As previously announced, NCBI’s Assembly and Genome record pages will be redirected to new NCBI Datasets pages in June 2023. The NCBI Datasets Command Line Interface (CLI) tools provide easy, straightforward programmatic downloads of assembled genome sequence data. We invite you to check them out and let us know what you think!
Features & Benefits of NCBI Datasets
- Get assembled genome sequence, annotation, and metadata, including transcripts and proteins, in one easy step.
- Querying is easy and flexible! Retrieve data using organism name, assembly accession, or BioProject accession.
- Request data for multiple assemblies in one request – it is now simpler and faster to download large amounts of data.
- Metadata is derived from multiple databases and metadata schemas are documented.
Continue reading “Download Assembled Genome Data Programmatically with NCBI Datasets”
The 2023 Nucleic Acids Research Database Issue features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below. Continue reading “Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue”
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!”
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!”
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”
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”
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”
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 email@example.com if you have any questions or concerns.
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”
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.)