Tag: PubMed Central (PMC)

A more modern PMC is coming – let us know what you think in PMC Labs!

We’re updating PubMed Central (PMC) to a give you a more modern and easier to use site and we want your feedback. The first phase of this work is now on PMC Labs for you to explore and provide feedback.

In the first phase we have focused on modernizing PMC’s platform to create a more stable and easy-to-update environment. This also includes some initial changes to the homepage (Figure 1), site organization, and article pages (Figure 2). Many of the updates you see on the Labs site create a similar look and feel for PMC and PubMed, reorganizing documentation to highlight the most accessed and important content first and consolidating redundant features to provide a smoother experience. Please visit PMC Labs to try out the PMC updates and provide feedback using the buttons on the lower right-hand side of the Labs pages (Figure 1). We will update the current PMC website with new features once we gather your input on the Labs site.

Figure 1. The PMC Labs homepage featuring the PMC full text search bar, links to the most heavily used documentation, information for distinct groups of PMC users (Authors, Publishers, and Developers), statistics on deposits, an updated “New in PMC section” (not shown), and a prominent Feedback link (circled) for you to provide comments and suggestions. Continue reading “A more modern PMC is coming – let us know what you think in PMC Labs!” →

Expanding access to coronavirus-related literature: the COVID-19 Initiative in PMC reaches 100K articles!

One important way the National Library of Medicine (NLM) is responding to the ongoing public health emergency is through the COVID-19 Initiative. This public-private cooperation between NLM and more than 50 scholarly publishers and societies allows you to access over 100,000 articles on COVID-19, SARS-CoV-2 and other coronaviruses through PubMed Central (PMC). This collection includes recently published discoveries, a history of coronavirus reports for comparison, international (globally comprehensive) content, and captures the breadth of research, analysis, and commentary. We make these articles available in human- and machine-readable formats to support public accessibility and analysis by researchers.

You can search this public health emergency collection in PMC or download the collection through the PMC Open Access Subset. The collection spans:

- More than half a century of research, including articles from the 1960s through the present (more than 60% of the articles included thus far were published in 2020 (Figure 1, top panel);
- Several languages, including content in English (~95%), German, French, and Spanish;
- Many publication types, more than half of them research or review articles (Figure 1, bottom panel).

Figure 1. The Public Health Emergency Collection articles by decade of publication (top panel) and by publication type (bottom panel).

People have viewed or downloaded articles in this PMC collection more than 80 million times since March reflecting the great demand for such an open and centralized collection. Artificial intelligence organizations, such as the Allen Institute for AI — builders of the COVID-19 Research Dataset (CORD-19), have also used the collection to develop new text and data mining techniques that can help answer high-priority scientific questions related to COVID-19.

To learn more about the initiative and NLM’s collaborators, see the Public Health Emergency COVID-19 Initiative overview and related FAQs.

NIH Preprint Pilot in PubMed Central

NLM is preparing to launch a pilot project to test the viability of making preprints resulting from NIH-funded research available via PubMed Central (PMC). The primary goal of the NIH Preprint Pilot will be to explore approaches to increasing the discoverability of early NIH research results. The pilot will begin the week of June 8, 2020 and will run for a minimum of 12 months. Lessons learned during that time will inform future NLM efforts with preprints.

In its role as the repository for peer-reviewed manuscripts supported by NIH, PMC already makes available more than one million published papers resulting from NIH-supported research. Building on NIH guidance (NOT-OD-17-050) to investigators that encouraged the use of interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work, NLM hopes this pilot will inform possible future steps to further accelerate discovery and access of papers that are developed with NIH funds and encourage the open and fast dissemination of NIH research results, when appropriate.

Continue reading →

CORD-19: A New Machine Readable COVID-19 Literature Dataset

Are you interested in mining literature about COVID-19 and the novel SARS-Cov-2 virus? You may want to check out the COVID-19 Open Research Dataset (CORD-19). CORD-19 is a collection of more than 13,000 full text articles that focus on COVID-19 and coronaviruses and that were assembled from PMC, the WHO, bioRxiv, and medRxiv. To produce this dataset, the National Library of Medicine partnered with colleagues from the Allen Institute for AI, the Chan Zuckerberg Initiative (CZI), Georgetown University’s Center for Security and Emerging Technology (CSET), Kaggle, Microsoft, and the White House Office of Science and Technology Policy (OSTP).

CORD-19 is available from the Allen Institute and will be updated weekly as new articles become available. The article data are formatted in JSON, making the collection ideal for computational methods such as data mining, machine learning, and natural language processing. We hope this collection serves as a call to action for the community to improve our understanding of coronaviruses and the human diseases they cause. Have a look and let us know what you think!

Changes to PMC Bulk Downloadable Open Access Dataset Files on March 18, 2019

As the final part of an announced FTP restructuring effort, we will remove the old PMC Bulk Open Access files on March 18, 2019 – but please note that the data is still available.

In August 2016, the PMC Open Access dataset was split into two groups: Continue reading “Changes to PMC Bulk Downloadable Open Access Dataset Files on March 18, 2019” →

Discovering associated data in PMC

In the NLM Strategic Plan released earlier this year, we noted that “[c]reating efficient ways to link the literature with associated datasets enables knowledge generation and discovery.” To that end, PMC is now aggregating data citations, data availability statements and supplementary materials, as available, in an Associated Data box. This box will only display on articles that have one or more of these features in the article.

To limit your search to records with an Associated Data box, you can use the new “Associated Data” facet on the search results page.

We hope that exposing this content in a consistent format and in an easy to find and easy to access manner, you will more readily find the datasets you need to further accelerate discovery and advance health. As part of our ongoing commitment to making data findable, accessible, interoperable, and re-usable (FAIR), we encourage you to contact us with your feedback on these updates and with any other suggestions you may have for improving discovery of related data in PMC.

Hey Professors! Get your free personal assistant — an NCBI Account!

Professors, we know you’re busy — really, really busy. You have to develop and teach your courses and labs, coordinate and run your journal clubs and seminars, direct your lab’s research efforts, write grants and publications, counsel and mentor your students, and stay current on everything related to your teaching and research topics.

NCBI has information that can help with all of this, but there are so many interesting records and so little time to organize them. Sign up (Help) for or log in (Help) to your free NCBI Account and let us help you get started and get organized!

Read on – or watch the video embedded below – to learn more about what you can do with your NCBI Account.

Continue reading “Hey Professors! Get your free personal assistant — an NCBI Account!” →

PubMed Health to be discontinued October 31, 2018; content will continue to be available at NLM

Update #2: As announced July 31, 2018, the PubMed Health website has been shut down as of October 31, 2018.

NLM thanks you for using PubMed Health over the years.

Update #1: As reported previously, the PubMed Health website will shut down on October 31, 2018. This decision was made so the National Library of Medicine (NLM) can consolidate its consumer health and comparative effectiveness resources to make them easier to find.

In an effort to consolidate similar resources and make information easier to find, the National Library of Medicine will be retiring its PubMed Health website, effective October 31, 2018, and providing the same or similar content through more widely used NLM resources, namely PubMed, MedlinePlus, and Bookshelf.

PubMed Health content falls into two general categories: consumer health resources and systematic reviews/comparative effectiveness research (CER). A similar range of consumer health information to that in PubMed Health is available from NLM’s MedlinePlus, while the systematic reviews and CER in PubMed Health are searchable through PubMed, which links to the full text (when available) in Bookshelf, journals, and/or PubMed Central.

Continue reading “PubMed Health to be discontinued October 31, 2018; content will continue to be available at NLM” →

Institutional Repositories in PubMed: a new quick way to free full text articles

New icons are starting to appear in PubMed that take you directly to free full text publications uploaded in an institutional repository (IR). Here’s an example:

This one is from Deep Blue, University of Michigan’s Library IR. When you see it on a publication like this one on Ebola, you can get free access to the publication there.

The icons only appear when there is no free full text available from the journal or PMC (PubMed Central). So far, only 4 IRs with eligible publications are participating – you can see which ones they are here. They already expand access to around 25,000 publications.

The NCBI program that enables this is LinkOut. You can read more about it in the NLM Technical Bulletin. IRs can apply by email to join LinkOut. And if you are an author at an institution with a repository, support your IR and enable more people to read your work.