Join us on October 20, 2021 at 12PM US eastern time learn about an updated version of the E-utilities API for PubMed that we will launch on April 4, 2022. With few exceptions, this update will not change the E-utility URLs you currently use but will bring the search results up to date with the web version of PubMed released in 2020 and improve reliability. Attend this webinar to learn about how these changes will affect your API calls to PubMed and to get your questions answered.
Date and time: Wed, October 20, 2021 12:00 PM – 12:45 PM EDT
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
EFetchwill 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.
Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!
Introducing GaPTools for dbGaP Submitters
This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.
ClinVar and our scientific and patient-care community rely on your submissions. With our new Application Programming Interface (API) for submissions, we’ve made it even easier for you to provide us with your most up-to-date classification of variants. The new RESTful API allows you to automate your submission workflow so that you can submit new records and update existing records faster. Setting up your account to use the API requires three one-time activities:
ClinVar Submission API Setup
Click on each of the steps in order to set up your account to use the API!
In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool? Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins in one shell command or API request. The API documentation is a good way to get started with programmatic access (Figure 1).
Figure 1. The Datasets API documentation showing a demonstration retrieving Gene metadata using RefSeq mRNA accessions. The API returns a readily processed JSON object.
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.
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
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.)
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.
Next Wednesday, July 11, 2018, NCBI staff will show you a set of simple exercises that use EDirect to explore aspects of a human gene. You can easily incorporate these examples into your undergraduate biology courses.
Date and time: Wed, July 11, 2018 12:00 PM – 12:30 PM EDT
The NCBI web BLAST service has several useful download formats, including tabular formats. All formats allow you to easily save your BLAST results for processing, editing, and annotating.
This video will show you how to use basic Unix tools and EDirect to expand and enhance your tabular saved BLAST results. You will also see learn how to add useful information like taxonomy and sequence titles.