Whilst the benefits for repository owners are obvious – e.g. massively increasing the visibility of your open access content – not many repositories are actually doing this. At the time of writing, in the UK there are only 4 other repositories in the LinkOut programme: University of Strathclyde, Imperial College London, the White Rose consortium & the London School of Hygiene & Tropical Medicine. Currently there are no other institutions that use Pure so I thought I would investigate and create some instructions.<\/p>\n
This blog post will help Pure administrators find URLs to full\u2010text open access items that have a PMID, but not a PMCID which can be used to send to NCBI.<\/p>\n
Step 1: find Pure records that have a PMID, and also have open access full-text.<\/u><\/strong><\/p>\n Note: Pure only holds PMIDs for records that have been imported from PubMed. Unfortunately, PMC IDs are not stored like other identifiers like ISBNs or DOIs. Set up a new report with the following filters:<\/p>\n Recommended values for data table:<\/p>\n This report will pull all records from Pure that have been imported from PubMed, and will show the Pure ID\/DOI\/PMID\/UUID and OA embargo date. The UUID will be used to generate a stable URL to the item page in the portal. Export the report as an Excel spreadsheet.<\/p>\n Step 2: Find out which Pure records with PMIDs also have PMCIDs<\/u><\/strong><\/p>\n If a paper has a PMC ID then it will have an open access version in PubMed Central and the LinkOut won’t be interested in including that record. You can use the online PMCID – PMID – Manuscript ID – DOI Converter to find out if the items in the Pure report have PMC IDs:<\/p>\n https:\/\/www.ncbi.nlm.nih.gov\/pmc\/pmctopmid\/<\/a><\/p>\n Cut\/paste PMIDs into the box, select CSV result format and convert 100 records at a time. Any more will likely to produce an error.<\/p>\n Ignoring the results with PMCIDs, cut\/paste the remaining PMIDs (Identifier not found in PMC) into a new column in the Pure report spreadsheet.<\/p>\n Step 3: Identify the Pure records which can be included in PubMed LinkOut.<\/u><\/strong><\/p>\n So far we have a list of records in Pure that have a PMID (which may or may not have PMCIDs), and a list of PMIDs that have been checked to make sure they don\u2019t have PMC IDs. What we need to do now is merge the data. There are a number of different ways to do this in Excel, but I chose to use the conditional formatting function to highlight duplicate PMIDs in Pure that are on the \u2018not in PMC list\u2019 we created. Filtering by colour will then give you a list of records which can be included in the PubMed LinkOut programme. I chose to remove the items which are currently under an embargo which can be identified from the Open Access embargo date, and removed using a filter.<\/p>\n All that is remaining to do is to tidy up the records and add the stable URL. This can be done by taking the UUID-4 value from the Pure report and concatenating with the handle server ID for Pure, for example:<\/p>\n Handle + UUID-4 = URL , e.g:<\/p>\n http:\/\/hdl.handle.net\/20.500.11820\/e22c7edc-9533-4ad3-ae44-3f706dd7682c<\/a><\/p>\n Now you have a list of URLs of items in Pure that have PMIDs – but crucially not PMCIDs – which you can submit to the LinkOut Programme. You can download a printable PDF version of these instructions here:<\/p>\n Pure PubMed LinkOut instructions<\/a><\/p>\n <\/p>\n <\/p>\n","protected":false},"excerpt":{"rendered":" Instructions for Pure users on how to find data to join PubMed LinkOut PubMed LinkOut is a service where you can send data to NCBI which will allow them to link PubMed records directly to your institutional repository: PubMed LinkOut … Continue reading \n
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