Don’t Let Your Search Get Lost In Translation

When conducting a literature search on a topic, many times the search is conducted in more than one database for more comprehensive results. And in the case of systematic reviews, such a practice is required.

Even more challenging, when it comes to systematic reviews, is that the searches in each database should be as similar to one another as possible. The process of taking an original search strategy from one database and making only necessary changes (controlled vocabulary, syntax, field codes), adapt the strategy to another database is referred to as “search translation.”

The Parts of a Search

There are several parts to complex literature searches that combine multiple elements: Boolean operators, nesting, controlled vocabulary, field codes, quotations, proximity, and special operators.

Boolean Operators

Boolean Operators (AND, OR, and NOT) are the basis of how to combine concepts to create a search.

While nearly all databases use Boolean operators in the same manner and meaning, it’s important to know when capitalization is necessary and when it is not.

Nesting

Nesting uses parentheses much in the same way they are used in Algebra — that is, whatever is inside the pair of parentheses must be done first, and from there a search (just like math), will be conducted from left-to-right.

Since nesting is about how to read and execute a search, it typically will not change between databases.

Controlled Vocabulary

Controlled vocabulary refers to the set dictionary of terms for that database, such as MeSH (Medical Subject Headings) and EmTree. MeSH is the National Library of Medicine’s controlled vocabulary, and they create the MeSH terms for PubMed. These terms may not always be identical to the MeSH terms found in MEDLINE on another platform though, and they require different identification.

Unfortunately there is no easy way to translate these terms, but using the built in databases (MeSH Database, MEDLINE Term Finder, EmTree Database, etc) you can quickly find the most closely aligned term to use.

Field Codes

Field codes are essentially the special codes for each database that tell the database where to search for that term. For example [tiab] in PubMed tells the database to search that term in the title and abstract fields only. In MEDLINE the title/abstract field code is .ti,ab, whereas in Embase it is :ti,ab.

Quotations

In order to search for a specific phrase searches must use quotations. However, depending on the database, they may require double quotations (“smart quotes”), straight quotations, or single quotations.

Proximity

Proximity operators (also called adjacency in some databases) are essentially a middle-ground between searching across an entire record and specific quotations. They allow the user to select how close they want to two terms to appear in a record. Every database uses slightly different proximity operators and syntax, and some have strict rules with how they can be used.

Special Operators

Special Operators are operators that can be added to search terms to modify what is searched. Examples of special operators are truncation and wildcards, which expand the variations of the specified term that are searched. An asterisk (*) is the common operator for truncation in many databases.

Where to Start

All the information on how to search each database according to its own rules and/or the rules of an online platform it resides on can be found in the database/platform’s Help section.

Typically, this translation of search strategies is done by a librarian manually but automated/semi-automated tools are being gradually introduced. A beta version of such tool (Query Translation) is currently available in Embase.com, the Elsevier interface of the Embase database. It will assist in “translating” PubMed searches into the Embase.com search syntax.

The tool allows entering a search term or the whole search strategy (query) and get it translated to Embase syntax.


Developments in Cancer Diagnostics, Treatment, Diet

At the very end of 2023, new developments in different areas of oncology were reported in the literature; a few are highlighted below.

New about old in cancer diagnostics and treatment

Drug repurposing is one of the established practices in cancer therapy. Researchers at the Icahn School of Medicine at Mount Sinai conducted an animal study aimed at using an allergy drug in cancer treatment. The study was published in Nature.

A new study established that needle biopsy, an indispensable tool for the diagnosis of breast cancer, itself triggered cellular changes that later promoted cancer spread. The study was published in Cell Reports Medicine.

A new retrospective cohort study showed that the use of proper diagnostic tools helped establish that patients with benign breast disease were more likely to get breast cancer than the general population. The study was published in JAMA Surgery.

Artificial Intelligence (AI) is increasingly used for prediction of cancer patients’ outcomes

A new study by Northwestern University researchers employed an artificial intelligence (AI) tool that ensured more precision in predicting outcomes in breast cancer patients, thus sparing them unnecessary chemotherapy treatments. The study was published in Nature Medicine.

Another AI model created at UT Southwestern Medical Center analyzed cell spatial organization to increase the precision of patient diagnoses and prognoses, paving the way to improved personalized treatment approaches. This study was published in Nature Communications.

Interesting approaches emerge in cancer treatment

Researchers from the Rare Cancers Genomics Team at the International Agency for Research on Cancer (IARC) and partner institutions created “mini-tumours”, small versions of a rare and “obscure” neuroendocrine cancer that can create a “test” environment for the investigation of the development of this cancer and the ways of treating it. The study was published in Cancer Cell.

Researchers from the U.S. found a way to destroy cancer cells by vibration, stimulating aminocyanine molecules with near-infrared light. That “caused them to vibrate in sync, enough to break apart the membranes of cancer cells.” The study was published in Nature Chemistry

A multi-institutional team of researchers has received federal funding to develop a bacterial therapeutic for precise and less expensive cancer treatment through a single dose.


New research into the dietary approaches to cancer was reported

Recent research into diet effects on cancer found that white navy beans had a beneficial effect on colon cancer survivors. This finding may have an impact on the prevention of colon cancer and better outcomes for colon cancer survivors. The results of a clinical trial were published in eBioMedicine.

A systematic review and meta-analysis of observational studies conducted by British researchers found that intake of raw carrots decreases cancer risk across different cancer types by 10-20%. The study was published in Critical Reviews in Food Science and Nutrition.

Another study on a dietary intervention established a beneficial effect of Flaxseed for decreasing breast cancer risk. The study was published in Microbiology Spectrum.

On the other hand, some foods may be harmful and increase cancer risk. A new prospective study found that higher intakes of alcohol and white bread are associated with increased colorectal cancer risk. This study was published in Nutrients.

And another study on the adverse effects of certain foods found that ultraprocessed foods may increase the risk of head and neck as well as esophageal cancers. The study was published in the European Journal of Nutrition.




2024 MeSH Update and PubMed Year-End Activities

Tis the season…for the National Library of Medicine’s (NLM) Annual MeSH Processing for 2024!!

Every November-December brings the much anticipated annual changes to PubMed’s MeSH (Medical Subject Headings) structure for the controlled vocabulary associated with MEDLINE.

Types of MeSH Updates

Some MeSH, subheadings, and supplementary concepts cease to be, some are renamed, new MeSH and subheadings are incorporated, and some MeSH change their location in the MeSH hierarchical tree structure (e.g. a MeSH moves under a different broader heading) or combine with other terms. Some Supplemental Concepts are also upgraded to a MeSH Descriptor status. Below are some of the types of changes and updates made during the Annual MeSH Update.

  • New MeSH Descriptors — brand new MeSH Descriptors
  • New Supplementary Concepts — brand new terms that currently do not warrant a full MeSH Descriptor
  • Changed MeSH Descriptors — MeSH terms that were modified (either by name or hierarchical location), also referred to as the “Preferred Term”
  • Upgraded MeSH Descriptors — terms that moved from Supplementary Concepts to MeSH Descriptors
  • Combined Terms — either MeSH Descriptors or Supplementary Concepts that were combined with other terms under a single term
  • Split Terms — either MeSH Descriptors or Supplementary Concepts that are split to expand the level of description and detail
  • Removed Terms — either MeSH Descriptors or Supplementary Concepts that were removed, either due to being combined, upgraded, or renamed

What’s New in 2024

The 2024 MeSH updates includes a variety of important and much-needed updates!

One of the biggest and most needed expansion in the 2024 update is that of the Psychological Stress concept, with dozens of new MesH Descriptors within the concept of Psychological Stress, including:

  • Coping Skills
  • Psychological Growth
  • Financial Strain
  • Psychological Recovery
  • School Shooting
  • Stress Experience

Impacts on Searching PubMed

MeSH structure changes may affect already saved searches, including My NCBI alerts; for example ceased in 2024 MeSH may be part of your search strategy designed/saved in the previous years and the deleted/ceased to be term will not retrieve any references.

If you have searches saved in your My NCBI account and/or you are getting PubMed e-mail alerts, or if you need to update your Systematic Review based on your previous search strategy, you may want to consult a Research Informationist to ensure your saved searches are not affected by the annual changes in the MeSH terminology. Don’t hesitate to ASK US!

A Note by the National Library of Medicine says: “Typically, NLM does not retroactively re-index MEDLINE citations with new MeSH heading concepts. Therefore, searching PubMed for a new MeSH term tagged with [mh] or [majr] effectively limits retrieval to citations indexed after the term was introduced. Searchers may consult the MeSH database to see the previous indexing terms most likely used for a particular concept before the new MeSH heading was introduced. For terms without previous indexing information, consider the next broader term(s) in the MeSH hierarchy. For more searching guidance, see the on-demand class MeSH Changes and PubMed Searching.