Tag: e-utilities

RefSeq release 214 is available!

RefSeq release 214 is available!

RefSeq release 214 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Foreign contamination screening
Introducing the new Foreign Contamination Screen (FCS) tool! If you produce assembled genomes, check out FCS, a tool you can run yourself to improve your genome assemblies and facilitate high-quality data submissions to GenBank. FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. See our previous blog post to learn how FCS enhances contaminant detection sensitivity. Continue reading “RefSeq release 214 is available!”

Coming soon: Updated PubMed E-utilities!

Coming soon: Updated PubMed E-utilities!

Important Note: This release is being postponed and will go live Monday, November 21, 2022.

PubMed will be moving to an updated version of the E-utilities  API on November 15, 2022. As previously announced, this updated version of E-utilities will use the same technology as the web version of PubMed released in 2020. So, search results returned by the updated ESearch E-utility  will now match those of the PubMed.gov website 

This update only affects E-utility calls with &db=pubmed. There are no changes to the E-utilities for other databases. You can refer to our previous post or watch our recorded webinar for more details on this update.   Continue reading “Coming soon: Updated PubMed E-utilities!”

PubMed API launch is pushed back

PubMed API launch is pushed back

As we previously announced, we will be moving to an updated version of the E-utilities API for PubMed. In preparation for this launch, a test server is currently available to allow you to test your API calls on the new service and report issues. Thank you for trying out the test server and continuing to submit your feedback!

To address your comments, finalize updates, and to give you more time to prepare for the API update, we are pushing back the release of the new API until later this year. Continue reading “PubMed API launch is pushed back”

Test Server for the PubMed API (E-utilities) is Now Available

Test Server for the PubMed API (E-utilities) is Now Available

Official update scheduled to launch June 2022 

As previously announced, we will be moving to an updated version of the E-utilities API for PubMed. We are planning to delay this change until June 2022 to give you time to test your API calls on the new service, report issues, and provide your feedback. Don’t wait until launch! A test server is available leading up to the release and ready for you to try! 

How do I use the test server? 

The test server is available through the following URL:

Test server: https://eutilspreview.ncbi.nlm.nih.gov/entrez/eutils/

Continue reading “Test Server for the PubMed API (E-utilities) is Now Available”

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 soon!

Updated PubMed E-utilities coming soon!

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 in late 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”