New PubMed Updates: User Guide, MyNCBI, and more


As you may have heard, we are working on a new version of PubMed, and we’ve recently released some new features that you can check out.

new user guide answers many common questions about how best to use the new site. We’ve also added links on the new PubMed homepage to many popular sites including the E-utilities, Advanced Search, and the MeSH database.

The action menu (Figure 1) now contains Collections and My Bibliography, allowing you to manage and share groups of citations. After running a search, you will also find a “Create alert” link under the search box that lets you set up automatic My NCBI email updates for your search.

Action menu on new PubMed

Figure 1. New PubMed search result page showing the new “Create alert” link and updated action menu.

Going forward, we will continue to develop new features leading up to the time when this new version of PubMed will replace the legacy PubMed. As this progresses, we would love to hear what you think about these new additions! Please use the “Feedback” button (available on every page of the new PubMed) to submit your comments, questions, or concerns.

NCBI on YouTube: new videos on PubMed, My Bibliography, sequence data and more


Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

Introducing the Genome Submission Wizard in Genome Workbench v3.0

Genome Workbench version 3 is a major upgrade, including the addition of the Genome Submission Wizard. This video guides you through the wizard, from uploading your genome data file to completion of the submitter report, which is ready to submit to GenBank using tools such as Submission Portal or BankIt. Note: An on-line tutorial is under “Manuals” on the Genome Workbench home page.

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August 14 Webinar: An updated PubMed is on its way!


On Wednesday, August 14, 2019 at 11AM, NCBI staff will show you PubMed Labs, a test site that will become the default PubMed early next year. You will get a preview of the new, modern interface, updated features including advanced search, clipboard, options for sharing results, and the new “cite” button. You’ll also learn about features that are still under development and how to give us your feedback on the new PubMed.

The August 14 webinar session is full. We will make the recording available and are offering an encore session on August 28, 2019. 

Register for the August 28 session.

Date: Wed, Aug 14, 2018
Time: 11:00 AM – 11:45 AM EDT

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

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.

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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.

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PubMed Journals will be shut down


Almost two years ago, we launched PubMed Journals, an NCBI Labs project. PubMed Journals helped people follow the latest biomedical literature by making it easier to find and follow journals, browse new articles, and included a Journal News Feed to track new arrivals news links, trending articles and important article updates.

PubMed Journals was a successful experiment. Since September 2016, nearly 20,000 people followed 10,453 distinct journals. Each customer followed 3 journals on average.

Though PubMed Journals will no longer exist as a separate entity, we hope to add its features into future NCBI products. We appreciate your feedback over the years that made PubMed Journals a productive test of new ideas.

NCBI Labs is NCBI’s product incubator for delivering new features and capabilities to NCBI end users.

June 13 NCBI Minute: Using EDirect to Query a Local Installation of PubMed


Next Wednesday, June 13, 2018, we’ll show you how to use EDirect to install PubMed locally and then search and retrieve records from the local instance. You will also see an analysis example that shows the significant speed improvement with the Local Cache and employs some advanced EDirect xtract options to aid with processing records.

Date and time: Wed, June 13, 2018 12:00 PM – 12:30 PM EDT

Click to register.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Formulas will be displayed in PubMed Titles and abstracts


Starting this month, we will begin displaying formulas in citation titles, abstracts and keywords in PubMed.

Previously, formulas were replaced with “[Formula: see text]” (see Figure 1).

PubMed abstract display without formula

Figure 1. Formula replaced with [Formula: see text] in the PubMed abstract display.

With this enhancement, you will now see formulas in the PubMed summary and abstract displays when these data are available in new citations (see Figure 2).

PubMed abstract showing chemical formula

Figure 2. Formula shown in the PubMed abstract display after June 1, 2018.

We will also be including the MathML 3.0 element tags in PubMed XML. To support the addition of MathML tagging in our XML, we have created a DTD, which you can download now. Existing content will be valid against the new DTD. You can also download sample XML files with MathML 3.0 tags.

EDirect for PubMed starts March 5


Beginning Monday, March 5, 2018, the National Library of Medicine (NLM) will present EDirect for PubMed, part of the Insider’s Guide to Accessing NLM Data.

This newly expanded series of interactive workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of five 90-minute sessions (plus an optional “office hours”), students will learn how to use EDirect commands to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. EDirect requires access to a Unix environment but we will send easy installation instructions for Windows and Mac computers before the class starts. No prior Unix knowledge is required; novice users are welcome! Continue reading

NLM Webinar: Insider’s Guide to Accessing NLM Data: Welcome to E-utilities for PubMed (Tuesday, February 13 at 1pm EST)


Want to do more with PubMed?

Want to extract just the PubMed data you need, in the format you want?

Dreaming of creating your own PubMed tool or interface, but don’t know where to start?

Join us on Tuesday, February 13 at 1pm EST for a one-hour introductory webinar designed to teach you more powerful and flexible ways of accessing NLM data, starting with the Application Programming Interfaces (APIs) for PubMed and other NCBI databases. This presentation is part of the Insider’s Guide, a series aimed at librarians and other information specialists who have experience using PubMed via the traditional Web interface, but now want to dig deeper. Continue reading