Tag: e-utilities

NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed

Missed a few videos on YouTube? Here’s the latest from our channel.

Customize the MSA Viewer to Make Your Analysis Easier

We’re constantly improving the Multiple Sequence Alignment (MSA) Viewer. This video demonstrates several new and popular features, including the ability to change data columns, hide selected rows, analyze polymorphisms, and more.

Continue reading “NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed”

Updated PubMed E-utilities coming in April 2022!

Updated PubMed E-utilities coming in April 2022!

Do you develop an application that uses the PubMed API? Do you need to access PubMed data programmatically? Then you’ll be interested to know that we will be launching an updated version of the E-utilities API for PubMed on April 4, 2022. This updated version will align the functions of the E-utilities with the web version of PubMed released in 2020. For example, search results returned by the updated ESearch E-utility will now match those of web PubMed. To be clear, this update only affects E-utility calls with &db=pubmed. The behavior of all other Entrez databases will not change.

Why are we doing this?

This release will fully transfer all E-utility functions to the technology stack that supports web PubMed. What this means for you is not only consistent behavior for both web and API PubMed interfaces, but also more reliable performance.

Will URLs for PubMed E-utility calls be changing?

Fortunately, for the most part, no! With only a few exceptions, current E-utility URLs for PubMed (&db=pubmed) will continue to function after we release the update. Here are the exceptions:

  • ESearch will only be able to access the first 10,000 records retrieved by the search query (&retmax <= 10,000; &retstart + &retmax <= 10,000)
  • EPost will only be able to accept up to 10,000 PMIDs in a single URL request.
  • EFetch will no longer support returns in ASN.1 format.

Will the output of PubMed E-utility calls be changing?

Again, in almost all cases, no. Here are the exceptions:

  • ESearch will now return exactly the same PubMed IDs (PMIDs) that are currently returned by web PubMed
  • EFetch will now return XML data by default (&retmode is not set) rather than ASN.1. In other words, the default value of &retmode will become “xml”.

What should you do?

  • If you manage code that creates PubMed E-utility requests, review the above changes to ensure that your code will continue to function after the update.
  • Verify your code on a test server that we will make public later this fall. We’ll update this blog about the details when they become available.
  • Attend our webinar about these changes on October 20 if you have questions or concerns.

What will happen to the current version of the PubMed E-utilities after the release on April 4, 2022?

Once we release the updated PubMed E-utilities, the current version of the PubMed E-utilities will no longer be available. All PubMed requests will use the same technology stack.

Please write to us at info@ncbi.nlm.nih.gov if you have any questions or concerns.

Join NCBI at PAG in San Diego, January 12–16, 2019

Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.

Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)

Continue reading “Join NCBI at PAG in San Diego, January 12–16, 2019”

September 12 NCBI Minute: Release Plan for NCBI API Keys

September 12 NCBI Minute: Release Plan for NCBI API Keys

Update: Webinar is now on September 12!

If you already registered for the September 5 date, you are automatically registered for September 12. You do not need to re-register. We welcome anyone else who would like to register.

As previously announced, NCBI has introduced API keys for the E-utilities. You will soon want to start using API Keys in your E-Utilities API calls as these will allow the fastest access to NCBI databases. In this webinar, we will review how API Keys work and will provide you with a schedule of brief testing periods and the timing of the full release of API key functionality.

Date and time: Wed, Sep 12, 2018 12:00 PM – 12:30 PM EDT

Register here: https://bit.ly/2v0wFMl

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.

(Webinar re-scheduled to September 12 because the presenter was called away unexpectedly.)

Release Plan for E-utility API Keys

As promised in our post this past spring, we are now announcing the scheduled release of API keys for the E-utilities API. If you’ve missed some of our original discussion of these keys, or have questions about how to get a key, you may want to check out this post.

In this post, we’ll be discussing three things:

  • The current status of API keys
  • Upcoming testing periods in September
  • Final public release on December 1, 2018.

Continue reading “Release Plan for E-utility API Keys”

Upcoming Changes to EST and GSS Databases

Upcoming Changes to EST and GSS Databases

Update: NCBI is now in the process of merging EST and GSS records into the Nucleotide database, and we expect to complete this process in early 2019. Accession.version and GI identifiers will not change during this process.

As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database. This change will provide a single point of access for all GenBank sequence data with a common look and feel.

Read more to learn about how this change affects these resources:

  • Websites (Entrez)
  • APIs (E-utilities)
  • FTP sites
  • Submission procedures
  • BLAST
  • TSA (have a look if you’re not familiar!)

Continue reading “Upcoming Changes to EST and GSS Databases”

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.

Continue reading “Testing Periods for New API Keys”

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

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)

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