New BLAST results page in NCBI LABS


NCBI Labs is showcasing an experiment to improve the BLAST results page. The goal is to provide a more useful BLAST output that better meets your needs and integrates with your workflows. The new results incorporate feedback from surveys and interviews with BLAST users. We think you’ll find the new results are more compact, easier to navigate, and expose useful formatting and other features that you may not have known about.

The results page has organism, percent identity, and E value filters in plain view and easily accessible. The Descriptions and Graphic Summary are on separate tabs, and the popular taxonomy view is on a fourth tab rather than on a separate web page. These changes along with other enhancements make the display more concise and easier to navigate. The figure below shows the new output format.

Blast_resultsFigure 1. The New BLAST Results with filters directly on the page and a more concise tabbed output that includes the taxonomy report. The Back to Traditional Results Page link re-loads the results in the standard format.

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NCBI implements new, natural language sequence search


In late May, we introduced a new type of search experience in NCBI Labs that uses natural language queries to make common tasks easier. The experience at NCBI Labs – where we experiment with potential new features and tools – proved successful. We’re pleased to announce that we added this simplified search capability to NCBI’s global search page. Some natural language queries now work in the “All Databases” search from the NCBI home page!

NCBI search bar, red arrow pointing to all databases

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As-you-type-suggestions come to NCBI Labs


In a recent post, we described a new way to search our databases in NCBI Labs. We have now added a suggestions dropdown to the search bar that should make life easier for many NCBI visitors.

The as-you-type suggestions are simple, natural language-like queries we described in the previous post. They’ll help you avoid typos and save time if you’re searching for organisms with long or hard-to-spell names.

These suggestions are meant to direct you to high value results. As we improve the search experience, you may notice changes to the suggestions. We welcome your feedback on ways to enhance this new feature.

Here’s a quick look at what to expect:

dropdown suggestions ncbi labs search

Figure 1. As-you-type suggestions appear in a dropdown. Note how “human” is recognized as homo sapiens. Many common organisms are supported in this manner, e.g. “mouse”, “cow”.)

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.

Test drive a new sequence search experience at NCBI Labs


We know it’s not always easy to find the sequence data you’re after at NCBI. Maybe it’s because you’re no expert at constructing queries, and you end up with no results or too many results. Or maybe you’re an Entrez wizard, but creating a query full of Booleans and filters seems like overkill when you could just write a short natural language query, like you’re used to doing in Google.  The next time you search for a gene, transcript or genome assembly for a given organism, try the new search experience we’re piloting in NCBI Labs.

In NCBI Labs, you can now search for sequences using natural language and get the best results.

NCBI Labs transcript search interface

Figure 1. The new interface for specified transcript search.

The improved search experience now available in NCBI Labs addresses 3 types of queries that commonly fail in searches at NCBI: organism-gene (e.g. human BRCA1), organism-transcript (e.g. Mouse p53 transcripts) and organism-assembly (e.g. dog reference genome). For each of these query types in NCBI Labs, we now return NCBI’s highest quality sequence sets or reference and representative assemblies in an easy-to-view panel.

Example queries are shown below to get you started.

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PubMed Labs is now part of NCBI Labs


About two years ago, NCBI launched PubMed Labs, a gathering place for discovering and experimenting with new features and content for NCBI’s family of websites.  Over those years, we launched a few experiments that have helped us learn more about our customers and how we can serve them better.

Today we’re happy to announce that we’re expanding PubMed Labs to a broader set of experiments called NCBI Labs.

Why are we doing this?

  • To better convey the breadth of upcoming experiments on data, services, and websites that NCBI offers now and hopes to offer in the future.  You can expect to see new features, content, and other experiments from NCBI Labs in the coming months.
  • To reserve the name “PubMed Labs” for an exciting new set of experiments around biomedical literature and especially literature search.

What Will Change?

This blog’s menu item and blog category “PubMed Labs” will now appear as “NCBI Labs”. Existing links will continue to work.  We won’t be updating the old blog posts, for the most part, although some links on existing sites (e.g. on PubMed Journals) may be updated to use the new name.

Find, Browse and Follow Biomedical Literature with PubMed Journals


Following the latest biomedical literature can be a challenge, but NCBI’s new PubMed Journals will help you keep up-to-date.

PubMed Journals lets you:

  • Easily find and follow journals of interest
  • Browse new articles in your favorite journals
  • Keep up-to-date with a Journal News Feed containing new arrivals, news links, trending articles, and important article updates (retractions and more!)

The PubMed Journals home page.

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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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