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


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

Try Our New, Experimental PubMed Search and User Interface in PubMed Labs


NLM needs your input. We are experimenting with a new PubMed search algorithm, as well as a modern, mobile-first user interface, and want to know what you think. You can try out these experimental elements at PubMed Labs, a website we created for the very purpose of giving potential new PubMed features a test drive and gathering user opinions.

Please note that PubMed Labs includes only a limited set of features at this time and not the full set of PubMed tools. The absence of a feature or tool on PubMed Labs does not mean we plan to eliminate it from PubMed; it simply means we are not testing it now!

The key elements we are testing are:

In PubMed Labs, search results are listed by best match. The best match button is at the top right; you can also click the "most recent" button (to the right of "best match") to sort by date.

  • A new search algorithm for ranking (ordering) the best matches to your query

Based on analysis of data obtained from anonymous PubMed search logs, we have developed a new algorithm that we believe does a much better job of sorting search results by their relevance, or “best match,” to your query. This new algorithm incorporates machine learning to re-rank the top articles returned.

We were so excited by results with this algorithm that we already implemented it in PubMed, but it is still experimental and we would very much appreciate hearing what you think. Part of our test in PubMed Labs is having best match be the default sort, instead of PubMed’s default of sorting by most recent articles. If you find that you prefer to sort by the most recent articles instead, it takes only a simple click of a button to do so.

Interested in specifics about the new algorithm? You can read more in this NLM Technical Bulletin.

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October 4th NCBI Minute: Create, link and share your bibliography (PubMed & ORCID)


On October 4, 2017, NCBI staff will present a webinar on author disambiguation and the advantages of using an ORCID ID.

Disambiguating common author names is tough in any field, but if your published research is cited in PubMed, we can help you find your citations, create a bibliography, and share your publication list with others.

In this webinar, we’ll also talk about the advantage of quickly registering for a free, unique identifier that will remain constant – even if your name changes.

Date & time: Wednesday, October 4, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI releases newly designed dbSNP RefSNP Report – Alpha version


NCBI dbSNP is pleased to announce a newly designed Reference SNP (RefSNP, rs) Report webpage to provide enhanced performance and presentation for access to individual RefSNP records. This Alpha version of the report enables browsing of submitted and computed RefSNP variant data from the redesigned dbSNP build system.

The new RefSNP report (alpha version). You can see all of the sections described in the blog post, like the summary section and the sidebar menu.

Figure 1. The dbSNP RefSNP Report Alpha for rs268.

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