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.
Is there a chance that one can still access ESearch results beyond the 10,000 limit in the future, in one way or another (paging, higher limit, etc.)?
The solution I see with the new APIs when the results exceeds 10,000 would be to artificially create chunks split by year, hopying each year does not exceed the limit. That seems a bit cumbersome.
Is the test server available yet?
The test server is not officially public. We’ll announce on this site when it’s ready, which should be in the next couple of weeks. We are planning to extend the deadline for the switch over until June.
Was the question about exceeding 10,000 articles answered somewhere? For systematic reviews retrieving the full set of matching pmids is important.
Thank you for asking. As with the web page, you cannot retrieve more than 10,000 PubMed ids in a single search. Try segmenting your search by publication date range, journal, or other facet, to limit your initial results set. See the PubMed help document (https://pubmed.ncbi.nlm.nih.gov/help/#narrow-search) for more suggestions.
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Yes, one workaround is to segment the search by date. The EDirect commandline programs have a built-in batch process that will allow you to get more than 10 thousand articles. For more information on the EDirect package see https://www.ncbi.nlm.nih.gov/books/NBK179288/
I can’t wait for the API update. Any news on the official launch date in June? Or any idea when the test server will be available?
The test server is available at: https://eutilspreview.ncbi.nlm.nih.gov/entrez/eutils/ The switch to the new API has been delayed. See https://ncbiinsights.ncbi.nlm.nih.gov/2022/06/22/pubmed-api-launch-delayed/
Hi,
Any update regarding this? Are test servers available yet?
The test server is available at https://eutilspreview.ncbi.nlm.nih.gov/entrez/eutils/ The change the new API has been delayed. See https://ncbiinsights.ncbi.nlm.nih.gov/2022/06/22/pubmed-api-launch-delayed/
Has the updated release date been finalized? Is it still this month?
The switch over to the new PubMed API has been postponed. See https://ncbiinsights.ncbi.nlm.nih.gov/2022/06/22/pubmed-api-launch-delayed/