Tag: 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 in April 2022!

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 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.

 

Read about NCBI resources in 2020 Nucleic Acids Research database issue

The 2020 Nucleic Acids Research database issue features papers from NCBI staff on GenBank, ClinVar and more. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

“Database resources of the National Center for Biotechnology Information”

by Eric W Sayers, Jeff Beck, J Rodney Brister, Evan E Bolton, Kathi Canese et al. (PMID: 31602479)

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. This article provides a brief overview of the NCBI Entrez system of databases, followed by a summary of resources that were either introduced or significantly updated in the past year, including PubMed, PMC, BookshelfBLAST databases and more!

Continue reading “Read about NCBI resources in 2020 Nucleic Acids Research database issue”

The new PubMed is here!

The updated interface includes a responsive design to improve the mobile experience as well as improved search capabilities using a best match sort.

PubMed includes the features you rely on for searching, saving, and sharing your results.

  • Access the same trusted database of more than 30 million citations for biomedical literature.
  • Use the default filters or customize the filter menu to meet your needs.
  • Save your search results to a file, email your results to yourself or a colleague, or send your results to a clipboard, collection, or your NCBI My Bibliography.
  • Save your search and create an email alert.

This version of PubMed will become the default in early 2020 and will eventually replace the legacy PubMed.  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.

We want to hear from you! What do you think of the new PubMed? Please submit your comments, questions, or concerns using the “Feedback” button available on each page of the new PubMed

New PubMed Updates: User Guide, MyNCBI, and more

As you may have heard, we are working on a new version of PubMed, and we’ve recently released some new features that you can check out.

new user guide answers many common questions about how best to use the new site. We’ve also added links on the new PubMed homepage to many popular sites including the E-utilities, Advanced Search, and the MeSH database.

The action menu (Figure 1) now contains Collections and My Bibliography, allowing you to manage and share groups of citations. After running a search, you will also find a “Create alert” link under the search box that lets you set up automatic My NCBI email updates for your search.

Action menu on new PubMed
Figure 1. New PubMed search result page showing the new “Create alert” link and updated action menu.

Going forward, we will continue to develop new features leading up to the time when this new version of PubMed will replace the legacy PubMed. As this progresses, we would love to hear what you think about these new additions! Please use the “Feedback” button (available on every page of the new PubMed) to submit your comments, questions, or concerns.

NCBI on YouTube: new videos on PubMed, My Bibliography, sequence data and more

Here are the latest videos on our YouTube channel. Subscribe to get alerts for new videos.

Introducing the Genome Submission Wizard in Genome Workbench v3.0

Genome Workbench version 3 is a major upgrade, including the addition of the Genome Submission Wizard. This video guides you through the wizard, from uploading your genome data file to completion of the submitter report, which is ready to submit to GenBank using tools such as Submission Portal or BankIt. Note: An on-line tutorial is under “Manuals” on the Genome Workbench home page.

Continue reading “NCBI on YouTube: new videos on PubMed, My Bibliography, sequence data and more”