Exploring Entrez Direct: Parsing the XML Output of E-utilities


Entrez Direct is a UNIX/LINUX command-line interface to E-utilities, the API to the NCBI Entrez system. One of Entrez Direct’s most useful features is its ability to parse and reformat complex XML data returns from EFetch. In this post, we will explore how to use these features to parse, reformat and process specific data from PubMed records downloaded in XML using EFetch. Though this post focuses on PubMed, the technique is universal and applies to any XML returned by E-utilities from any database. The example explored here is also presented briefly in the Entrez Direct documentation; here we’ll dive in a bit depeer to see how it works. Let’s get started!

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My Bibliography and SciENcv: How to Delegate Authority to Others to Edit/Create Your Profile and Collections


As a My NCBI account holder, you can invite other individuals to act as your delegate and grant them the ability to view and edit your My Bibliography collection (including Other Citations), as well as the ability to view, edit, and create profiles in your SciENcv.

Inviting a Delegate

The first step is to send a delegate invitation from your NCBI Account Settings page. After you’ve logged in to your NCBI account, click on your username in the top right corner of the screen to access your Account Settings. Then, under the “Delegates” section, click “Add a delegate” and enter the email address for your intended recipient. You can have multiple delegates on your account, and you can control what each delegate has access to from the Delegates section of your Account Settings page.

Acting as a Delegate

If a colleague invites you to become a delegate on their NCBI account, you will receive an email invitation. After you’ve accepted the delegation invitation, you will see your colleague’s Bibliography appear in your Collections list on your My NCBI landing page:

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Designing exon-specific primers for the human genome


A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.

Here are the steps to follow to design primers to amplify exon 15 from human BRCA1:

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Advice for NIH Grantees: How to comply with the NIH Public Access Policy


“The NIH public access policy requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMed Central immediately upon acceptance for publication.” – http://publicaccess.nih.gov/

To comply with NIH Public Access Policy, here are the steps you should take:

Determine if the Public Access Policy applies to your publication

Generally, the NIH Public Access Policy applies to any peer-reviewed journal article that was accepted for publication on or after April 7, 2008 and that arose from NIH funding in Fiscal Year 2008 or later.

Determine Applicability for Your Publication

What does the NIH consider to be a ‘journal’?

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New SciENcv Features Allow Users To Create and Download Multiple Biosketches


NCBI’s recent update to the SciENcv feature in MyNCBI gives researchers the ability to create multiple biosketches for grants from federal agencies engaged in scientific research, allowing a more tailored and convenient approach to the grant application process.

What is SciENcv?

SciENcv (Science Experts Network Curriculum Vitae) is designed to help researchers assemble an NIH biosketch by extracting information from NIH eRA Commons and PubMed. The SciENcv interagency working group includes NIH, as well as DOD, DOE, EPA, NSF, USDA and the Smithsonian. You can access SciENcv if you have a My NCBI account. My NCBI accounts are free and offer many useful features, such as saving searches, automated e-mail alerts and My Bibliography.

 Create your biosketch

Based on user suggestions, we’ve made it possible to create biosketches in three ways: from scratch, from an external source, or by duplicating an existing profile (see Figure 1). While the eRA Commons data feed is currently the only external data option, we plan on adding other external data sources in a future release of SciENcv.

Figure 1. Three ways to create your NIH biosketches in SciENcv

Figure 1. Three ways to create your NIH biosketches in SciENcv

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Sequence updates in human genome assembly GRCh38: filling in the gaps


In a previous blog post, we explained several important concepts about the human reference genome.  We presented a region of human chromosome 17 as an example of a location where the genome sequence was not fully assembled.  In this post, we are going to revisit the same gapped region to see how the Genome Reference Consortium (GRC) changed this part of the genome in GRCh38, the updated human reference assembly released in December 2013.  This region represents just one of the more than 1,000 changes and improvements that the GRC introduced in GRCh38.

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Making Custom Databases for Web BLAST


An easy way to speed up your BLAST analysis is to search a smaller database targeted to sequences of interest. We’ll describe here a few ways to create such custom databases on the BLAST web pages.  For this Quick Tip we’ll use the pages in the Basic BLAST section of the BLAST home page.

BLAST parent databases

Generating a custom database begins with selecting the appropriate parent database. The BLAST Guide provides database descriptions to help with choosing a database.  You select the parent in the Database pull-down menu, shown in Figure 1. Selecting the database is really your first opportunity to customize.

BLAST Parent Database Pull-down Menu

Figure 1. The database selection pull-down lists: top panel, nucleotide databases; bottom panel, protein databases

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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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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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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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