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07 de Dezembro, 2010

Some PUBMED search tricks: an example on how to find all existing vitamin D intervention studies

Autor: O Primitivo. Categoria: Ciência


I recently saw on Nige’s Diet & Nutrition Blog a wonderful list of all Vitamin D3: Studies from 2005 to present. I think he did a fantastic job in collecting all these studies. But they certainly will be outdated very soon, as several vitamin D studies are now being published on a daily basis. So my idea here is to find out if there is some way to have this list automatically updated, and accessible by some permanent, short URL address. Yes, there is an easy solution for this and I’ll explain below how it is done in 7 easy steps (I’m writing this article in english specially to Nigel, who might find this interesting).

1. First we need to select a list of keywords that appear in the title of all vitamin D studies. I would choose these four keywords: vitamin D; 25-hydroxyvitamin; cholecalciferol; 1,25-dihydroxy. I believe this covers 99,99% of all vitamin D published studies, or maybe 100%. Some other keywords, like "bone density" could also be linked to vitamin D studies that don’t mention "vitamin D" in the title of the article, but I’m excluding this keyword as it could also not be related at all to our objectives.

2. Second, we go to Pubmed search engine. Then we click "Advanced Search". In the Search Builder box, we select Title. And we then write the first keyword "vitamin D" (without the brackets). Then select "OR" and click "Add to Search Box". Now write the second keyword in the Search Builder Box, "25-hydroxyvitamin". Click again "Add to Search Box". Do the same for the last two keywords in the list, cholecalciferol and 1,25-dihydroxy. The Search Box on top should now show (((vitamin d[Title]) OR 25-hydroxyvitamin[Title]) OR cholecalciferol[Title]) OR 1,25-dihydroxy[Title]. Now click Search and you will get a list of the latest +15.590 vitamin D studies. This is quite an impressive listing, which demonstrates the recent importance that is being given to vitamin D research.

3. Now we want to find the full URL that produces the search results we just obtained above. For this purpose, now click "Advanced Search" and then the "Details" link. The Query Translation box contains the following string: ((vitamin d[Title] OR 25-hydroxyvitamin[Title]) OR cholecalciferol[Title]) OR 1,25-dihydroxy[Title]. Click the URL button and you will obtain, in the address bar of the browser, the corresponding URL: "font-size: medium;">4. This is a pretty long URL address, we need a smaller, handy URL to send to our friends and to post on blog posts. This can be achieved with the Bit.Ly utility, which is a method to compress long URLs into smaller ones. Just click here, then copy/paste the long URL above into the Bit.Ly "Shorten Links Here" box, then click the "Shorten" button, and "voila" our final short URL is If you click this link it will get you to all most recent vitamin D studies available. This can be done, of course, for any other keywords you main find interesting.

5. Our search can be further optimized. For example, if you are not a professional researcher, with university access to full papers, and this is my case, you may want to limit/filter your search to only free articles. For this purpose, click the "Free full text" link on the top right, and will get a listing of +3295 freely available vitamin D related articles. And now for some further filtering, I don’t want epidemiological/observational studies, I only want intervention studies with vitamin D. For this, click the link again and then click the"Limits" link located above the Pubmed search box. In the "Type of studies" options, select "Clinical trial" and also "Randomized clinical trial". Finally click the "Search" button in the end of the page (not the "Search" button on top of page).

6. This last search will produce +758 results of vitamin D intervention studies. I don’t know what you think of this but I think these simple search methods are pretty powerful, and cool. To get the full URL of this search, just do as above, click the "Advanced search" link, and then the "Details" link. The corresponding string in the Query Translation box is this one: ((vitamin d[Title] OR 25-hydroxyvitamin[Title]) OR cholecalciferol[Title]) OR 1,25-dihydroxy[Title] AND (Clinical Trial[ptyp] OR Randomized Controlled Trial[ptyp]). Now click the URL button and the full URL will be available in the address bar of your browser, just as we did above. A very long URL: "font-size: medium;">7. Now lets reduce this URL using the Bit.Ly utility gain. Click here, then copy/paste the long URL above into the "Shorten Links Here" box, click the "Shorten" button, and "voila", our final short URL is This permanent short link will give you the current list of all intervention studies related to vitamin D. I don’t know many other tricks using the Pubmed searching features, so if you know of any other cool methods please let me know.

Tags: 1.25-dihydroxy, 25-hydroxyvitamin, cholecalciferol, pubmed, search, tricks, vitamin D

1 comentário a este artigo.

1 | Nigel Kinbrum

07 de Dezembro, 2010, 17:36


Hi. Thanks for that.

Another trick is to create an RSS Feed after setting the search terms & limits.

I shorten links by using the html text tags (minus the first & last space characters).

Cheers, Nige.

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