Reading Articles Referenced Within OpenWetWare

To paraphrase Sigmund Freud,

“Sometimes a reference is just a reference…”

But not all the time. By the time we’re reading an OpenWetWare (OWW) page and notice a reference to a published paper, we’ve come to the page through a search engine. At this point, a reference is no longer a starting point for a new search. It’s now contextually enlivened information.

We want to read it now. Our interest has already been qualified. Searching is behind us. Is this the time to go to another site to read about the article and to find more? For me, at this point, I want to decide how relevant an article is by reading it. “Let me decide!”.

PubMed’s website is where OWW references typically end up. The PubMed ID (PMID) is a common identifier for research articles for most biological research output. The US NIH acts as a proxy for redirecting us to the actual article. If we have rights to read it via online subscription, we eventually get to see it.

As we’ve experienced far too often, getting to the article through PubMed isn’t direct. The process looks something like this:

  1. You see a citation.
  2. You want to read it.
  3. You click the link.
  4. You read the reference.
  5. You click the link.
  6. You go to the publisher’s site.
  7. You click the link.
  8. If your institution has a subscription, you read the article.

Enter Pubget.

Pubget is a service that cuts through this process. It allows you to click on a link and read the article.

Using it, the process gets collapsed to this:

  1. You see a citation.
  2. You want to read it.
  3. You click the link.
  4. If your institution has a subscription, you read the article.

Note the steps. Once click is now required. The rest is all about thinking, wanting, and reading. So. What if some of the power of this service were to be brought to bear within OpenWetWare?

Based upon a request last week, we looked into how Pubget works. With no official affiliation with Pubget, I’ve added a number of features to OWW that now make this possible in an almost invisible manner.

What do you have to do to take advantage of Pubget

If you’re a member of OWW, you can start by going to your preferences page to set your institution. Just log in, click on the “My Preferences” link at the top of the page, and go to the ‘Misc’ tab. It’s the last tab on the right. Look for the list of participating universities here:

Select the name of the institution where your lab is located. Like Pubget itself, this feature will only work when you’re physically working on that network. Once you set this, you need never change it until you graduate! If you’re at home and not at work, pubmed will use the default setting: any subscriptions by your university will be unavailable util you get back to the lab. This isn’t part of OWW’s Orwellian plot to keep you at your bench for as much of your life as possible. It’s a technical issue. At MIT, we use browser certificates that extend this so that I still get access to the same content at home. I’m sure this isn’t universal. But try it and see how it works. We’re evaluating how we can extend this capability over time for other universities. If your university uses VPN connections, you are virtually on your lab’s network: all subscriptions will continue to work.

Even if your university isn’t on the list, this feature will allow you access to the full text of all open source journals such as those published via PLoS.

The effect is that a growing number of OWW lookup features will use this label to pre-set the URL’s you use to ‘cut to the chase’ and make content available when you click and not a few seconds later. If you want to review several articles, those few seconds do add up quickly. In addition to this, Pubget provides a search interface that ‘knows’ the format of many of the most important journals.

What parts of OWW can use Pubget?

General OWW text.

Try this. Edit an OWW article you’ve created containing a pubmed reference. Reformat the reference to use this format:

PMID 12345

Save the document. The text is now a clickable reference. If you’ve set your preference, the article will be opened for you to read if it’s available as a PDF file as well as associated reference information. You can use the PubMed search to find related content as well. Any existing pages using the ‘PMID’ tag will beave the same way.

Biblio References

If you use the Bibio extension for publishing citations, a Pubget link is now present if there’s already a pubmed reference for it. Just click on the link to to read the text.

Pubget Gadgets

A Pubget gadget is a code snippet you can create at the pubget site to provide a search using their service. To create one, go to the pubget site and create it using this url:

To paste it onto your page, do the following:

  1. Create the widget on the Pubget page.
  2. Copy the widget to your clipboard after you create it.
  3. Paste the html code onto an OWW page.
  4. Place an  “<html>” tag right before the code you pasted.
  5. Place an “</html>” tag right after the code you pasted.
  6. Save the page.
  7. Instant widget!

RSS Feeds

A side effect of the way pubget works is that RSS feeds, already supported within OWW, can use the same feature. To create and RSS feed that uses Pubmed, do the following.

  1. Open one of your OWW pages for editing.
  2. Create an RSS feed using the with a search term inside of it like this:<xfeeds>OpenWetWare</xfeeds> (replace OpenWetWare with your text)
  3. Add the ‘bubget’ attribute (pubget=”Y”) inside of the “<xfeeds> tag. The sequence will now look like this:   <xfeeds pubget=”Y”>OpenWetWare</xfeeds>
  4. Save the OWW page

This will now tell the xfeeds extension in OWW to map all of the URL’s in the returned RSS feed to use your specified university tag. The references will now direcly load when you click on them.

There’s a shortcut to do this if you have a page name you want to use as the search term. As an example, consider your user page.

  1. Edit your user page.
  2. Find a place you want to insert the search feed.
  3. Insert the following tag: “{{PubgetRSS}}” (no quotes but with the curly braces)
  4. Save the page. Done!

If anyone sees other places this capability would fit, please let me know.

Also, if anyone has a problem using this feature, let me know. I’m not trying to push one company versus another. But the service to OWW this offers seems worth the effort.



  1. Jakob’s avatar

    Looks very promising. Very few non-US institutions though. How can those be added to PubGet? Or how can PubGet used if the institutions is not yet listed in the list?



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