How Europe PMC built a database of life science preprints

What is it about?

Preprints are early versions of research papers. The main difference is that preprints have not been reviewed by experts in the field. Preprints allow scientists to share their results quickly. They are free to read and publish. Authors can receive early feedback and continuously improve their work. However, finding and assessing preprints can be difficult. There are more than 60 different preprint platforms to search through. Only some of those support programmatic access and advanced analyses. This study explains how Europe PMC (PubMed Central) has built a database of life science preprints.

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Photo by Growtika on Unsplash

Photo by Growtika on Unsplash

Why is it important?

This publication highlights the benefits of including preprints in Europe PMC. It also addresses limitations and technical challenges of this process. Benefits of including preprints in Europe PMC. 1. Improved visibility. Europe PMC aggregates preprints from different sources. It offers a single search for preprints and journal articles. Users can also set up email alerts for new relevant preprints.. This makes it easier to find and follow preprinted research. 2. Increased trust. Europe PMC follows a set of criteria when selecting new preprint sources. This is important to ensure that preprints in Europe PMC meet scientific standards. Europe PMC displays feedback from different review groups available for preprints. This helps readers to assess preprint quality themselves, even without traditional peer review. Europe PMC also highlights other trust indicators for preprints. For example, support from a funding organisation, associated open data, and so on. Altogether, these steps help build trust in preprints as legitimate research outputs. 3. Integration into research workflows. Europe PMC offers tools to cite preprints or claim them to your author profile. The Article Status Monitor tool can check for various updates to preprint records. For example, it can check if there is a new preprint version, a published journal article based on a preprint, or if a preprint is withdrawn. This helps researchers track changes to preprints, which is important for proper citation. 4. Supporting preprint analyses. Europe PMC supports systematic reviewers that want to include preprints in their meta-analyses. In Europe PMC users can create complex, custom queries for preprints. In addition, Europe PMC searches the full text of preprints. This increases recall and helps find specific study types. For programmatic users Europe PMC offers a RESTful API (Application Programming Interface) and a bulk download option. Preprints in Europe PMC can be accessed in a standard, machine-readable format. This is crucial for text-mining and machine-learning purposes. It also supports creation of new tools and cross-platform integrations. For example, FlyBase offers a search for preprints relevant to the Drosophila community. This feature is built using Europe PMC APIs. Technical challenges of including preprints in Europe PMC. 1. Distributed access points. To combine preprints from many sources Europe PMC relies on Crossref. Crossref is a DOI registration agency used by many preprint platforms. Yet, some platforms don't use Crossref. One important example is arXiv preprint server. Getting preprints from servers that don't use Crossref would need more resources. 2. Limited metadata. Metadata is information about the article, for example title, journal, author affiliations. Europe PMC needs to know the preprint title, abstract, posted date, and author names. This is important to make preprints discoverable and useful to readers. Unfortunately, some preprint servers do not share all this information with Crossref. 3. Divergence of practices and standards. There are many different ways in which preprint platforms handle preprints. They may have different approaches to versioning or withdrawals. Europe PMC needs to address these differences when combining preprints from different sources.