Frequently Asked Questions

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Q - What is the easiest way to browse our database?

A - For those who wish to easily find some interesting articles relevant to genetics/genomics and health, simply click on one of the large red-colored buttons on our homepage, such as the one with selected articles for members of The Public (https://nutrigenetics.net/Home/ThePublic.aspx). All article titles shown are links to the corresponding PubMed.gov records. For casual visitors who have not logged in, 7 recent article titles are displayed; but after logging in (which is free on weekends, U.S. Pacific time as shown on the login page), then literally hundreds of interesting article titles are shown for extremely easy browsing.

 

Q - What makes our database unique?

A - Our database is a large subset of PubMed article references relevant to human genetics and related "omics," but further indexed using a controlled vocabulary. Our use of standardized terminology is especially helpful for identifying genes and genetic variants. It also allows users to generate their own alphabetical list of subtopics for any given topic, or even more importantly, for combinations of multiple topics. Sequential, stepwise use of such indexes ("drill-down indexing") allows discovery of otherwise hidden relationships between genes, health conditions, and potential risk modifiers. See tutorial.

 

Q - Since our database is a subset of PubMed, what benefits are provided over using PubMed alone?

A - Besides our lists of "selected recent titles" found via our homepage links, our database provides the following advantages:

  1) Drill-down discovery of otherwise hidden relationships between genes, health conditions, and potential risk modifiers (see online tutorial);

  2) Umbrella topics like Pharmacogenetics or Nutrition, which contain all articles mentioning drugs or diet-related items, respectively, so that when viewing an index, there is less chance of overlooking an important relationship;

  3) Standardized terminology (controlled vocabulary) is helpful for all topics, but especially for both finding genes and gene variants;

  4) Synonyms for many topics are provided in our Indexes, which is helpful for recognizing the alternative terminology used by the various authors;

  5) Grouping of gene variants with their corresponding genes when viewing an Index is extremely helpful, especially for articles mentioning isolated "rs numbers";

  6) All rs numbers cited within PubMed for human gene variants are included in our database (except for newest items pending), and all articles mentioning them in titles or abstracts can be found by creating an Index or a Search using the following umbrella topic: rs Numbers Cited;

  7) Gene variants testable by direct-to-consumer companies are indicated with a double-asterisk in the Indexes. This is extremely helpful for those who have already been tested, or who may wish to be tested, or for Professionals who may wish to recommend or evaluate such testing;

  8) For Health Conditions, our Indexes indicate with a double-asterisk those topics which represent potential risk modifiers/environmental variables which can, in some cases, modify risks either beneficially or detrimentally. Genes/gene variants which are mentioned are also displayed;

  9) For Risk Modifiers/Environmental Variables, our Indexes indicate which health conditions, and which genes/gene variants are also mentioned;

 10) For Genes/Gene Variants, our Indexes indicate which health conditions, and which risk modifiers/environmental variables are also mentioned. (Note: Genes/gene variants are grouped separately at the bottom of our Indexes.)

 

Q - What is PubMed®, and how extensive is our subset?

A - PubMed® is the online version of the National Library of Medicine's database of health-related journal articles from around the world (PubMed.gov). Our database contains a genetics-related subset of well over 1,700,000 references spanning the years 2000 to the present, with an average of more than 150 newly-published articles being added every single day.

 

Q - What criteria is used to select articles for inclusion in our database?

A - We consider all of the PubMed articles which mention human genes, genetics, polymorphisms, mutations, or gene expression in their titles or abstracts, or in PubMed's own indexing system of MeSH terms (Medical Subject Headings). This is further augmented by our own proprietary search criteria which includes terms like genomics, epigenetics, nutrigenetics, nutrigenomics, pharmacogenetics, pharmacogenomics, plus many more, including any of the numerous rs numbers (reference SNP ID numbers) for genetic variants such as rs9939609, etc., as further described in the NCBI SNP database at: https://www.ncbi.nlm.nih.gov/snp/ (note that this database is often described as dbSNP; note also that "SNP" usually refers to "single nucleotide polymorphism" and is commonly verbalized like the word "snip" -- however, the dbSNP database itself is now using "SNV" for "single nucleotide variants" since this term is more general, and applies to both common variants like polymorphisms per se, and to uncommon substitutions which are often called mutations).

 

Q - Search results show the article titles, but can the journal citations also be displayed?

A - Yes; to display more complete citations for "Search" results, simply click on "View Printer-Friendly Version", located just below the Go button, which then shows the journal name, the year/volume/page(s), and the PubMed ID number (PMID) for each article title.

 

Q - Many of the citations in our database are marked as "Free." How can these be downloaded?

A - Click on the journal title, which takes you to PubMed. Click on the link found there which says "Free," or on the link to the publisher's website.

 

Q How can an article copy be obtained if it's not free?

A You can request an "inter-library loan" through your local reference librarian, or you can click on one of the links found on the article's PubMed page, and purchase a copy online.

 

Q - What percentage of the articles cited in our database are available as free downloads?

A - Overall, approximately 40% of all of the articles cited in our database are available as free PDF downloads (more than 700,000 free articles total).

 

Q - Can search results be limited to only those articles for which free downloads are available?

A - The term "Free" (but without the quotation marks) can be used as one of the topics of a search (for article titles with links to PubMed), but "Free" is not functional when creating an index. Knowing which articles are available as free PDFs (or free full-text) can be helpful when looking for general background information, but limiting your search results to only those articles which are free can easily result in missing many potentially important articles.

 

Q - Is the database at Nutrigenetics.net curated manually, or automatically, and how often does it get updated?

A - We use a proprietary combination of both manual and semi-automated processes for identifying relevant PubMed records, and for indexing them. PubMed initially uses full-text indexing, followed sometime later with the addition of MeSH terms for most of their articles. In contrast to full-text indexing, the Nutrigenetics.net database uses only standardized terminology (controlled vocabulary) for indexing. Although this requires extra effort, it thereby enables our database users to create their own user-defined list of subtopics (index) for any given topic, or for any given combination of topics. Some delay in indexing is therefore unavoidable, and the frequency of indexing for specific topics is variable. It should be noted, however, that we do not aspire to replace or compete with PubMed, but rather to augment and further enhance it. Our controlled-vocabulary indexing and cross-reference tools for synonyms are not otherwise available in PubMed, and are especially helpful for genes -- and in particular, for genetic variants. We’re steadily adding new topics to our database, and further enhancing our indexing, including deeper searches and cross-referencing of additional variations in terminology. Please submit any suggestions or requests you may have to info@nutrigenetics.net.


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