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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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:

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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).

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).

Figure 1. The PubReader format as seen in three common displays (widescreen desktop, smart phone and tablet).

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