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Bridging the PubMed Gap for Genetics and Health

Posted by: Ron Martin on 3/6/2010

PubMed® is a valuable online resource freely provided by the National Library of Medicine which allows users to browse through more than 19 million journal article citations.

Although many visitors to their site at www.pubmed.gov use simple free-text searches to find relevant articles, more dedicated users can learn advanced searching techniques as explained by various tutorials found there.

For highly specific queries, the number of search results can be kept to a manageable number of citations.  However, for larger result sets, PubMed® does not provide a way to sort the results by subtopics.

A breakout by subtopics could help identify not only individual variables of interest, but also general classes of variables like health conditions, or risk modifiers like drugs or dietary practices, or lifestyle variables such as exercise or tobacco use, or genetic variables such as mutations or gene expression, etc.

Although this seems like a worthwhile objective for PubMed's future, in the meantime, an impressive model for such as a system has already been developed by Nutrigenetics Unlimited Inc., and is available at www.nutrigenetics.net.

The display of subtopics enables users to quickly scan through the numerous relationships which always exist in any large search result, rather than be limited to scratching the surface of recent articles only, or limited to only a narrowly-focused subset in order to keep the list short.

The key is to index each article using a controlled vocabulary of standardized indexing terms, which also allows subtopic breakouts – not only for individual topics, but also for combinations of multiple topics of the user's choosing.

For instance, when starting with a single topic, an alphabetical list (index) of subtopics can be viewed which also reports the number of citations for each subtopic, and further displays major synonyms – to assist the user in recognizing related content that would otherwise be obscured.  Subtopic listings can also be created "on-the-fly" for combinations of topics.  Stepwise use of such listings enables "drill-down" for discovery of relationships between topics which would otherwise easily escape attention.

The database at nutrigenetics.net contains an extensive subset of more than 300,000 citations from PubMed® spanning the last 10+ years, with links to more than 90,000 free PDF article copies.  These citations are relevant to the interplay between genetics, health, and our environment – including but not limited to nutrition.  Included are citations relevant to health conditions, genetic testing, nutrition research, nutrigenetics, nutrigenomics, gene expression, lifestyle, stress, pharmaceuticals (pharmacogenetics), and specific genes and gene variants – plus social environment, mental health, behavior, ethics, and much more.

Big advantages to using the nutrigenetics.net database include: 

  1. controlled vocabulary,
  2. user-selectable subtopic listings (indexes), and
  3. cross-referencing with synonyms while searching and when viewing subtopics. 

Use of the controlled vocabulary goes a long way toward solving the problem of inconsistent terminology, but the display of synonyms is an important feature which enables users to recognize relevant text which may otherwise be overlooked.  Without such assistance, inconsistencies in terminology is especially challenging for genes and gene variants.


The controlled vocabulary is loosely based on the National Library of Medicine's Medical Subject Headings (www.nlm.nih.gov/mesh/MBrowser.html), together with the use of standardized gene symbols  (www.genenames.org) and synonyms (www.genenames.org and www.ncbi.nlm.nih.gov/omim).

The nutrigenetics.net database is making the relationships between our genetics (nature) and our environment (nurture) much more accessible to everyone, including students, educators, journalists, companies, librarians and researchers as well as to physicians, nurses, pharmacists, dietitians, dentists, genetic counselors, and other health professionals. The goal is to inform the public, equip professionals, and encourage public/professional partnerships.

 

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