files are ready for loading.


    1. It then takes 48 hours for the files to load, you will receive a notification from NCBI that the files have been processed.


    1. NCBI also recommend access via a different URL so PubMed recognises we’re from UWA and activates the Find It @ UWA links:


    1. The FindIt@UWA button now appears on the abstract view of article to which we have access:

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