Keeping up with literature using RSS feeds

In my recent (and very successful) attempt to procrastinate writing my manuscript, I completely revamped my strategy for staying on top of scientific literature. So far I’ve deemed the transition extremely successful 😀 so in further attempt to procrastinate I’ll share my newly found insights.

Like the majority of people that I’ve surveyed (i.e. three colleagues), I used to learn about new publications through email subscriptions to different journals. Other than the Nature-Science-Cell trinity, I was also subscribed to a handful of field-specific journals, several esoteric journals that nobody cares about but me, and bioRxiv (don’t worry, only neuro preprints). In addition, I also set PubMed to send me weekly emails about new papers which match my preset search criteria and I got emails from ResearchGate whenever an author I’m stalking published a new paper.

The problem is evident. I got a lot of emails. What’s worse is that journals can be weekly, bi-weekly, monthly or just plain random (with all the haphazard special editions and news feeds and what-not) and preprints are perpetual. The flow of mails was large and unsystematic, and I unless I tackled them fairly regularly it was tricky to keep track of what I’d seen or save articles for later.

I finally decided that enough was enough. I wanted all of my alerts in one place in one format and synced across all of my devices. The solution – RSS.

What is RSS?

RSS is a backronym for “Rich Site Summary” or “Really Simple Syndication”. An RSS feed contains updated content from a website (e.g. news, social media, blogs, online journals) in a standard format. You can aggregate multiple RSS feeds from different sources into an RSS reader app which automatically syncs new feeds. Readers also let you mark articles as read, save them for later, share them with others, organize them as you please and generally reduce the amount of chaos in the world.

*A backronym is a phrase that claims to be the source of an acronym, sort of a folklore etymology.

Setting up your own RSS protocol requires two things: (1) Choosing an RSS reader and (2) Adding RSS feeds

(1) Choosing an RSS reader

I’m no techie, so I won’t even go there. A quick Google search will provide you with dozens of recommendations, comparisons and endless rants about all of the readers with all of the features for all of the operating systems.

I chose a reader called feedly since it met all of my own criteria, namely:

  • The free version allows me to add a sufficient number of RSS sources (up to 100)
  • It’s compatible with all of my devices (I’m an Apple user, but it also works with Windows, Android etc.)
  • The layout is simple and minimalistic
  • Bonus: it integrates with other applications like Evernote and OneNote, so I can quickly save content to my favourite notes app (#teamOneNote).

To get feedly, you’ll first need to open an account. Afterwards you can either download the feedly extension for Google Chrome or download the feedly app. I installed the desktop app for MacOS and the iOS app for iPhone/iPad.

(2) Adding RSS feeds

After you’ve selected a reader, you can get started with adding RSS feed sources. In feedly, this means creating a “feed” (a topical collection of RSS feed sources), and adding the desired sources inside. I made a feed called “Papers” and added my sources by pasting their RSS URLs into the search bar (more on how to generate these later), but you could also search for your favorite journals or topics directly.

Which RSS feeds to add

We all have slightly different interests and a very different tolerance for general scientific jabber, but I’ll share my own current practice and take from it what you will.

(1) The ‘big name’ journals (Nature, Science, Cell, etc.)

Did you know that a near-complete 3.8 million year-old cranium was found in Ethiopia and recently identified as belonging to hominin species Australopithecus anamensis?

You should. And if you don’t – you’re probably not subscribed to Nature.

Whether or not you want to live under a rock (pun intended) is up to you, but being the nerds that we are we tend to care about general scientific advances. They also give us quick topics of conversation when we’re trying to maneuver regular social interactions .

Regardless, you probably want to monitor when big papers in your field appear in general journals. In any case, these are some major journals that I follow and their RSS feed URLs:

  • Nature: http://www.nature.com/nature/current_issue/rss
  • Science: http://www.sciencemag.org/rss/current.xml
  • Cell: http://www.cell.com/cell/current.rss
  • PNAS: http://www.pnas.org/rss/current.xml

(2) Lower impact journals, field-specific journals and journals read by me and the editor’s mother, e.g.:

  • Nature Methods: http://www.nature.com/nmeth/current_issue/rss
  • Nature communications: http://feeds.nature.com/ncomms/rss/current
  • Nature biotechnology: https://www.nature.com/nbt.rss
  • PLoS Biology: https://journals.plos.org/plosbiology/feed/atom
  • Cell reports: http://www.cell.com/cell-reports/current.rss
  • Nature Neuroscience: https://www.nature.com/neuro.rss
  • Neuron: http://www.cell.com/neuron/inpress.rss
  • Journal of Neuroscience: https://www.jneurosci.org/rss/current.xml
  • ACS Nano
  • Glycobiology
  • Matrix biology

(3) Customized PubMed searches

I want to have the option to see all of the latest publications in the aforementioned journals. However, I also want to make sure that I’m up to date on papers that are highly relevant for me, both in those journals and in others that I’m not following.

I’m assuming the majority of you know how to do a PubMed search that includes keywords, journals or authors e.g. (AMPA[Title]) AND Choquet, Daniel[Author]). You can build a specific PubMed query here. Instead of clicking search, under the search bar click “create RSS” (note: this doesn’t work for me on Safari but does work on Chrome). Open the xml and copy the resulting URL into your feedly search bar:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=1xohA8CjI3Mid0GGMPFAVrZImwF4DEqUvXWszNyfHu3vy0gg2x

I use PubMed to search for keywords (in paper titles or content) that are directly related to my research topic, or to stalk my favourite authors. You can also use this to follow your colleagues ResearchGate style, but then you could also just talk to them directly using your mouth and voice.

(4) bioRxiv

Subscribing to bioRxiv is essentially the same as a peer-reviewed journal, but I thought it deserved its own paragraph so that I could rant a bit.

Sven Truckenbrodt has already shared how instrumental it was for him to publish his research in bioRxiv in this post. The number of preprints being uploaded to bioRxiv is steadily growing and the results are disseminated almost instantly through social media. So if you’re not on Twitter and such, you’ll be miles behind the latest research without following bioRxiv. If it makes you feel more assured, about two thirds of preprints do end up being published and their popularity on the archive correlates quite well with the impact factor of the journal they’re ultimately published in[1]. Needless to say, I’m a fan of the Rxivs.

You can create a bioRxiv RSS feed URL for different topics here. For more advanced users, you can use their export API to make more specific searches.

Reading RSS feeds

Now that you have all of your feeds aggregated in a single reader app, you can unsubscribe from all of those aggravating mails pouring into your inbox every week. No more “News and alerts” or “My NCBI” until the end of time 😀

As for actually reading the feeds, you can do that at your leisure however suits you best. For me, whenever I have a few minutes to kill, I’ll scroll through the titles and triage them. If something isn’t interesting, I’ll immediately mark it as “read” and hide it from the feed. Otherwise, I’ll either click to read the abstract (or if I have the time, go to the webpage for the full paper) or mark it to “read later”. On a phone it’s even more efficient – you can swipe left à la Tinder to mark an item as read and quickly sift through unwanted articles.

Will there be redundancy? Yes. But I don’t see that as a disadvantage. If something pops up on multiple sources, that probably means it’s important for you. Anyhow, swiping away an article you’ve already seen takes a fraction of a second.

Once I’m sitting at my laptop and have some more time, I’ll look through papers I’ve saved for later and open them on the journal’s website for some more proper reading and to save to my reference manager (Mendeley, which I wrote about in this post).

One app to rule them all

I’ve made it clear that I derive a lot of pleasure from reducing entropy. But other than that, I really do feel that I’ve been more successful at staying on top of literature since switching to an RSS reader. It was also immensely satisfying to unsubscribe from all the email updates and see my clean empty inbox.

If I’ve managed to convince you to convert, I’d be happy to hear what you think and even more happy if you find any more tricks and tools for improvement.

 

[1] Abdill, R.J., and Blekhman, R. (2019). Tracking the popularity and outcomes of all bioRxiv preprints. Elife 8, 1–21.

Tal Dankovich

PhD candidate, Neuroscience, University Medical Center Göttingen (UMG)

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