Stay on top of the literature by automating PubMed feeds

Piles of scientific papers. Despite the ever-rising bar to publish scientific papers, it seems that the scientific community is accelerating with the rate of publication, rather than slowing down or even maintaining pace. This is no doubt due to the increasing numbers of online-only journals that promise rapid acceptance times with minimal formatting and production overhead. At times it may feel impossible to actually keep track of where a field is going because by the time you've read last week's hotlist papers, there are suddenly another five showing up on PubMed, Google Scholar or Web of Science. On top of that, if you haven't checked "that one" journal in a while, you may end up missing an important paper until its already old news because you didn't choose just the right keywords in your search. Well, suffer no more. The following how-to guide will help you to stay on top of papers in your field by utilizing two important resources: PubMed's search engine (without question the most trustable source for legitimate primary sources for the biological [and other] sciences) and IFTTT ("If This, then That"), a website that helps you to automate tasks through the internet. The best part: it's all free.

A how-to guide on using IFTTT to automate scientific literature searches with PubMed:

Step 1. First, go to PubMed.com and input search terms that usually pick up papers that you are interested in. This may be a single keyword, combinations of keywords, or maybe even the name of a specific PI that you want to follow. For the purpose of this guide, I will search for "mitochondria AND apoptosis": Screen Shot 2016-01-24 at 8.13.00 PM   Step 2. Directly under the search bar, click "Create RSS" and update the dropdown field to 100: Screen Shot 2016-01-24 at 8.14.06 PM   Step 3. Click "Create RSS" and you will be presented with an orange button that says "XML" Screen Shot 2016-01-24 at 8.14.56 PM   Step 4. Once you click the XML button, select the address bar and copy the entire address of the XML/RSS feed to your clipboard (Control/Command + C): Screen Shot 2016-01-24 at 8.15.52 PM   Step 5. Make an account at IFTTT.com. It's free and takes just a few moments. (This blog is unaffiliated with IFTTT, it's just a very nice tool)   Step 6. Login to your account, to the immediate right of the search bar at the top click "My Recipes" Screen Shot 2016-01-24 at 8.27.54 PM   Step 7. Once at "My Recipes" click the big blue button at the right that says "Create a Recipe" Screen Shot 2016-01-24 at 7.49.21 PM   Step 8. Click the bright blue "this" link Screen Shot 2016-01-24 at 7.57.14 PM   Step 9. Scroll down and choose the RSS/orange "Feed" icon Screen Shot 2016-01-24 at 7.58.15 PM   Step 10. You will be presented with two options, choose the left option that says "New feed item" Screen Shot 2016-01-24 at 8.00.03 PM   Step 11. Paste in the copied XML/RSS address and click "Create Trigger" Screen Shot 2016-01-24 at 8.29.59 PM   Step 12. Click the bright blue "that" link Screen Shot 2016-01-24 at 8.31.46 PM   Step 13. Scroll down and choose the "Email" icon Screen Shot 2016-01-24 at 8.33.06 PM   Step 14. Click "Send me an email" Screen Shot 2016-01-24 at 8.33.53 PM   Step 15. You may leave the next area as-is and click "Create Action," or you can add keywords to the subject/body that you might use for organizing your email inboxes. I leave it as-is and just sort all emails coming from IFTTT into its own inbox. Screen Shot 2016-01-24 at 8.34.48 PM   Step 16. Click "Create Recipe" and you're done. Every day, as your recipe runs, it will email you with one new email (with title, author list, journal, abstract and PMID) for each item on your PubMed RSS feed directly to the address that you registered at IFTTT. Screen Shot 2016-01-24 at 8.36.48 PM

A few notes:

  • Of course you can use the RSS feed taken from PubMed and use it in an RSS reader. The reason that I use email is that I have a GMail account as my primary email, and it's tough to beat the Google search functionality. Plus, I am often in my email, so having all of these abstracts and PubMed links directly at hand is extremely convenient.
  • You also don't have to use the Email automation function in IFTTT. If you prefer, you can choose to do Evernote, Google Drive, etc. I have found Email to be useful for the reasons listed above, but be creative and find something that works best for you.
  • It takes about one day from when you create the recipe for it to start sending you email, so do not be disheartened if you do not immediately get emails from your PubMed feed.
  • Depending on how broad or specific your search terms are you may end up with dozens or hundreds of new papers each day, so choose wisely. I generally have just the key protein or specific disease I am interested/studying at the time.
  • Some days you will get no emails, some days you will get many. If you have multiple feeds, then some days you will have thirty from one and two from another. If you study a very, very specific protein that only has a few labs in the world focusing on it, it may take weeks or months for a new paper to be sent to you.
  • You will only get emails from your feed once per day. For me, this is usually early morning.
  Hopefully this guide will keep you up to date on the publications in your field. I have found it extremely helpful in the past when a paper comes out that happens to "scoop" a portion of a manuscript I am writing, so I can quickly rephrase some of my experiments to highlight its unique relevance and avoid having to explain to reviewers later why I am not just reiterating the same point as an already published paper. Unfortunately, this has happened numerous times, including being notified of a paper that covered almost 75% of the exact section of my dissertation I had been writing in that moment. I hope that does not happen to any of you, and with this method of keeping up on the literature, I think you will be well prepared to predict the direction of your field and hopefully avoid such situations more effectively. Happy reading, JRY  

1 thought on “Stay on top of the literature by automating PubMed feeds”

  1. I wonder about organ transplantasjon and stem cells. I have the idea of using better technology for having the patient supported by machines or even i readed of animal supported functions? I n this time you get could be possible to use the sick organ for stem cell repair.I wonder about an article i readed.they used stem cells in a heart donated.

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