New Spin on Mystery Location Game with Periscope

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Author: Judy

The Basic Concept

The conventional Mystery Hangout or Mystery Skype has two classes simultaneously using the platform of choice, Google Hangout or Skype, to guess the location of the other school using yes/no questions. Many are familiar with the concept and plenty of information can be found online for running these class activities. Now Periscope offers a new spin on the idea.

Screen shot from the Twitter feed of the app

Two colleagues in advance who both have the Periscope app on their devices (iPhone, Android, iPad, etc.) make arrangements in advance. One colleague at Location 1 is in a place that does not obviously give away the location but has some hints available to show as the game progresses. In the classroom where students will be trying to guess the location, the teacher, library-media specialist, or IT coach has the selected device hooked up for projection and joins the Periscope just as the colleague starts the broadcast.

Some Tips

1) In advance of the Mystery Periscope (aka Mystery Scope), the “scoper” could put on a website or blog some pictures that won’t give away the location but offer some enticement to generate student interest. This step can also be skipped.

2) The “scoper” is on site at the location. The beauty of using the app as opposed to the standard Mystery Hangout or Mystery Skype is the “scoper” can easily move around, be on location out-of-doors, and make adjustments of what to show on the camera as the guessers text in questions.

3) The “scoper” could be prepared as the guessers come close to identifying the location to show a famous landmark at the site of the scope. Once the location is guessed, the “scoper” can tell about the landmark and more about the location. At this point, the students can continue to prepare questions or responses for the person showing the broadcast, who can text in to the “scoper” the students’ suggestions to keep the momentum going.

4) ** Important** The “scoper” needs to turn off Location setting in Periscoper before starting the broadcast.

See the first icon (up arrow) in the below image. The “scoper” would click and toggle until “precise location is turned off ” before the broadcast is started.

The second icon can be tapped if the “scoper” wants the broadcast private and wants to select who can see it from the list of followers, with the list popping up of followers once the icon is tapped. The third icon allows the user to determine who can chat (text in comments): anyone or just those selected by the “scoper.”

5) Time zones, which are often a hangup in organizing Mystery Location events with Skype or Google Hangout are less of an issue when using Periscope. The person doing the broadcast can go live any time that is convenient. Granted, this is just one class or perhaps more joining in to guess the location, but the person doing the broadcast is not in a school setting and nor should the person be at home. A setting convenient for the “scoper” that will be of interest to the students should be used. For instance, if I were doing the scope for young students in elementary school, I might be at Monterey Aquarium or the Bronx Zoo. For older students in a social studies class, I might be on the mall at Washington DC ready to show and speak about the Lincoln Memorial after the students figured out the location from me just standing on the mall but not showing any of the monuments until the location were identified.

How I Can Help

I am willing and able to go to landmarks, places of interest, and places that will generate discussion for the students viewing the scope. For instance, I could be on site at one of the landmarks in my own state or a neighboring state and because I travel often, I could arrange the scope per where I will be and input from the person who will be showing the scope to the specified audience.

Guess the Location

I am throwing in some screen captures from recent Periscopes I have done. Most of my broadcasts start with my location, but I would change  the format for a Mystery Location and not use that as a opening.

So here are some images from places I recently scoped with Periscope. See if you can figure out where I was.

Not quite enough information to figure out the location, at least in most cases, but images like these can be put on a blog in advance to pique student interest before the Mystery Location Scope. They can also be captured afterwards in a blog post to continue the discussion and add more information based on student interest and comments during the scope.
For more ideas about using Periscope, see my blog post, “Around the World in 24 Hours.” That post suggests ways to use the app for cultural experiences, studying famous places, and learning about natural wonders of the world.
For now, I simply offer the idea of a new spin on the conventional Mystery Skypes and Google Hangouts by using Periscope, which gives the person on the other end the freedom to move around and decide where to go based the comments texted in during the scope. The use of Periscope’s hearts can also figure in, with the person who is showing the broadcast tapping on the screen to send hearts based on how well the students are guessing the location.
So have you used Perisocpe yet? What are your thoughts and ideas for using this app? Do you think the app could put a new spin on Mystery Location games? 
Here are two examples of a Periscope I created and uploaded to YouTube, while in DC. Now the app also offers a way to save both the scope and comments, but at the time that I created these two, was not yet launched. I offer these two example to point out how a scoper working with a class on a Mystery Location game can offer insights into historical places and monuments. 

This post is crossed posted on one of my other blogs.

No Minced Words & a Few Sniffles Were Detected at UX Speakeasy

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Author: Lisa C. Kaczmarczyk

Some people were feeling emotional at last night’s UX Speakeasy.  If the amazing artwork didn’t get you, the starry sky would have done it for sure. It was a lovely outdoor venue at SILO in Maker’s Quarter in the heart of downtown San Diego. Perfect setting for this particular event. Last night was primarily a going away celebration for Aaron Irizarry who is one of the founding members of the group.

About 3 years ago, Aaron was one of 13 women and men who decided that San Diego really needed to build community for  UX (User Experience) professionals. I’ve been told there was a feeling that

something was missing – people worked in UX in San Diego but didn’t know each other, didn’t hang out together, didn’t realize there were quite a few jobs in UX, didn’t recognize the opportunities to build a career here in UX.

Clearly they were on to something because in no time the group was maxing out space in larger and larger venues. These days we have to regularly put limits on monthly meetings in the range of 80-100 people because it’s hard to find space to fit everyone interested in attending. The original group of 13 put themselves out in pursuit of a vision, and according to a tribute last night, Aaron was in the thick of all the early activities, taking leadership positions sometimes on short notice. In those days, there weren’t the teams of volunteers and enthusiastic members there are today.

So when Aaron spoke about his experiences here, and said to the crowd “Be grateful you have a community of people you can connect with on a regular basis” I wasn’t surprised to see some people looking almost teary eyed.

A secondary, and related reason for the meetup last night was the coincidentally timed release of Aaron’s Book “Discussing Design”. An overarching theme of his conversation about it was the importance of learning to have the “right” conversations. By way of example, Aaron explained how community contributed to the appearance of this book. He said that a casual conversation led to a blog post, which led to a conference proposal, which led to the book being written. Things happen when we share and explore ideas, pursue opportunities and do it with others in community.

Sometimes it wasn’t clear to me when Aaron was speaking about the book or on a wider scale, but it doesn’t really matter because the point is the same: it’s critically important that technical professionals learn how to communicate better about our work. When people speak in buzz words or stock phrases no one knows what is really going on.

Aaron said he wanted to vomit – or something to that effect – when someone says “Can you make that pop more?”.  Rather…find out: What is working, not working exactly? What is it that makes you feel it isn’t going to work for our persona?

Never one to mince words, Aaron continued,

 “We need to set the ground work for those conversations. We need to learn how to talk about our work. It doesn’t matter how skilled you are, you’ll just be another talented asshole”.

Although he was focused on Design, I was thinking more broadly. Conversations are hard; confrontations suck (that’s Aaron again being direct about what we all know). I’d like to read Aaron’s book because it appears to be about the topic of setting the ground for those hard conversations. I’d like to read Aaron’s perspective on the matter. I’d like to see how it is similar and different from other writings on technical and science communication.

Bringing the conversation back around to why all 80+ of us were there last night, Aaron wrapped up his farewell remarks by reminding everyone that they need to understand the value of this community; it’s not just a monthly party. It’s an opportunity for support and finding new ways to frame important conversations.

An Innocent Visit to a Women in Tech Group Leads to An Unplanned Time Warp

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Author: Lisa C. Kaczmarczyk

Why are we still asking the same questions about women and technology?

Somewhere along the line when I wasn’t paying attention, I passed through an unseen door into a place where I’m now looking backwards as much as forward when it comes to women in tech. I have been noticing this for quite some time but it really smacked me in the face a few weeks ago when I attended a meeting of a new, small, group of mostly tech industry professionals. Women, the vast majority of whom were in their 20s and 30s.

Without planning it, the few of us who were not Millennials found ourselves clumping together randomly throughout the evening. Not all at once, but over and over I found myself having similar conversations with post 40-somethings about differences in our perspective about the issues and concerns of women in tech. We compared notes about what happens when you’ve been around long enough to see what lies beyond the ideal of a meritocracy in tech.

The larger group formed, from what I can tell, rather spontaneously, as a result of a few women wanting a smaller more intimate space for women than currently exists in larger social & networking groups. This was their second meeting and part of the conversation was about what topics they cared most about. Creating a female oriented space. Work-Life Balance. Designing Your Environment (where “environment” is broadly defined to refer to “world” and “life”).  Several people noted that they weren’t into some of the more traditionally male associated networking activities that center around “hanging out and drinking and kegs”.

Now that I find myself a holder of “institutional memory” I am having weird flashbacks.

Back in the 1980s (the oh so distant past when it comes to tech) I remember having very similar discussions from the context of wanting to break into the tech industry, to be accepted for what I could do rather than what I might look like (i.e. female). Business wasn’t about social activism was it? I flip flopped from wanting to be one of the guys in order to be accepted, to wanting to have a place to talk about why that approach never seemed to really work. Determined to succeed by being the best technically and assuming that if I ignored my gender everyone else would have to as well.

Anyone remember Andrew Dice Clay? The guys in my group of developers thought he was hysterical and watched his misogynist Stand Up at off site socializing events, checking with me to see if I was going to fit in by laughing along with them. I remember “Lisa, what do you think? He’s funny, right? … See, Lisa is ok with it”. I was offended but didn’t say a word. I had lots of reasons. Reason: I needed a job. Reason: I should let things roll off. Reason: I was afraid of not being accepted. However, I was a feminist outside of the office. I once took off for a weekend to attend a rally in Washington DC and when I came back, someone found out, and two of the guys refused to speak to me for weeks. It was a lousy way to tackle work life balance.

There was a divided opinion at the recent women’s meeting about whether it was better to go along with male dominated structures and systems, or whether it was better to take explicitly women focused approaches when working for change. The arguments pro and con were the same ones I heard 25 years ago. The concerns about the effect on men were the same ones I heard 25 years ago. The implicit fears about what taking a stand or speaking out would mean for one’s career were the same ones I heard 25 years ago.

Several of the women at the meeting worked for a company that makes a cutting edge tech product for athletes. They were discussing their jobs enthusiastically. One of the women listening to them pointed out that the demographic for that company’s products is 18-30 year old males. A discussion ensued about why that was, and if the company could expand their market demographic in order to stay competitive. No longer the only player in their market, the competition is heating up. The entire group discussed what men or women might do with the company’s products. No one in the room (that I remember) had bought the product for themselves, although a few had bought it for a male they knew. It seemed clear to me that here was an opportunity to do something good for business and for women in tech by, at the very least, changing the product’s marketing.

As I later surmised, fears of rocking the boat are sometimes subtle. There wasn’t much enthusiasm for altering the existing product or marketing. So I asked if any of the women working in this male dominated tech company on a male oriented product, had any thoughts about the contradiction (?) of their employment situation while we were sitting here in a group explicitly devoted to supporting women in the tech design business?

The initial response was a shocked look and a pause. Then “We have to focus on our target user”. Oh, to know history! In a competitive environment, that phrase is the reason many initially successful companies decline and become irrelevant. Nothing related specifically to gender there; it’s a business and marketing basic.  Yet someone added, unprompted and dismissively : “It isn’t a business issue”.  I had to restrain myself from beating my head on the table.

Sadly, that wasn’t the last of my throwback moments. Later in the same discussion someone said, as a reason for not changing the existing product / marketing: “Women aren’t interested in technology”. As Millennials love to say: OMG.

If I had ever been in doubt about whether or not there were still serious issues for women starting out in tech, (and for the record, I wasn’t), the fact that we are having the same conversations, the same fears and denials as we had in the 80s would have dispelled them.

By the way, in the 1980s I remember women who were then in their 40s and 50s saying the same darned things about how they were hearing many of the same darned questions and conversations they heard in the 1960s about women with career ambitions in business.

Oddly enough, I initially attended this meeting not knowing if this was the right place for me. It had not so much to do with the idea of a women focused group, but more because of the fact that I felt so much older than most of the women there. I have experiences and perspective that only come with having been around the block a few times.  I wasn’t sure if there was a place for me in this group of women. How ironic. After decades spent as one of very few women in my tech world, I found myself one of very few mid career professionals in a room full of tech women. Neither situation is ideal or particularly comfortable.

Well…I come away from that meeting with more questions and more to think about than I came in with. But one thing I am more sure about than ever: as long as people (women or men) are still asking the same questions about women and technology in a male dominated environment, groups like this one are needed. I hope we can find a way to move forward so that 25 years from now the current group of women in tech don’t find themselves having the same deja vu.

Is Being a Connected Educator Addictive?

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Author: Judy

Now that I’m using an increasing variety of tools to stay connected as an educator, I am wondering if the allure is addictive. Do I need to check each of these daily, or even more than once a day, and oh, sometimes hourly or less?

  • Twitter
  • Voxer chat groups
  • Periscope
  • Instagram
With ease of access to all of these on my iPhone, I am wondering what is overkill, and I have named just a few of the apps I use daily. Each leads me somewhere else via posted links or live streamlining videos. A Twitter chat alone can be not just the hourlong, but far longer if I check all the links to resources shared or to an archive with Storify.

Watching a Periscope and texting in comments is another half hour or hour shot.

Is all of this time worth it? Then, there is the never-ending stream of invites to webinars and following conferences online via Twitter and notifications to check a Periscope live-stream broadcast.

Look all those hearts coming in from a recent Periscope I watched and screen captures, tweeting out to the broadcaster my appreciation.

We say we want to be connected educators and it helps us grow professionally and connects us with educators and resources globally. We become better educators because we are connected and learn from all those others and resources at our fingertips. But do we go through withdrawal symptoms when we need to disconnect?
Last week, I dropped my iPhone in a park when taking photos. The phone was lost for a few hours. I had used iCloud to lock the phone and put out a text message alert on the phone to call a number if found. At first, I was somewhat relieved to know my phone might be gone for a day or two while I waited to decide if I wanted to buy another one and upgrade to an iPhone 6 or iPhone 6+. I almost felt a sense of relief, though I would still have my laptop and iPad to connect, but the phone really functioned as my quick 24/7 access, anytime, any place. 
Well, my dilemma ended when about two hours later I got the anticipated call my phone was found. Did I rush to get it? You bet. After all of this debating, I decided if I had to have one addiction (other than coffee in the morning) being a connected educator was the one.
Now another commitment I need to make is to do more blogging. But every time I look at one of my blogs, I am reminded they need a makeover. Look at all those Blogger scrabbled labels hanging out on the side (Index) and all the side Gadgets that just need to go. But instead of spending time cleaning up my blogs, I am off to another online place to stay connected.
I thank my PLN (personal learning network) for getting me to this point increasingly over the time of being a connected educator 24/7, or at least almost 24/7. So is it a complete addiction when the first thing I reach for in the morning before the cup of coffee is the phone to check notifications!
Oh and I do promise to clean up all those labels and other gadgets on the sidebar if I can just break myself away from checking Voxer messages, tweeting back and forth on Twitter, checking new posts to Instagram, and you following another Periscope broadcast. Oh, and I did I mention Flickr, where I need to get to now to find a Creative Commons images to add to this post.

flickr photo shared by giulia.forsythe under a Creative Commons ( BY-NC-SA ) license

So how do others feel about being a connected educator? Do the pros outweigh the cons? So you take a tech sabbatical sometimes and disconnect?

The San Diego Women’s Hackathon Codes++

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Author: Lisa C. Kaczmarczyk

Just over 65 young women descended upon several computer labs and their adjoining classrooms at California State University San Marcos on Saturday. Yes, it was the third instantiation of the San Diego Women’s Hackathon. The event was organized and implemented so that everything appeared seamless by Dr. Youwen Ouyang, a Professor in the Computer Science Department, and Shauna Ruyle, a marketing consultant and Cal State San Marcos graduate. They were supported by approximately 10 student volunteers and 18 adult mentors, many of whom were themselves technical women.

The Hackathon has been growing at quite a clip since I wrote about the inaugural event a year ago, as witnessed in part by the growing list of sponsors, which included Intuit Corporation, Equinox Center, Girl Develop IT, 4BoneHealth and CompTIA. Students came from as away as Riverside County and the south side of San Diego proper. Grouped into teams, and given the choice of two coding tasks that aim to make the world a better place, they hit the ground running.

Sporting my “Media” badge I spent the day zipping around talking to the participants, student volunteers and mentors. Much of the time however, I hung out and observed the dynamics of the coders that were so noticeably different from the dynamics in the computer labs I’ve spent so many hours in over the years.

The coding challenges were supplied by two of the event sponsors: 4BoneHealth and the Equinox Center. The teams that chose the first challenge had to create an app or game to educate their peers about the importance of getting enough calcium – and how to do so. The teams that chose the second challenge had to create an app to help people learn about the current drought in southern California. As if to encourage conversation about the usual lack of precipitation, Saturday it rained all day.

According to the official website, Hackathon participants were age 16 and up. However, I’m pretty sure I saw two girls who looked to be about 9 and 11. They were both firmly attached to mice and keyboards and one of them was right smack in the middle of a group of older participants as they all plotted and strategized. Go Girls! In addition, there were at least a few women who were returning to school to study computer science after having spent some years working in other occupations. They too were seamlessly integrated into their teams. 

So why did these women decide to get up in the dark, drive as much as an hour or more in the rain to hang out on a college campus? On a Saturday? The slightly older ones had a variety of reasons, but many of the younger first time participants said things like this: “I had nothing else to do” “My teacher told me about it” “I’m going to take a class in it”. Interesting.

Would they have come today if boys had been participants too? “NO”. That much was quite clear. One of them added: “You mean to a normal one?”  Hmmm.

A few hours later, what did these same, younger first time participants have to say? “At first it made

no sense, but now these lines of code make sense”. “It’s cool”. Aha…

Many of the groups spontaneously formed into organizational patterns that closely mimicked a technique known in pedagogical circles as Pair Programming. Well researched, this cooperative approach to learning to code has been shown to have many benefits for learning. Especially in many non-traditional populations. Read: women and girls. Yet, in traditional classrooms there is often resistance to Pair Programming because it defies the stereotypical solo, competitive, programmer behavior.

The vast majority of the groups I observed functioned amazingly well, without overt or even subtle power plays and jockying for dominance. I watched them resolving differences of opinion by sharing

and compromising, rather than having one person aggressively attempt to take control. If you have spent any amount of time in the sometimes anti-social world of male dominated tech, you know just how unusual this can be.

There were poignant moments. I spoke with one participant who seemed a bit sad. She told me she was “passionate about everything” related to engineering and computer science and felt that she should know already what aspect of these she wanted to pursue. Mind you, this young woman was in high school. We talked for a few minutes and I hope that by the end of our conversation she was able to view her wide ranging interests as the valuable and often unique interdisciplinary perspective that it is. In our globally interconnected technical world, we need young women like her.

There is a lesson in that encounter for those of us who have “succeeded” and now want to nurture and mentor those coming along after us.

At the end of the day, everyone piled into a room to eat dinner and watch the project presentations. Each group got up on stage and made a pitch to the audience and the judges. They fielded questions from the judges about their technical choices, most difficult moments, how they resolved team challenges and why they made certain design decisions. Every group had completed a significant portion of a project, even those groups whose members had little to no prior coding experience. They were justifiably proud of themselves. I noted as well how virtually every group made sure each member presented a portion of their pitch. It had been a very long day but energy radiated from the stage.

I asked many of the participants if they would attend another hackathon? Yes…definitely, absolutely, I can’t wait. But not if boys are there. Why not? They just looked at me like I was slightly odd for even asking.

Fortunately, the next San Diego Women’s Hackathon in October is a mere 6 months away.

UX Speakeasy Confessions

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Author: Lisa C. Kaczmarczyk

I just have five grand

Make me an iPhone UI? 
Who am I, Steve Jobs?!

Ponder it.
It should resonate at a sub-cellular level.
Not yet? Were you there last night? No matter. It will come to you. 
This motivational Haiku (5 – 7 – 5) was the product of the Black group’s UX Confession at last night’s

San Diego UX Speakeasy meetup. Their task was to discuss and divulge about experiences when “The person who hired you wanted to design it them-self” and report back out to the larger group.

No more needs to be said. It should all be as clear and satiating as the ever present snow melt flowing from the Sierra Nevada range.
Get back to me with your revelations. This team took the Silver (2nd Place) award so you know their creation was profound. 
One of the other groups contained a recruiter who was no doubt the inspiration for that team’s Bronze (3rd Place) win. Unfortunately I can’t report what they said because it was so deep I was awash in the avalanche of buzz word nouns liberally dusted with high powered adjectives and superlatives. Superbly done team Bronze!
 I can only presume (hope) this was the Purple group whose discussion and presentation task was around “Your new client or boss insisted that UX and UI were the same”. 
AKA: A statement leading to The Resume Kiss of Death. 
Oh… Bronze winning Purple’s job descriptions were an April Fool’s Joke. They were, right?
Then there was the  Gold (1st Place) winning confessional entry. Most appropriately it went to a team

that tightly and with laser focus captured the essence of the Crazed Boss. That person we all know who doesn’t understand … well you decide:

The essence of this group’s meme was captured shorthand in a chirpy UX Speakeasy twitter feed post: 5 pm Friday Product Manager says: Design it Enterprise social mobile sexy it has to pop design it and code it by Monday. No Sweat
Poetic in its own right isn’t it? I think their prompt was “Your boss wanted the UI to be as intuitive as their iPhone”. Oh wait… that sounds like the iPhone Haiku. Perhaps it was “The person who hired you wanted to design it them-self”. No wait… We used that on already. Should we have? With only a little imagination it could apply to “When you got negative user feedback and a manager said “the user opted in, they asked for it!”. But maybe closer to “Your product team insists that epics and user stories are the same”.
Incredible how so many of last night’s confessional prompts apply to so many situations with so little cognitive effort. 
Having thought at great and complex length about the matter, I suspect that the actual cue was: “When the product manager wanted mockups before any requirements were defined”
Keep pondering the meaning of this profound instructional creation and get back to me with your revelations. Especially if your memory of the evening is somewhat altered from mine. After all, it isn’t often we get such an educational and deeply stimulating experience wrapped up in the guise of something as innocently innocuous as hanging out at an Irish Pub.
But don’t sweat the little stuff: If you don’t see all the pieces falling into place – ask around the meetup attendees. They all seemed to get it. By the way: last night was our 400th meetup. Something to be very proud of. We’ve grown in a few short years from 13 starry eyed visionaries to some 4 digit and growing kick butt professionals. Cheers!

Please read “It’s time to reboot bioinformatics education”

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Author: nsaunders

I guess I’ve been around bioinformatics for the best part of 15 years. In that time, I’ve seen almost no improvement in the way biologists handle and use data. If anything I’ve seen a decline, perhaps because the data have become larger and more complex with no improvement in the skills base.

It strikes me when I read questions at Biostars that the problem faced by many students and researchers is deeper than “not knowing what to do.” It’s having no idea how to figure out what they need to know in order to do what they want to do. In essence, this is about how to get people into a problem-solving mindset so as they’re aware, for example that:

  • it’s extremely unlikely that you are the first person to encounter this problem
  • it’s likely that the solution is documented somewhere
  • effective search will lead you to a solution even if you don’t fully understand it at first
  • the tool(s) that you know are not necessarily the right ones for the job (and Excel is never the right tool for the job)
  • implementing the solution may require that you (shudder) learn new skills
  • time spent on those skills now is almost certainly time saved later because…
  • …with a very little self-education in programming, tasks that took hours or days can be automated and take seconds or minutes

It’s good (and bad) to know that these issues are not confined to Australian researchers: here is It’s time to reboot bioinformatics education by Todd Harris. It is excellent and you should go and read it as soon as possible.

Filed under: bioblogs, bioinformatics, blogroll, education

PubMed retraction reporting update

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Author: nsaunders

Just a quick update to the previous post. At the helpful suggestion of Steve Royle, I’ve added a new section to the report which attempts to normalise retractions by journal. So for example, J. Biol. Chem. has (as of now) 94 retracted articles and in total 170 842 publications indexed in PubMed. That becomes (100 000 / 170 842) * 94 = 55.022 retractions per 100 000 articles.

Top 20 journals, retracted articles per 100 000 publications

Top 20 journals, retracted articles per 100 000 publications

This leads to some startling changes to the journals “top 20″ list. If you’re wondering what’s going on in the world of anaesthesiology, look no further (thanks again to Steve for the reminder).
Filed under: R, statistics Tagged: pmretract, pubmed, retraction, rmarkdown

PMRetract: PubMed retraction reporting rewritten as an interactive RMarkdown document

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Author: nsaunders

Back in 2010, I wrote a web application called PMRetract to monitor retraction notices in the PubMed database. It was written primarily as a way for me to explore some technologies: the Ruby web framework Sinatra, MongoDB (hosted at MongoHQ, now Compose) and Heroku, where the app was hosted.

I automated the update process using Rake and the whole thing ran pretty smoothly, in a “set and forget” kind of way for four years or so. However, the first era of PMRetract is over. Heroku have shut down git pushes to their “Bamboo Stack” – which runs applications using Ruby version 1.8.7 – and will shut down the stack on June 16 2015. Currently, I don’t have the time either to update my code for a newer Ruby version or to figure out the (frankly, near-unintelligible) instructions for migration to the newer Cedar stack.

So I figured now was a good time to learn some new skills, deal with a few issues and relaunch PMRetract as something easier to maintain and more portable. Here it is. As all the code is “out there” for viewing, I’ll just add few notes here regarding this latest incarnation.

  1. Writing in RMarkdown has several advantages:
    • There are the usual advantages of literate documents – seeing the code together with the results, reproducibility.
    • Parsing PubMed XML files directly using R is an easier, more “lightweight” process than storage, retrieval and visualisation via a dedicated database.
    • The output is a single HTML file which is easy to distribute or host: for example here at Github and here, published to Rpubs using RStudio. Grab it yourself, use it however you like.
  2. There are a couple of slow procedures (several minutes) that are better run from separate R scripts than from the RMarkdown document, for debugging purposes. These are (a) downloading PubMed XML and (b) retrieving total articles per year across five decades. Those scripts are here at Github. The RMarkdown document then reads their output.
  3. This project allowed me to explore the rCharts package. I had long wondered why, given the excellent plotting capabilities of R, anyone would want to provide a wrapper to javascript plotting libraries. The answer of course is that with tools such as RMarkdown, we can generate documents in HTML format where interactive javascript shines.
  4. Highcharts is still my library of choice. I know the cool kids use D3 but (a) I know Highcharts better and (b) I find the transformation between data and its graphical representation most intuitive in Highcharts. That’s just how my brain works, not a reflection of the other libraries.
  5. The publishing procedure is not quite so fully-automated as it was using Rake; this shell script is my best attempt so far. However, it’s easy enough to compile and publish the document using RStudio whenever the notification feed updates.
  6. A couple of enhancements:
    • The clunky, confusing zoomable timeline showing retractions on specific dates has been replaced by a non-zoomable version showing retraction counts per year.
    • There’s always been some confusion as to whether we’re looking at data for retracted articles or their associated retraction notices – so now both types of data are shown, in separate clearly-labelled and coloured plots.

That’s it, more or less. Enjoy and let me know what you think.

Filed under: programming, R, statistics, web resources Tagged: pmretract, pubmed, retraction, rmarkdown, rpubs

Just how many retracted articles are there in PubMed anyway?

View the article’s original source
Author: nsaunders

I am forever returning to PubMed data, downloaded as XML, trying to extract information from it and becoming deeply confused in the process.

Take the seemingly-simple question “how many retracted articles are there in PubMed?”

Well, one way is to search for records with the publication type “Retracted Article”. As of right now, that returns a count of 3550.


retracted <- entrez_search("pubmed", ""Retracted Publication"[PTYP]")
[1] "3550"

Another starting point is retraction notices – the publications which announce retractions. We search for those using the type “Retraction of Publication”.

retractions <- entrez_search("pubmed", ""Retraction of Publication"[PTYP]")
[1] "3769"

So there are more retraction notices than retracted articles. Furthermore, a single retraction notice can refer to more than one retracted article. If we download all retraction notices as PubMed XML (file retractionOf.xml), we see that the retracted articles referred to by a retraction notice are stored under the node named CommentsCorrectionsList:

            <CommentsCorrections RefType="RetractionOf">
                <RefSource>Ochalski ME, Shuttleworth JJ, Chu T, Orwig KE. Fertil Steril. 2011 Feb;95(2):819-22</RefSource>
                <PMID Version="1">20889152</PMID>

There are retraction notices without a CommentsCorrectionsList. Where it is present, there are CommentsCorrections without PMID but always (I think) with RefSource. So we can count up the retracted articles referred to by retraction notices like this:

doc.retOf <- xmlTreeParse("retractionOf.xml", useInternalNodes = TRUE)
ns.retOf <- getNodeSet(doc.retOf, "//MedlineCitation")
sources.retOf <- lapply(ns.retOf, function(x) xpathSApply(x, ".//CommentsCorrections[@RefType='RetractionOf']/RefSource", xmlValue))

# count RefSource per retraction notice - first 10
head(sapply(sources.retOf, length), 10)
# [1] 0 1 1 1 1 1 1 1 1 1

# total RefSource
sum(sapply(sources, length))
# [1] 3898

It appears then that retraction notices refer to 3 898 articles, but only 3 550 of type “Retracted Publication” are currently indexed in PubMed. Next question: of the PMIDs for retracted articles linked to from retraction notices, how many match up to the PMID list found in the downloaded PubMed XML file for all “retracted article” (retracted.xml) ?

# "retracted publication"
doc.retd <- xmlTreeParse("retracted.xml", useInternalNodes = TRUE)
pmid.retd <- xpathSApply(doc.retd, "//MedlineCitation/PMID", xmlValue)
# "retraction of publication"
pmid.retOf <- lapply(ns.retOf, function(x) xpathSApply(x, ".//CommentsCorrections[@RefType='RetractionOf']/PMID", xmlValue))

# count PMIDs linked to from retraction notice
sum(sapply(pmid.retOf, length))
# [1] 3524

# and how many correspond with "retracted article"
length(which(unlist(pmid.retOf) %in% pmid.retd))
# [1] 3524

So there are, apparently, 26 (3550 – 3524) retracted articles that have a PMID, but that PMID is not referred to in a retraction notice.

In summary
It’s like the old “how long is a piece of string”, isn’t it. To summarise, as of this moment:

  • PubMed contains 3 769 retraction notices
  • Those notices reference 3 898 sources, of which 3 524 have PMIDs
  • A further 26 retracted articles have a PMID not referenced by a retraction notice

What do we make of the (3898 – 3550) = 348 articles referenced by a retraction notice, but not indexed by PubMed? Could they be in journals that were not indexed when the article was published, but indexing began prior to publication of the retraction notice?

You can see from all this that linking retraction notices with the associated retracted articles is not easy. And if you want to do interesting analyses such as time to retraction – well, don’t even get me started on PubMed dates…

Filed under: bioinformatics, programming, publications, R, statistics Tagged: ncbi, pubmed, retraction