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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Essentials of Glycobiology, Third Edition & New Glycan Website Now Available at NCBI


Glycobiology—the study of the structure, biosynthesis, biology, and evolution of glycans (the sugar chains synthesized by all living cells)—is a rapidly growing field in the natural sciences, with broad relevance to many areas of basic research, biomedicine, and biotechnology.

NCBI has two new glycobiology resources: the third edition of a definitive work in the field, Essentials of Glycobiology, and a new NCBI Glycans website that includes links to some useful external resources as well as the Symbol Nomenclature for Glycans (SNFG).

essentials of glycobiology

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Identifying and Correlating Chemical Names & Synonyms


This blog post is intended for people who refer to chemical names/symbols and synonyms in databases like PubMed and PubChem, or in their own scientific papers. There is a similar post for gene symbols and names.

During the research and publishing process, scientists need to refer to their chemicals-of-interest. While there are standardized nomenclatures (IUPAC, SMILESInChITM, etc.), different labs sometimes use different names for the same chemical.

The NCBI PubChem project has set up a system to identify and correlate these various names as well as ‘alias’, ‘synonym’, or ‘also known as’ terms that have been used in the literature.

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Streptococcus pyogenes “A to Zs” Covered in New Book, Freely Available on NCBI Bookshelf


The University of Oklahoma Health Sciences Center has published an open-access book called “Streptococcus pyogenes: Basic Biology to Clinical Manifestations” that provides a comprehensive review of research on the bacteria. The university’s first online, open-access book, “Streptococcus pyogenes” is freely available on NCBI’s Bookshelf, at http://www.ncbi.nlm.nih.gov/books/NBK333424/.
S.pyogenes Book on the NCBI Bookshelf

Streptococcus pyogenes (Group A Streptococcus) is responsible for diseases such as scarlet fever, pharyngitis, impetigo, cellulitis, necrotizing fasciitis and toxic shock syndrome, as well as the sequelae of rheumatic fever and acute poststreptococcal glomerulonephritis. The book aims to provide an up-to-date and comprehensive review of research on Streptococcus pyogenes, including its basic biology, epidemiology, genetics and pathways that facilitate group A streptococcal infections. Continue reading

PubMed Also-Viewed: Quickly find related articles


You’ve seen it before on shopping web site: you load a page displaying an item you want and see a list of other items that people bought with the one you’re viewing.

PubMed is free, but finding the important articles on a topic can cost a lot of time. To help you keep on top of the literature – with a little help from your fellow PubMed users – we are introducing a new type of link called “Articles frequently viewed together”. For some PubMed abstracts, you may see this link in the “Related Information” section in the right column.

PubMed Also-Viewed feature

Figure 1. The PubMed Also-Viewed feature.

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Setting Up Automatic NCBI Searches and New Record Alerts


Do you regularly perform PubMed searches to find new articles on your topic of interest?

Would you like to know when new sequence records become available for your gene?

Is it important to be alerted when new bioactivity assays are available with inhibitor data for your enzyme?

With a free My NCBI account, you can easily set up a series of e-mail alerts to notify you of such new information. You can read more about the many other functions of My NCBI.

Here’s how to set up these alerts:

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Early Developments in the PubMed Commons Pilot


It’s been an exciting and productive time since the PubMed Commons beta launch. We’ve learned a great deal, both here working under the hood and from the conversations in social media and blog posts.

We are working on answers to questions that people are asking, via our Twitter account and by revising and expanding information on the PubMed Commons page soon. And we will try out a Twitter chat: so keep your eye out on @PubMedCommons for the announcement.

There are now about 1,000 people signed up in the Commons. Remember, any author in PubMed can join, from anywhere in the world. Check out our step-by-step guide. Once you are in, you can invite others. So please spread the word!

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Joining PubMed Commons: A Step-by-step Guide


In our previous post we wrote about a new service called PubMed Commons that allows researchers to add comments to individual PubMed records. As we described in that post, PubMed Commons is currently a beta pilot release, and requires interested people to join the system before they can view or add comments. This post will describe how to join PubMed Commons.

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PubMed Commons: A New Forum for Scientific Discourse


NCBI has released a pilot version of a new service in PubMed that allows researchers to post comments on individual PubMed abstracts. Called PubMed Commons, this service is an initiative of the NIH leadership in response to repeated requests by the scientific community for such a forum to be part of PubMed. We hope that PubMed Commons will leverage the social power of the internet to encourage constructive criticism and high quality discussions of scientific issues that will both enhance understanding and provide new avenues of collaboration within the community.

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Removing Duplicate Citations from My Bibliography


My Bibliography is a component of the My NCBI service and allows authors to create an online collection of their published work. While editing their bibliographies, authors can import citations for their articles directly from PubMed, and the system will automatically check for duplicates and will remove citations imported more than once.  However, authors may still end up with duplicates in certain situations, and sometimes it is not obvious how to remove these duplicates. In this post we will describe three situations where duplicates may persist and will discuss ways to remove them.

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