Germany’s Plan for an Open and Independent PubMed Safety Net

A few months ago, I wrote about reasons to be concerned about the reliability of PubMed under the new regime at the National Institutes of Health (NIH). PubMed is a critical biomedical literature database, with a range of associated services. It’s produced by one of the institutes of the NIH, the US National Library of Medicine (NLM). I listed several questions: Could PubMed go down more often, and for longer? Might services no longer be free? How else could the quality and reliability of its services be degraded? Could junk science flood flood in, if (when?) the NLM is no longer a reliable gatekeeper?

If there are only short-term service delivery problems, we will be fine using Europe PMC – but we would need more than that if PubMed was severely affected. (You can read more about this and some of the technical issues I discuss below in my earlier post.)

Now, Germany has stepped up to this challenge. On May 2, the German National Library of Medicine (ZB MED), announced they were planning to develop an “open, reliable, and sustainable” alternative to PubMed. And today they held an open virtual meeting to discuss their plans for “resilient and independent life science research infrastructure.”

The meeting was impressive, moderated by Eva Seidlmayer, with introductory talks by the project leaders, Miriam Albers and Konrad Förstner, and a lively Q&A session. The talks were recorded, and will be going online along with a summary of the Q&A session and translations. This session was in German: An English session may be organized in a few weeks if there’s interest.

Having worked at PubMed, I have some idea of how complex “replacing” it would be. I was hopeful, but a little worried, to be honest. I need not have worried! What they’re doing is ambitious for sure, but it’s both responsible and exciting.

The big vision is to move past the reliance on any single country’s investment in this core life sciences infrastructure: It’s not to have a duplicative, parallel structure in Germany, nor to simply transplant a centralized system from the US to Germany. The goal is a fully open source, federated, safety net, embedded within the international community, with a strong global network of support. If PubMed as it is now falls, then this “PubMed 2.0” could carry the load forward. And if PubMed powers on, then aspects of what’s developed would be available for the NLM and any other services to use.

Everyone hopes, of course, that there will be no emergency. But as the scientific community has lost confidence in the security of centralized US infrastructure, ZB MED has leapt in to get basic infrastructure rolling while building an international network at the same time.

While PubMed’s output is open, PubMed itself isn’t open source. ZB MED has started an 18-month project to effectively reverse-engineer the basic functionality of the literature database, and make it all fully open source, so that if needed, a full service “PubMed 2.0” could be developed. The basics they are building for initially are the current corpus, the daily serving of meta-data on new literature, MeSH (the Medical Subject Headings that tag the literature), and some of the API utilities that researchers and other services rely on.

Plan A is to re-create the current model of publisher-submitted data, including abstracts. Plan B is a fallback to using CrossRef meta-data, which is available for about 90% of what currently feeds into PubMed. In their 18-month building process, they are working on both. ZB MED is clearly very sensitive to the community concern about being suddenly left high and dry: They are moving as quickly as they can to have an emergency substitute as soon as possible, even though that would of necessity be a very no-frills, basic service.

Working with the library and scientific community, ZB MED aims to have “beta” versions to release as soon as possible for people to test and respond to. They are not starting from this cold. ZB MED already runs LIVIVO, a life sciences search engine; they do the German translation of MeSH; and much more. They are keeping a close eye on PubMed, monitoring changes to PubMed and to MeSH.

One of the exciting roads this project is setting off on is moving beyond the English language limits of PubMed, too. ZB MED could make a major contribution here, even if PubMed is never compromised.

As well as developing the open source PubMed safety net, ZB MED is preparing plans to continue additional PubMed functions, should the NLM no longer be able to do the jobs – ongoing development of MeSH, and an editorial committee process for determining which journals are included in the database.

ZB MED has begun negotiations with publishers this month, and several gold Open Access publishers have already indicated their willingness to submit their meta-data to this project. In the Q&A part of the meeting, there was discussion about the challenge of getting commercial publisher participation. It’s going to take a lot to convince publishers to contribute, and getting the library/government consortia that pay for institutional subscriptions to include this in their contracts may be critical: Access to this kind of meta-data is an issue already raised in the Barcelona Declaration.

ZB MED has gotten started on the technical work, the community building, and the negotiations as a matter of urgency – so much urgency, in fact, that they didn’t wait for all the funding to be nailed down. It’s critical that support and pressure for the goal of independent, open source infrastructure of the life sciences literature comes from as many directions as possible. There’s a template for letters of support from institutions etc here. Please spread the word, and make sure your institutions and countries get behind this initiative!

The project is called OLSPub, for open life science publication database, and its internet home is here. There’ll be more to see there soon, and if you’re not already on the mailing list, at the moment you can join it by sending an email to Dr Albers, whose details are on the website.

You can follow ZB MED on Mastodon, on Bluesky, on LinkedIn, and on Instagram. Their YouTube channel is here.

You can keep up with my work at my newsletter, Living With Evidence. I’m active on Mastodon: @[email protected] and on Bluesky.

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Disclosures: I am not a medical librarian or information specialist. I worked at NCBI at the National Library of Medicine (NIH) from 2011 to 2018 on PubMed projects, predominantly PubMed Health and PubMed Commons (both of which no longer exist). I speak German, and translations in this post are my own.

The photo of ZBMed at the top of this post is by Raimond Spekking via Wikimedia Commons, CC BY-SA 4.0.