Tag: PubMed Central (PMC)

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.

NIHMS Users: Do You Know How Often Your Paper is Being Accessed Via PMC? Here’s How to Find Out.

If you’re reading this, you probably already know that NIH and some other institutions have public access policies that require that peer-reviewed publications resulting from their funding be made available to the public. But did you know that if you complied with your funding agency’s public access policy by depositing your author manuscript in NIH’s PubMed Central (PMC) archive via the NIH Manuscript Submission (NIHMS) system, you can easily obtain statistics on how frequently your paper is being accessed? Continue reading “NIHMS Users: Do You Know How Often Your Paper is Being Accessed Via PMC? Here’s How to Find Out.” →

Advice for NIH Grantees: How to comply with the NIH Public Access Policy

“The NIH public access policy requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMed Central immediately upon acceptance for publication.” – http://publicaccess.nih.gov/

To comply with NIH Public Access Policy, here are the steps you should take:

Determine if the Public Access Policy applies to your publication

Generally, the NIH Public Access Policy applies to any peer-reviewed journal article that was accepted for publication on or after April 7, 2008 and that arose from NIH funding in Fiscal Year 2008 or later.

Determine Applicability for Your Publication

What does the NIH consider to be a ‘journal’?

Continue reading “Advice for NIH Grantees: How to comply with the NIH Public Access Policy” →

Verifying Article Compliance for NIH Public Access

Are you trying to find out if your article complies with the NIH Public Access policy and/or find a PubMed Central ID (PMCID) for your article? If so, this post describes a simple method for finding the PMCID for an article and thereby verifying Public Access compliance.

First, let’s start with a bit of background. To comply with the NIH Public Access Policy, you need to make sure that your peer-reviewed articles that resulted from NIH funding (full or partial) and that were accepted for publication on or after April 7, 2008 are available in the PubMed Central (PMC) database with a PMCID. Please be aware that PMC is not the same as PubMed. PMC is NCBI’s full-text digital archive, while PubMed contains only citations and abstracts. It is not enough for your citation to be available in PubMed with a PubMed ID (PMID); you must have a PMCID to satisfy NIH Public Access policy.

To check that your article has a PMCID and is compliant, proceed as follows:

Continue reading “Verifying Article Compliance for NIH Public Access” →

New PubReader View For Full-Text Articles

NCBI’s new PubReader display format in PubMed Central (PMC) makes full-text research papers not only more readable but also more portable.

Whether you’re using a desktop, laptop, tablet or smart phone, PubReader adapts to your device, displaying full-text articles in a user-friendly format that minimizes scrolling and maximizes intuitive navigation and portability (see Figure 1).

Continue reading “New PubReader View For Full-Text Articles” →