Tag: PubMed

Coming soon: Updated PubMed E-utilities!

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 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”

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

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 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
  • Register

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 webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

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.

Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI

Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI

This post is in support of the CDC’s Fungal Disease Awareness Week — September 20-24, 2021.

The impact of fungal diseases on human health has often been neglected, but increased association of fungal infections with severe illness and death during the COVID-19 pandemic has brought fungal diseases into the spotlight.

According to the CDC, the most common fungal co-infections in patients with COVID-19 include aspergillosis or invasive candidiasis including healthcare-associated infection from Candida auris.  Other reported diseases are mucormycosis, coccidioidomycosis and cryptococcosis. Aspergillosis is commonly caused by Aspergillus fumigatus, mucormycosis by Rhizopus species, coccidioidomycosis by Coccidioides immitis and C. posadasii and cryptococcosis by Cryptococcus neoformans.

This post explores several NCBI resources that have relevant information about the fungal pathogens implicated in these COVID-19 related illnesses.

Assembled genomes

Correctly identified and annotated genome assemblies are available for the fungal taxa implicated as co-infections in COVID-19 patients are summarized in table below.  These and  many other fungi are also available as curated RefSeq genome assemblies.

Continue reading “Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI”

New PubMed updates and retirement of legacy PubMed on October 31

The new PubMed has been the default now since May, and more than 99% of you are using the new site. The recent NLM technical bulletin has details on features that we have added to the new PubMed based on your requests.

Legacy PubMed, which has been available in parallel with the new PubMed, will be finally taken down after October 31, 2020.  We will continue to provide API access to PubMed through the E-utilities, which uses the legacy system, for the foreseeable future and until we can transition to an API that accesses the new system.

We understand that it can take time to adapt to changes and find favorite features in a new interface. Several learning and training resources are available to help you use the new PubMed: Continue reading “New PubMed updates and retirement of legacy PubMed on October 31”

The New and Improved PubMed® — We Are Listening

Today marks 5 weeks since the new PubMed was made the default version. Throughout this process, we promised to listen, and we heard from you!

This was a huge change

We know change isn’t always easy, especially with major changes to a familiar service or product. We are staunch believers in making incremental changes whenever possible: releasing small improvements, observing the effects, gathering user feedback, and then using that data to make further modifications. This time, an incremental approach to improving PubMed wasn’t feasible. We needed to make major changes under the hood (new databases, cloud delivery, new web architecture, etc.) for PubMed to be sustainable going forward.

User feedback is invaluable: it has played an enormous role in updates over the 24 years PubMed has been in existence, and it continues to do so. To prepare for new PubMed, we launched the beta version in 2017, then called PubMed Labs, as a way to set up the new framework and solicit feedback from our users. During development and since, we reached out to our stakeholders with presentations, webinars, handouts, FAQstoolkits, and tutorials, including a series of four 90- minute online classes, How PubMed® Works, many of which continue to be available.

We understand that not everyone had a chance to put the new PubMed through its paces, and we’re grateful to those of you who provided feedback along the way, whether it was by sending questions or comments using the feedback button, by discussing with us how you accomplish your work with PubMed, or by filling out a survey.

For some, when the new version of PubMed became the default last month, it was a huge shift. The ways in which you were accustomed to working with the system changed. We heard from some of you that you were used to a particular feature being available on PubMed and now you don’t know where to find it.

Continue reading “The New and Improved PubMed® — We Are Listening”

Try the new PubMed on your mobile device

Our new, responsive PubMed site replaces PubMed Mobile. You now have the full PubMed experience on any size screen, including the ability to save and email citations, use the Clipboard, and send citations to My NCBI Collections on your mobile device.

pubmed 2
Figure 1. The new PubMed on mobile.

Also, the new, responsive PubMed will replace the legacy desktop site for PubMed in late spring 2020. NLM will continue adding features and improving the user experience, ensuring that PubMed remains a trusted and accessible source of biomedical literature today and in the future.

For more information about the development of the new PubMed, please see the NLM Technical Bulletin.