How a novel machine learning system is bridging the gap between advanced models and expert insights to accelerate protein research Proteins are essential molecules with many critical roles in the body. Determining a protein’s 3D structure helps scientists understand its functions within cells. This is crucial for advances in biology, medicine, and drug design. Our […]

Europe PMC and Open Targets develop Lit-OTAR framework unearthing over 48 million unique associations that can be leveraged for drug discovery Identifying drug targets is a critical and intricate part of drug discovery. This requires scientists to look at many sources of evidence. They use them to find links between drugs, targets, and diseases. This […]

Europe PMC POSI update – 2 years on  Two years have sailed by since Europe PMC adopted the Principles of Open Scholarly Infrastructure (POSI) in February 2021. POSI is a set of guidelines for open scholarly infrastructure providers and outlines how these organisations should be run and sustained. It offers a framework to uphold transparency […]

Europe PubMed Central (Europe PMC) is an open access repository of life science research, including peer-reviewed journal articles and preprints. It contains over 41 million abstracts and 8.7 million full-text articles, adding over 1.7 million new articles annually. To facilitate information discovery and foster literature–data integration, Europe PMC has incorporated text-mining approaches into its workflows.  […]

Europe PMC now includes the full text preprints supported by Europe PMC funders Open science is at the heart of Europe PMC, providing access to open content and data. Recognising the role that preprints play as a way for life science researchers to openly and rapidly share their findings, Europe PMC has made over 420,000 […]

In July 2020, Europe PMC began indexing the full text of COVID-19 preprints. The initiative supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, has now made over 15,300 full text COVID-19 preprints searchable and free to read, alongside peer reviewed articles. Number of full text COVID-19 preprints in Europe PMC […]

More than 4,500 Research Square preprints discoverable alongside peer-reviewed research Research Square’s collection of more than 4,500 full-text COVID-19 preprints have been indexed in Europe PMC, an open-access repository of more than 1 million biomedical research works. The overall effort, jointly supported by Wellcome, the UK Medical Research Council, and Swiss National Science Foundation, expands […]

We are excited to announce the recent release of metagenomics annotations for Europe PMC publications. Thanks to the machine learning framework of Dr. Maaly Nassar for the joint EMERALD project between Europe PMC and MGnify teams, recognising metagenomics key terms in literature can now provide detailed biome descriptions for unravelling microbial implications in a variety […]

This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations. Highlighting annotations in the text enables users to easily scan the article and […]

In this pandemic, researchers have responded by publishing results rapidly, often through preprints. In fact, up to half of the publications in Europe PMC on COVID-19 are preprints rather than peer-reviewed journal articles. Currently, the full text of these preprints are scattered as PDFs on preprint servers, or, available as a non-standard set of documents […]

From algorithms to the bench Text-mining holds the promise of helping researchers to overcome information overload. It is a familiar premise: an avalanche of scientific knowledge is being produced and shared. Teaching machines to “read” might soon be the only manageable way to digest large amounts of information into useful facts. To extract bits of […]

We are excited to announce the launch of Europe PMC Annotations API, which provides programmatic access to annotations text-mined from biomedical abstracts and open access full text articles. The Annotations API is a part of Europe PMC’s programmatic tools suit and is freely available on the Europe PMC website: https://europepmc.org/AnnotationsApi. The exponential growth in scientific […]

Jo McEntyre, EMBL-EBI; Thomas Lemberger, EMBO; Mark Patterson, eLife; Kristen Rattan, Collaborative Knowledge Foundation; Alfonso Valencia, Barcelona Supercomputer Centre. The use of preprints in the life sciences offers tantalising opportunities to change the way research results are communicated and reused, and the work of ASAPbio has been key in engaging the scientific community to promote […]

Manual curation is vital for maintaining quality information in biological databases. However, with the exponential growth in biological data this approach is both challenging and time consuming. We wanted to create a scalable and sustainable process which could complement manual curation.    We recently launched a new service – SciLite – that allows text-mined annotations to be […]

Evidence Finder (EvF) provides a new way of searching Europe PMC that will help you find the most relevant articles more quickly. By surfacing “facts” based on biological concepts, EvF enhances the Europe PMC search, targeting relevant sentences from within full text articles. Over the next few weeks, we will be running an experiment on […]

New copyright exceptions to text and data mining for non-commercial research have recently come into effect and this is welcome news for UK researchers and research, argues Ross Mounce. Here he provides a brief overview of the past issues discouraging text and data mining and what the future holds now that these exceptions have been […]

Europe PMC has added protein and chemical structures from Protein Data Bank (PDB) and ChEBI via the BioEntities tab. There are some amazing examples in this paper, which was a collaboration between scientists in America, the Netherlands and UK: ‘Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120’ The paper investigates […]

We are pleased to announce a new feature in Europe PMC that allows you to track data citations in the scientific literature. It is now possible to search for papers that cite database records for several core life science databases, such as the European Nucleotide Archive, ArrayExpress, and PDBe, as well as dataset DOIs used […]

There is a new prototype tool available for browsing on Europe PMC labs: Acromine. Developed and hosted by the National Centre for Textmining, University of Manchester, Acromine suggests expansions of acronyms and presents articles specific to those expansions. The new tool is presented on an interface similar to the look and feel of Europe PMC. […]

UKPMC Labs is a new component of the UKPMC website, which will showcase novel applications based on UKPMC content. The first application to be featured on the Labs website is EvidenceFinder, an application that surfaces “facts” based on a user’s search terms from full text articles. The user is presented with a list of questions […]

Text mining features in databases are an increasingly popular way to extract useful information that could otherwise remain hidden. A new resource has become available to allow researchers to search for particular chemical compounds in biomedical literature. This task is often confounded by multiple names for particular chemicals being used in publications. Similarly, sometimes the […]