Testing Periods for New API Keys


You’ll want to pay attention to this if you regularly use the E-utilities API. As we announced last fall, we are in the process of introducing API keys for the E-utilities. This post will update the schedule of this process and outline our release plan, which will include a series of testing periods.

So what’s happening?

We’re learning a lot from you!

Thanks for all of your feedback! Ongoing conversations with our users are helping us plan this release in a way that will benefit everyone as much as possible. Please continue to reach out to us with ideas and suggestions!

The effective date for release of API keys has been pushed back.

We will not be activating API keys on May 1, 2018 as originally announced. That date is being moved to be no earlier than September 1, 2018.

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April 25 NCBI Minute: Revised Release Plan for the New NCBI API Keys


As previously announced, NCBI is introducing API keys for the E-utilities. This NCBI Minute will review these keys and their benefits for API users, and will update the schedule for when we will activate these keys. We will also describe plans for a test site and a series of testing periods during which these keys will be fully active. These periods are an ideal opportunity for developers to test their products in this new environment.

Please register and join us for this webinar to be presented on Wednesday, April 25, 2018 at noon, Eastern time.

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Bioinformatics paper uses NCBI open data to analyze drug response


study (PMID: 28158543) published in the July 2017 issue of Bioinformatics collects, classifies and analyzes single nucleotide variants (SNVs) that may affect response to currently approved drugs. They identified 2,640 SNVs of interest, most of which occur rarely in populations (minor allele frequency <0.01).

The researchers used protein sequence alignment tools and mined open data from multiple information resources accessed through E-utilities including PubChem Compound (Kim et al., 2016 PMID: 26400175), NCBI Gene (Maglott D, et al., 2014. PMID: 25355515), NCBI Protein (Sayers, 2013), MMDB (Madej et al., 2012 PMID: 22135289), PDB (Berman et al., 2000 PMID: 10592235), dbSNP (Sherry et al., 2001 PMID: 11125122), and ClinVar (Landrum et al., 2016 PMID: 26582918).

Questions, comments, and other feedback may be sent to Yanli Wang.

NLM Webinar: Insider’s Guide to Accessing NLM Data: Welcome to E-utilities for PubMed (Tuesday, February 13 at 1pm EST)


Want to do more with PubMed?

Want to extract just the PubMed data you need, in the format you want?

Dreaming of creating your own PubMed tool or interface, but don’t know where to start?

Join us on Tuesday, February 13 at 1pm EST for a one-hour introductory webinar designed to teach you more powerful and flexible ways of accessing NLM data, starting with the Application Programming Interfaces (APIs) for PubMed and other NCBI databases. This presentation is part of the Insider’s Guide, a series aimed at librarians and other information specialists who have experience using PubMed via the traditional Web interface, but now want to dig deeper. Continue reading

November 8 NCBI Minute: New API keys for better E-utilities & EDirect access to NCBI data


On Wednesday, November 8, 2017, we will present a webinar on API keys for E-utilities. In this webinar, you’ll learn how to get and start using your API key with the E-utilities and the command line EDirect programs.

Date and time: Wednesday, November 8, 2017 12:00-12:30PM EST

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

New API Keys for the E-utilities


This post was updated on February 2, 2017.

If you regularly use the E-utilities API, we have important news for you: NCBI is now providing API keys for the E-utilities! After May 1, 2018, NCBI will limit your access to the E-utilities unless you have one of these keys. Obtaining an API key is quick, and simple, and will allow you to access NCBI data faster. If you don’t have an API key, E-utilities will still work, but you may be limited to fewer requests than allowed with an API key.

What is an API key?

An API key is a unique string that you include in your HTTP requests that identifies you to NCBI servers. Think of the API key as a ‘turbocharger’ that lets you get more data, faster, from NCBI.

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October 4th NCBI Minute: Create, link and share your bibliography (PubMed & ORCID)


On October 4, 2017, NCBI staff will present a webinar on author disambiguation and the advantages of using an ORCID ID.

Disambiguating common author names is tough in any field, but if your published research is cited in PubMed, we can help you find your citations, create a bibliography, and share your publication list with others.

In this webinar, we’ll also talk about the advantage of quickly registering for a free, unique identifier that will remain constant – even if your name changes.

Date & time: Wednesday, October 4, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Blastdbinfo: API access to a database of BLAST databases


NCBI offers extensive collections of sequences through its BLAST services (http://blast.ncbi.nlm.nih.gov) for comparing and identifying DNA, RNA and protein sequences. NCBI now deposits descriptions of these sequence collections, known as BLAST databases, in a special database called blastdbinfo that you can access through the Entrez Programming Utilities (E-Utilities). Using blastdbinfo, you can enable a program to find an appropriate database and then send BLAST searches to that database using either the BLAST URL API or standalone BLAST (installed locally).

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