Author Archives: Dina

LibKey Now Flags Both First and Second Order Retractions

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Over the last decade, many in the scholarly research community have been sounding the alarm about journal article retractions being on the rise, for example:

Most prominent of these voices has been Dr. Ivan Oransky, co-founder of the Retraction Watch Database:

Thanks to an increase in awareness of this issue, new technologies have been developed to help alert library discovery tool users whenever they come across retracted items while searching. The thinking is that researchers should have the opportunity to closely examine retracted publications – and even publications that cite retracted papers but are not retracted themselves – as the research being reported within them may be compromised in some way.

One such tool, LibKey, that MSK community members can use via the library’s OneSearch catalog, flags retracted article citations whenever they appear in search result lists – see:

Starting in Summer 2025, LibKey expanded its retraction notification capabilities to also include “data about articles which cite one or more retracted articles”.

As per the LibKey (Third Iron) vendor’s newsletter:

“If a paper cites one or more retracted articles, LibKey will display an interstitial screen indicating which citations have been retracted”. 

For example – see:

If you have any questions or want additional guidance related to retractions, checkout “About Article Retractions” or feel free to Ask Us at the MSK Library.

From a PubMed Record to NCBI’s Gene information Portal

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PubMed – the National Library of Medicine’s database of biomedical literature that will celebrate its 30th anniversary in January 2026 – is an incredible resource that’s freely available to all.

So much so in fact that many other search tools, including Google Scholar and most of the generative AI research assistants that are popping up at a dizzying speed, heavily rely on PubMed for their content needs, especially since the National Center for Biotechnology Information (NCBI) has always been eager to build APIs and other tools to help facilitate collaborative relationships with developers of other research tools.

One of the downsides, however, of discovering PubMed’s content solely via other search engines and tools is that users miss out on some of the incredible value-added links to other information that appear within each PubMed record. This is particularly true for searches on topics with a genetic information or bioinformatics aspect.

Take this example (inspired by NLM training exercises):

You are interested in exploring how the CYP2r1 gene might impact vitamin D deficiency risk.

A basic search in PubMed might look something like this:

Clicking on the Title to view the Full Abstract view, users can scroll below the abstract text to see the MeSH terms and other Related Information – see:

The Related Information links include a link to NCBI’s Gene information portal which:

“integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.”

The Gene record can also include GeneRIFs or a “Gene Reference into Function”.
See https://www.ncbi.nlm.nih.gov/gene/about-generif for a more detailed description.

“GeneRIF provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene.”

As per https://www.ncbi.nlm.nih.gov/books/NBK3841/#EntrezGene.Bibliography:

“A GeneRIF is a concise phrase describing a function or functions of a gene, with the PubMed citation supporting that assertion.”

Filtering out the references that address a specific gene’s function can be a useful time-saver when literature searching.

For those who find the Gene records a bit overwhelming and prefer to stay within the familiar PubMed environment, limiting PubMed search results to those items that have been added as Gene RIFs can be filtered out in a PubMed search by adding “pubmed gene rif” [Filter].

For example, adding it to the PubMed search string:

“CYP2R1 gene” AND “vitamin D” AND “pubmed gene rif” [Filter]

If you have any questions or want additional guidance on designing specialized literature searches, feel free to Ask Us at the MSK Library.

Effective July 1, 2025 – New NIH Public Access Policy

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It was announced on April 30, 2025, that the 2024 NIH Public Access Policy, originally planned to come into effect at the end of 2025 will now be effective as of July 1, 2025.

A key difference between the 2008 and the new 2024 NIH Public Access Policy has to do with how quickly a full-text PMC version of the research article is required to be made publicly available.

In the 2008 version of the policy, the PMC copy had up to 12 months after official publication to become publicly available. The 2024 version of the policy removes the 12-month publisher embargo option and requires the article’s PMC version to become available immediately upon official publication. The new policy will apply to all NIH-funded research articles submitted for journal publication starting on July 1st.

From: https://www.nih.gov/about-nih/who-we-are/nih-director/statements/accelerating-access-research-results-new-implementation-date-2024-nih-public-access-policy

“While the 2008 Policy allowed for an up to 12-month delay before such articles were required to be made publicly available, in 2024, NIH revised the Public Access Policy to remove the embargo period so that researchers, students, and members of the public have rapid access to these findings.”

From: NOT-OD-25-101- Revision: Notice of Updated Effective Date for the 2024 NIH Public Access Policy:

“NIH’s default position is maximum transparency regarding research and research findings. This Notice updates the Effective Date of the 2024 NIH Public Access Policy, NOT-OD-25-047, to July 1, 2025 at which time it will replace the 2008 Public Access Policy. All other aspects of the Policy remain the same.“

From: NOT-OD-25-047 – 2024 NIH Public Access Policy:

“Regarding submission to PubMed Central, compliance with the Policy may be achieved through either:

  • Submission of the electronic version of the Author Accepted Manuscript to PubMed Central upon its acceptance for publication, for public availability without embargo upon the Official Date of Publication, or
  • Submission of the Final Published Article to PubMed Central from journals or publishers with formal agreements with NLM, upon the Official Date of Publication, for public availability without embargo.“

Learn more about how to comply with the NIH Pubic Access Policy or Ask Us your questions.