Author Archives: Dina

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.

ClinicalTrials.gov – Discovery Tool and Research Data Source

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As ClinicalTrials.gov celebrates its 25th anniversary, reaches its half-million registered studies milestone, and completes its modernization, it’s a good time to appreciate this invaluable research tool that has been around since 2000. In 2008, NLM launched the ClinicalTrials.gov results database, which now (as of 12/2024) has >70K registered studies posted with results.

Openly available to all with “about 90 thousand visitors per day and 2 million unique visitors every month”, ClinicalTrials.gov is a registry where individuals can identify both ongoing and completed registered trials from “50 States and in 229 countries and territories”.

Some functionality that has been added over the last few years (related to how you can search the database using Complex Search Queries and how you can download and use the search results/records from ClinicalTrials.gov) has made this database increasingly attractive as a data source for answering research questions.

From: https://clinicaltrials.gov/find-studies 

In addition to having search functionality that allows for very precise searching, it is now possible to download search results from ClinicalTrials.gov in the RIS file format that can be imported into citation management tools like EndNote and Covidence (used for managing systematic review projects).

It is important to note that the data fields included in the RIS download (which is not customizable), differ from those included in the CSV file download data fields (which a user can select from a menu of options), which differ from the JSON format (which can include every available data field for each study being downloaded). The ClinicalTrials.gov API option allows the ClinicalTrials.gov database to be accessed on a large scale, automated way by researchers and developers.

From: https://clinicaltrials.gov/find-studies/how-to-use-search-results

Examples of research projects that have leveraged ClinicalTrials.gov data:

  1. Alhajahjeh A, Rotter LK, Stempel JM, Grimshaw AA, Bewersdorf JP, Blaha O, Kewan T, Podoltsev NA, Shallis RM, Mendez L, Stahl M, Zeidan AM. Global Disparities in the Characteristics and Outcomes of Leukemia Clinical Trials: A Cross-Sectional Study of the ClinicalTrials.gov Database. JCO Glob Oncol. 2024 Nov;10:e2400316. doi: 10.1200/GO-24-00316. Epub 2024 Dec 2. PMID: 39621951.

  2. Chen D, Parsa R, Chauhan K, Lukovic J, Han K, Taggar A, Raman S. Review of brachytherapy clinical trials: a cross-sectional analysis of ClinicalTrials.gov. Radiat Oncol. 2024 Feb 13;19(1):22. doi: 10.1186/s13014-024-02415-8. PMID: 38351013; PMCID: PMC10863227.

  3. Falade AS, Adeoye O, Van Loon K, Buckle GC. Clinical Trials in Gastroesophageal Cancers: An Analysis of the Global Landscape of Interventional Trials From ClinicalTrials.gov. JCO Glob Oncol. 2024 Aug;10:e2400169. doi: 10.1200/GO.24.00169. PMID: 39173083.

  4. Pearce FJ, Cruz Rivera S, Liu X, Manna E, Denniston AK, Calvert MJ. The role of patient-reported outcome measures in trials of artificial intelligence health technologies: a systematic evaluation of ClinicalTrials.gov records (1997-2022). Lancet Digit Health. 2023 Mar;5(3):e160-e167. doi: 10.1016/S2589-7500(22)00249-7. PMID: 36828608.

  5. Yang A, Baxi S, Korenstein D. ClinicalTrials.gov for Facilitating Rapid Understanding of Potential Harms of New Drugs: The Case of Checkpoint Inhibitors. J Oncol Pract. 2018 Feb;14(2):72-76. doi: 10.1200/JOP.2017.025114. Epub 2018 Jan 3. PMID: 29298113; PMCID: PMC5812307.

Questions? Ask Us at the MSK Library!