Using the Pathogen Detection pipeline, we recently found new Shiga toxin 2 (stx2) subtypes in isolates from the United States collected as part of the Centers for Disease Control and Prevention (CDC) routine disease surveillance. Our pipeline relies on AMRFinderPlus to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. We screened over 60,000 E. coli and Shigella genomes for Shiga toxin, a factor associated with food borne illness. These analysis results and full AMRFinderPlus results for now over 270,000 E. coli and Shigella genomes are available in the MicroBIGG-E browser. Continue reading “NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype”
Tag: PubMed Central (PMC)
The role of a library in a digital world continues to evolve and expand. NLM’s PubMed Central (PMC) has a large and diverse user base that includes students and the public, as well as researchers, clinicians, and librarians. We recognize that these different audiences have varying levels of familiarity with PMC as an archive of literature published by other organizations, as well as with NLM, the National Institutes of Health (NIH), and the scholarly publishing process. That’s why we recently updated how we describe, display, and share articles in PMC to provide our users with more context and help them more accurately cite the correct source of an article made available in PMC.
Here are the updates made to PMC:
The 2023 Nucleic Acids Research Database Issue features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below. Continue reading “Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue”
Legacy view will no longer be available effective late-March 2023
You asked, we listened! We appreciate your feedback since the launch of the updated PubMed Central (PMC) website in March 2022, and we made several improvements to help you better access PMC. These updates include:
- Streamlined functionality to get formatted citation information that includes the PubMed format (NBIB file), that works easily on both web and mobile, and is consistent across the PubMed and PMC sites (see number 1 in the image below).
- Updated functionality to easily add an article to your My NCBI collections through PMC’s new “Collections” button (number 2 below).
- An improved “Resources” section that allows easy access to articles similar to the one you are viewing, other papers that cite that article, and links to related data records in other NCBI databases (number 3 below).
New article view in PMC. Updates are illustrated with yellow number squares: 1) “Cite” button provides formatted citation information; 2) “Collection” button adds the article to My NCBI collections; 3) “Resources” button finds related articles; 4) “Feedback” button to communicate with NCBI. Continue reading “New Enhancements to PMC Website”
Phase 2 expands the scope of the preprints included in PubMed and PMC
Last month, the National Library of Medicine (NLM) announced plans to extend its NIH Preprint Pilot in PubMed Central (PMC) and PubMed beyond COVID-19 to encompass all preprints reporting on NIH-funded research. The second phase of the pilot, launching later this month, will include preprints supported by an NIH award, contract, or intramural program and posted to an eligible preprint server on or after January 1, 2023. Continue reading “Next Phase of the NIH Preprint Pilot Launching Soon”
We have launched a fresh look and feel to the PubMed Central (PMC) website, which marks the first step of an ongoing modernization effort. The updated website will allow us to make continuous enhancements to PMC based on your feedback.
What Has Changed?
Now when you visit PMC’s homepage, you will see:
- A redesigned and reorganized homepage
- Easy-to-navigate help documentation
- A similar look and feel between features in PMC and PubMed
- A streamlined article display
Figure 1 highlights features of the new PMC article display. You can also find the most up-to-date version of this information in PMC’s User Guide. Continue reading “New PMC Website Design is Live!”
On March 21, we will be launching an updated PMC website with a modern design. You can try the updated version on PMC Labs now, and it will become the default design of the PMC website following launch. Be sure to check the banner at the top of the PMC website for updates on an exact cutover date.
This update represents the first phase of an overall PMC modernization that will help us update PMC in a quicker and more responsive fashion. New features and functionality will be deployed on an ongoing basis.
In advance of the official update, we wanted to remind you of a few details about what’s changing: Continue reading “Updated PMC Launching Soon!”
In June, we announced the arrival of PMC Labs, where you can test drive the work underway to create a more modern PMC website. Since then, we’ve continued to talk to users, gather input, and make ongoing adjustments based on your feedback.
We hope that the planned updates will create an easier navigation and reading experience, while keeping all the features you use most within PMC. If you haven’t had a chance to try out the changes, there’s still time to give input using the green feedback button in the lower right-hand corner of the site.
To enhance machine access to biomedical literature and drive impactful analyses and reuse, the National Library of Medicine (NLM) is pleased to announce the availability of the PubMed Central (PMC) Article Datasets on Amazon Web Services (AWS) Registry of Open Data as part of AWS’s Open Data Sponsorship Program (ODP). These datasets collectively span 4 million of PMC’s 7 million (total) full-text scientific articles.
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!”