Changing of the Guard: A New Acting Director for NCBI

We wanted to take a moment to announce an important internal development at NCBI. After an illustrious, 32-year career, Dr. James Ostell retired from federal service on March 31, 2020.

Dr. James Ostell

Dr. James Ostell

Dr. Ostell (or “Jim” as we all know him) came to NCBI at its very inception in 1988 and spent the majority of his time at NCBI as the Chief of the Information Engineering Branch. In this role he was responsible for designing, building, and deploying virtually all of the public production services that NCBI provides. In 2017, he became NCBI’s second Director, and championed initial efforts to move NCBI services to cloud environments. During his long tenure, Jim oversaw the growth of NCBI from a handful of people wondering how to confront the coming era of biological data to a vibrant center of some 700 staff serving more than 7 million users each day. We celebrate Jim’s leadership in building these services that continue to provide free and reliable access to data that are critical to biomedical research and the NIH mission to enhance human health.

We are also pleased to welcome Dr. Stephen Sherry as the new Acting Director of NCBI.

Dr. Stephen Sherry

Dr. Stephen Sherry

Dr. Sherry (or “Steve”) joined NCBI in 1998 and has led the development of several NCBI resources including dbSNP, dbVar, dbGaP, ClinVar, and SRA. He has also played a central role in the ongoing move of the SRA dataset onto cloud architectures. Steve has long-standing interests in storing population genetic data in ways that make these data useful to researchers while preserving the privacy of study participants.

As we wish Jim a fond farewell, we hope you will join us in welcoming Steve to this new role.

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

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Identifying Chemical Targets – Finding Potential Cross-Reactions and Predicting Side Effects

This blog post is directed toward researchers using PubChem.

You’ve identified a chemical that you’d like to use in your research as a chemical probe for a receptor or an enzyme inhibitor. However, chemicals are known to be able to bind to multiple protein targets, commonly known as “cross-reactivity”. In biological activity assays, this can cause problems with measuring the activity of a specific protein or pathway. If the chemical is employed as a medicant in living organisms, interactions with molecules other than the intended target can cause “side effects”.

At NCBI, the PubChem BioAssay database stores biological activity assay information that makes it possible to find experimentally measured targets for millions of chemicals. This blog post describes a workflow to download a table of gene/protein targets for a particular chemical.

Tamoxifen compound page.

Figure 1. Tamoxifen compound page.

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NCBI homepage update includes action buttons, category pages

The NCBI homepage now has six prominent buttons on it: Submit, Download, Learn, Develop, Analyze, and Research. Each of these buttons leads to an action page devoted to a particular set of services.

Figure 1. The NCBI homepage. The new action buttons are outlined in red.

Figure 1. The NCBI homepage. The new action buttons are outlined in red.

We’ve also included a blue feedback button on the left side of the Download, Learn, Develop and Analyze pages so that you can tell us what you think.

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