Europe PMC in 2023.

Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.

Searching and Evaluating Publications and Preprints Using Europe PMC.

In the field of life sciences there is a growing need for literature analysis tools that help scientists tackle information overload. Europe PubMed Central (Europe PMC), a partner of PubMed Central (PMC; National Library of Medicine, 2022), is an open access database of over 41 million life science publications and preprints, enriched with supporting data, reviews, protocols, and other relevant resources. Europe PMC is a trusted repository of choice for many life science funders (Europe PMC, 2022a), offering a suite of innovative search tools that allow users to search and evaluate the literature, including finding highly cited articles, preprints with community peer reviews, or papers referencing a proteomics dataset in the figure legend. In addition, Europe PMC utilizes text-mining to help researchers identify key terms and find data and evidence in the literature. First-time users often do not utilize the wealth of tools Europe PMC offers and can feel overwhelmed about how to perform the most effective search. This protocol, describing how to search and evaluate publications and preprints using Europe PMC, demonstrates how to carry out more efficient and effective literature searches using the tools provided by Europe PMC. This includes discovering the latest findings on a research topic, following research from a specific author, journal, or preprint server, exploring literature on a new method, expanding your reading list with relevant articles, as well as accessing and evaluating publications and preprints of interest. © 2023 EMBL-EBI. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Finding articles and preprints on a topic of interest Basic Protocol 2: Accessing an article Basic Protocol 3: Browsing the article Basic Protocol 4: Evaluating the article Basic Protocol 5: Refining search results Basic Protocol 6: Finding research by author Basic Protocol 7: Finding a specific article Basic Protocol 8: Finding information about a methodology Basic Protocol 9: Finding evidence of biological interactions, relations, and modifications Basic Protocol 10: Finding data behind a publication Basic Protocol 11: Expanding a reading list and building a bibliography Basic Protocol 12: Staying on top of the current literature.

Europe PMC in 2020.

Europe PMC (https://europepmc.org) is a database of research articles, including peer reviewed full text articles and abstracts, and preprints - all freely available for use via website, APIs and bulk download. This article outlines new developments since 2017 where work has focussed on three key areas: (i) Europe PMC has added to its core content to include life science preprint abstracts and a special collection of full text of COVID-19-related preprints. Europe PMC is unique as an aggregator of biomedical preprints alongside peer-reviewed articles, with over 180 000 preprints available to search. (ii) Europe PMC has significantly expanded its links to content related to the publications, such as links to Unpaywall, providing wider access to full text, preprint peer-review platforms, all major curated data resources in the life sciences, and experimental protocols. The redesigned Europe PMC website features the PubMed abstract and corresponding PMC full text merged into one article page; there is more evident and user-friendly navigation within articles and to related content, plus a figure browse feature. (iii) The expanded annotations platform offers ∼1.3 billion text mined biological terms and concepts sourced from 10 providers and over 40 global data resources.

Europe PMC in 2017.

Europe PMC (https://europepmc.org) is a comprehensive resource of biomedical research publications that offers advanced tools for search, retrieval, and interaction with the scientific literature. This article outlines new developments since 2014. In addition to delivering the core database and services, Europe PMC focuses on three areas of development: individual user services, data integration, and infrastructure to support text and data mining. Europe PMC now provides user accounts to save search queries and claim publications to ORCIDs, as well as open access profiles for authors based on public ORCID records. We continue to foster connections between scientific data and literature in a number of ways. All the data behind the paper - whether in structured archives, generic archives or as supplemental files - are now available via links to the BioStudies database. Text-mined biological concepts, including database accession numbers and data DOIs, are highlighted in the text and linked to the appropriate data resources. The SciLite community annotation platform accepts text-mining results from various contributors and overlays them on research articles as licence allows. In addition, text miners and developers can access all open content via APIs or via the FTP site.

Cox26 is a novel stoichiometric subunit of the yeast cytochrome c oxidase.

The cytochrome c oxidase (COX) is the terminal enzyme of the respiratory chain. The complex accepts electrons from cytochrome c and passes them onto molecular oxygen. This process contributes to energy capture in the form of a membrane potential across the inner membrane. The enzyme complex assembles in a stepwise process from the three mitochondria-encoded core subunits Cox1, Cox2 and Cox3, which associate with nuclear-encoded subunits and cofactors. In the yeast Saccharomyces cerevisiae, the cytochrome c oxidase associates with the bc1-complex into supercomplexes, allowing efficient energy transduction. Here we report on Cox26 as a protein found in respiratory chain supercomplexes containing cytochrome c oxidase. Our analyses reveal Cox26 as a novel stoichiometric structural subunit of the cytochrome c oxidase. A loss of Cox26 affects cytochrome c oxidase activity and respirasome organization.