Category: NCBI Labs

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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Introducing the new Virus Sequence Search Interface

BLAST is a powerful search tool, but often a search is just the beginning of the journey. We put ourselves in the shoes of a researcher who has just sequenced a handful of samples from the latest viral outbreak and tried to understand what information would be most useful. We also reached out to researchers in the field and asked: a) what questions do they really want to answer? and b) how can NCBI best provide the answers? Based on insights from those questions and answers, we developed the new Virus Sequence Search Interface (Fig. 1). The Search Interface is an NCBI Labs project, which means it is an experimental project, and we may modify the resource based on your feedback and experiences.

Figure 1. The Virus Sequence Selection Interface. — **Figure 1.** The Virus Sequence Selection Interface. The Virus Sequence Selection Interface accepts as input nucleotide and protein accessions, as well as FASTA and plain-text formatted sequences. The user selects either “Nucleotide” or “Protein,” depending on the sequence type, and selects the virus type from the pull-down menu below the text entry field.

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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:

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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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!)

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Fast Sequence Inspection with ORFfinder + SmartBLAST

This blog post is intended for all BLAST users.

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

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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.

**Figure 1.** The PubMed Also-Viewed feature.

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SmartBLAST: Faster BLASTp search results in a graphical view

BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the query, it treats all subject sequences the same, regardless of the quality of the sequence data or its annotation, and also does not allow easy comparisons between different subject sequences.

For example, the subject sequences may fall into multiple groups of similar sequences, or all of the subject sequences may be more similar to each other than to the query. A common way to obtain this information is to construct a multiple sequence alignment of the query and some or all of the subject sequences, but to this point, BLAST has not provided such alignments directly.

Enter SmartBLAST! SmartBLAST is a new and experimental NCBI tool that makes it easier to complete common sequence analysis tasks, such as finding a candidate protein name for a sequence, locating regions of high sequence conservation, or identifying regions covered by database sequences but missing from the query.

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Introducing NCBI Labs

Welcome to NCBI Labs!

NCBI Labs is all about you. It’s a new NCBI initiative for creating innovative and relevant products by involving you, our user community, from the beginning.

NCBI Labs is about experimentation. It’s a place where you’ll find early versions of new tools, experimental content, and proposed features, as well as an opportunity to suggest ideas to us.

NCBI Labs is about learning. It’s a place where the focus is on figuring out what works, where failure is OK because it’s a learning experience, and where any idea is welcome that can improve our services for our users.

NCBI Labs is about conversation. It’s a place where we can share future plans with you, and you can tell us how we’re doing. It’s a place where we all can come together to create resources that will benefit the broader scientific community.

Join the conversation!

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