How PubMed is Democratizing “Expert” Literature Searching

In May 2020, the U.S. National Library of Medicine (NLM) officially launched their updated version of PubMed, making it the default that will replace the legacy version going forward. First released in January 1996, as the Internet was just becoming available to the masses, PubMed has seen multiple redesigns over its almost 25 years of existence. New features have been added and improved upon continuously, with some of these changes more obvious to regular PubMed users than others. 

Millions of people around the World search this freely-available biomedical bibliographic database daily, with both experienced and non-experienced searchers in the mix. One noteworthy change to the updated version (which will likely go unnoticed by most searchers unless they choose to do an Advanced search and look at the Details by clicking on the carrot symbol >), is that PubMed’s search translation functionality (or automatic term mapping) has also been further enhanced.

In fact, the folks at NLM may now have come closer than ever before to elevating the PubMed search queries entered by less experienced searchers to truly “expert searcher” level search statements.

Here’s an explanation – an “expert searcher” typically approaches a comprehensive literature search by making these considerations regarding the concept(s) of interest: they will compile synonyms/subject headings, alternate/foreign spellings, singular and plural forms, and multiple term endings (suffixes), as well as, develop appropriate logic statements (using Boolean operators) to correctly combine these search terms.

Simply by inputting a term or two in the PubMed search box and clicking on the “Search” button, a non-expert can go from, say:

Search: lymphedema prevention 

…a two keyword query that then gets translated behind the scenes by the PubMed search engine into a rather sophisticated search strategy.

Legacy PubMed was already helping improve searches by mapping to relevant Medical Subject Headings (MeSH) and to foreign spellings, for example, it would have run this search translated to:

(“lymphoedema”[All Fields] OR “lymphedema”[MeSH Terms] OR “lymphedema”[All Fields]) AND (“prevention and control”[Subheading] OR (“prevention”[All Fields] AND “control”[All Fields]) OR “prevention and control”[All Fields] OR “prevention”[All Fields])

 …however, the updated version of PubMed has expanded the translation functionality to also search for singular/plural forms, as well as, incorporate a bit of truncation (ie. prevent*), allowing for relevant alternate term endings, as in the case here with “prevention”, see:

 ((((“lymphedema”[MeSH Terms] OR “lymphedema”[All Fields]) OR “lymphedemas”[All Fields]) OR “lymphoedema”[All Fields]) OR “lymphoedemas”[All Fields]) AND (((((((((((((((((“prevent”[All Fields] OR “preventability”[All Fields]) OR “preventable”[All Fields]) OR “preventative”[All Fields]) OR “preventatively”[All Fields]) OR “preventatives”[All Fields]) OR “prevented”[All Fields]) OR “preventing”[All Fields]) OR “prevention and control”[MeSH Subheading]) OR (“prevention”[All Fields] AND “control”[All Fields])) OR “prevention and control”[All Fields]) OR “prevention”[All Fields]) OR “prevention s”[All Fields]) OR “preventions”[All Fields]) OR “preventive”[All Fields]) OR “preventively”[All Fields]) OR “preventives”[All Fields]) OR “prevents”[All Fields])

Note: If for some reason a searcher wishes to turn off this query term(s) translation functionality, using quotation marks around each term will keep the automatic term mapping from occurring. For example:

Search: “lymphedema” “prevention” 

…now drops the mapping/translating, and only turns into:

“lymphedema”[All Fields] AND “prevention”[All Fields]

…versus inputting it as a phrase surrounded by quotations:

Search: “lymphedema prevention” 

…which will now stop considering the space between the two terms as an implied Boolean operator AND, and so will keep its integrity and be run only as:

“lymphedema prevention”[All Fields]

See this NLM handout for more Tips for Using PubMed or take one of the MSK Library’s New PubMed classes to learn more.


Interim Research Products

The scholarly communication landscape, especially over the last five years, has been changing rapidly. A noteworthy “new kid on the block” that has recently seen a big increase in availability, visibility, and use, is a category of resource type often referred to as “Interim Research Products”.

Interim research products are basically research documents that are shared publicly prior to their final publication in a peer-reviewed scholarly journal. In other words – keeping in mind that there are multiple definitions by different stakeholders that continue to evolve in this space – they are: research products that become part of the public scientific record without yet having been confirmed by peer review.

Most common among them are preprints and preregistered protocols. Recent discussions of these two types of interim research products that may be of interest:

1: Xu J, Zhang L. Will Medical Preprints Change Oncology Practice? JAMA Oncol.2020 Feb 20. doi: 10.1001/jamaoncol.2019.5972. [Epub ahead of print] PubMed PMID:32077893. 

2: Schiavo JH. PROSPERO: An International Register of Systematic Review Protocols. Med Ref Serv Q. 2019 Apr-Jun;38(2):171-180. doi:10.1080/02763869.2019.1588072. PubMed PMID: 31173570.

Funding agencies like the National Institutes of Health (NIH), among others, have started encouraging the use of interim research products as they may potentially improve the rigor of research work and speed up the dissemination of research results, not to mention allow for more transparency in the research process.

For example, the rapid sharing and dissemination of research findings is a critical goal of the National Cancer Institute (NCI)’s Cancer Moonshot Initiative as a way to accelerate cancer research. Specified in their documentation is the requirement “that all publications and data resulting from Cancer Moonshot funded initiatives will be required to be immediately accessible“. 

From their Cancer Moonshot Public Access and Data Sharing Policy website: 

“Much of the urgency highlighted by the Cancer Moonshot and in the Blue Ribbon Panel’s recommendations to the National Cancer Advisory Board (NCAB) in 2016 emphasizes that the rapid availability of cancer publications and the primary data behind it promotes dissemination of new knowledge, enhances reproducibility, and accelerates the ability of researchers to build upon cancer research to make new discoveries.” 

With this aim in mind, the Cancer Moonshot Initiative uses a broader definition of “publication” and “publish” than is traditionally used on their funding information website, and one that is more inclusive of interim research products. More specifically:

  • Publication: A “Publication” includes (a) published research results in any manuscript that is peer-reviewed and accepted by a journal1 or (b) a complete and public draft of a scientific document (commonly referred to as preprint).2
  • Publish: To “Publish” means to report in a publicly accessible manner.

For more information about finding and citing interim research products, be sure to Ask Us at the MSK Library.

Staying Active During the Pandemic

As the “pause” period in our region extends, it’s more important than ever for everyone to stay active as best they can to maintain their optimum physical and mental health. There are already published articles appearing in PubMed on this topic – for example these recent papers:

1: Chen P, Mao L, Nassis GP, Harmer P, Ainsworth BE, Li F. Coronavirus disease (COVID-19): The need to maintain regular physical activity while taking precautions. J Sport Health Sci. 2020 Mar;9(2):103-104. doi: 10.1016/j.jshs.2020.02.001. Epub 2020 Feb 4. PubMed PMID: 32099716; PubMed Central PMCID: PMC7031771.

2: Jiménez-Pavón D, Carbonell-Baeza A, Lavie CJ. Physical exercise as therapy to fight against the mental and physical consequences of COVID-19 quarantine: Special focus in older people. Prog Cardiovasc Dis. 2020 Mar 24. pii: S0033-0620(20)30063-3. doi: 10.1016/j.pcad.2020.03.009. [Epub ahead of print] PubMed PMID: 32220590; PubMed Central PMCID: PMC7118448.

3: Altena E, Baglioni C, Espie CA, Ellis J, Gavriloff D, Holzinger B, Schlarb A, Frase L, Jernelöv S, Riemann D. Dealing with sleep problems during home confinement due to the COVID-19 outbreak: practical recommendations from a task force of the European CBT-I Academy. J Sleep Res. 2020 Apr 4. doi:10.1111/jsr.13052. [Epub ahead of print] PubMed PMID: 32246787.

The US Department of Health and Human Services, Office of Disease Prevention and Health Promotion, has also released some guidance on “Staying Active While Social Distancing”, as has the American College of Sports Medicine. Their “Exercise is Medicineinitiative has created the Rx for Health series which is available in multiple languages and now includes handouts on: Being Active During the Coronavirus Pandemic and Keeping Children Active During the Coronavirus Pandemic that are intended to be distributed to patients by healthcare providers.

Stay safe, active, and be well everyone – and if you need any research help, just Ask Us!