Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools

As part of our ongoing effort to enhance your experience, we are updating the NCBI Datasets application programming interfaces (APIs). Beginning in June 2024, the v2alpha APIs will be promoted to the stable v2 version. At this time, the v1 API, the command-line interface (CLI) version 13 and older versions, and the Python library v1 … Continue reading Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools

Coming Soon to ClinVar! Somatic Variants & Changes to the XML

Do you rely on ClinVar XML files for your application or analytical pipeline? We are significantly updating ClinVar’s XML format to support the inclusion of new somatic variation data provided by submitters. In the coming months, you may need to make changes to your tool or pipeline code to continue to use the ClinVar XML. … Continue reading Coming Soon to ClinVar! Somatic Variants & Changes to the XML

Coming soon: Updated PubMed E-utilities!

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 … Continue reading Coming soon: Updated PubMed E-utilities!

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 … Continue reading PubMed API launch is pushed back

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

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Oct 20 Webinar: Introducing the updated PubMed E-utilities (API)

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 … Continue reading Oct 20 Webinar: Introducing the updated PubMed E-utilities (API)

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 … Continue reading Updated PubMed E-utilities coming in April 2022!

NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

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 … Continue reading NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Automate your workflow with the ClinVar Submission API

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 … Continue reading Automate your workflow with the ClinVar Submission API

Programmatic access to Gene Data using Datasets command-line and 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 … Continue reading Programmatic access to Gene Data using Datasets command-line and API