The Distant Librarian

Some Sci-Hub stuff

Sci-Hub popped up a couple of times today, along with a link to a tool I hadn't seen before.

1. Tools to liberate scholarly articles, help sources understand journalism and publish printable online zines. Mentioning the existence to journalists
2. They Know We Know They Know: Does Sci-Hub Affect Library Subscriptions? which in turn led to the
3. Sci-Hub Stats Browser, which is a dated snapshot of just how comprehensive the Sci-Hub database is. This is data supporting the article, Sci-Hub provides access to nearly all scholarly literature.

Wow.

Review: A funder-imposed data publication requirement seldom inspired data sharing

We've been doing a lot of talking about Data Management Plans at MPOW, and I recently came across the following article from PLOS One: A funder-imposed data publication requirement seldom inspired data sharing.

In it, the authors take a look at 315 research projects that had been funded by the Exxon Valdez Oil Spill Trustee Council (EVOSTC) between 1989 - 2010 to see how many data sets could be obtained. This is an interesting funding agency, as it funded research from many different disciplines, including the Social Sciences. As you might guess, the number of retrieved data sets is pretty darn low (26%), but the single biggest reason was that the authors were unable to reach the original researcher. I guess that shouldn't surprise me as much as it did. The other thing I found surprising is that they found slightly lower retrievability for research that was conducted after the EVOSTC enacted a formal data policy in 1995. I guess that's the sound bite for the article title!

But the other thing we've been talking about at MPOW is what kind of reward might entice researchers to post their data, and this article addressed that as well:

"Inherent in all of the above hurdles to data recovery is the absence of a reward structure for sharing data. There is no reward for the time investment required to learn how to curate data or construct data packages (including well documented and formatted error-free data, with project and file level metadata) in cases where original data curation was insufficient. The focus in science has traditionally been on production and citation of publications, and as such, a process for identification and citation of manuscripts has been well developed. Similar attribution and recognition of data would incentivize the archiving and sharing of data in the scientific community. One way publications are tracked and cited is through the use of digital object identifiers (DOIs), a tool that is also increasingly being used to attribute data. DOIs are particularly important for data identification because unlike manuscripts, data can be regularly updated or exist in multiple formats or subsets, so identifying specific versions of the data via a DOI is key to data proper data attribution and use. Although the use of data DOIs is a relatively new practice, they should facilitate more routine data citation as compared to traditional methods. Incorporating data citations into a scientists’ overall research output alongside journal publications should further incentivize data sharing."

So they're making some claims that they can't back up with this research, but which certainly makes sense. The one thing that might get researchers to post their data sets is better recognition in the tenure and promotion process of the work that's involved in making this information available online.

As a snarky aside, I wonder if the EVOSTC website has seen a redesign since it was first launched? :-0

Archive of tweets from Semantic Web in Libraries (SWIB) 2018

Here is an archive of tweets from this year's Semantic Web in Libraries (SWIB) conference. You can search and filter the results here,  and explore nifty visualizations here. All this courtesy of the excellent (and free) TAGS project.

A disturbing story on academic freedom and predatory publishing

While I had actually read the article in question shortly after it first came out, I was unaware of the fallout until earlier this morning. This is a story you should be aware of.

How I learned of it: Investigation launched into alleged academic freedom violations at Thompson Rivers University

What I had missed: B.C. economist in grim battle against deceptive scholarship and Suspended B.C. prof who exposed fake journals welcomes investigation.

In a nutshell, Dr. Derek Pyne wrote a paper in early 2017 titled, The Rewards of Predatory Publications at a Small Business School, in which he looked at how many of his colleagues in the business school at Thompson Rivers University had published articles in predatory journals. Quite a few, as it turned out. From his conclusion (emphasis mine):

Predatory journals have become an increasing problem when it comes to assessing and rewarding researchers for the merit of their publishing records. In addition, the presence of predatory journals makes it difficult for non-experts to judge the quality and validity of published research. This paper finds that, at least at one university, there are few incentives not to publish in predatory journals. In addition, when the opportunity cost of forgone income from extra teaching is significant, publishing in ranked journals is costly.

Of course it's understandable that his colleagues and administrators would be embarrassed by this paper, but apparently he has been suspended from his position, and the university as a whole, for bringing this information to light. I say apparently, because so far Thompson Rivers University hasn't provided any actual reason. Well, they do say all this.... Despite what you'll find in the preceding link, this appears to be completely against the concepts of academic freedom and tenure, like seriously TRU?

So this post is just to make sure y'all are aware of this sorry situation, and I now have an alert on his name so will let you know when it's been resolved. Of course these are my opinions and not those of my employer, yadda yadda yadda.

November 7 Updates:

Here's a good 15-minute audio summary of the whole situation: 10/3 podcast: A B.C. economist is in hot water for exposing fake journals

And here's an article from The Economist I missed from this past summer which mentions Dr. Pyne's paper, but appears to have come out just before his suspension: Some science journals that claim to peer review papers do not do so 

November 20, 2019 Update:

Report: Academic Freedom Breached at Thompson Rivers University

First look at NVivo Transcription

Almost exactly a year ago I took a quick look at three automated transcription tools, and today there's another one to add to the mix, though this one's not free. NVivo has launched an automated transcription service and I'm impressed! I uploaded the same audio clip I used in last year's shootout, a 40-second snippet from the inauguration of George W. Bush, and here's what NVivo made of it:

Please raise your right hand and repeat after me. I George Walker Bush do solemnly swear. George Walker Bush do solemnly swear that I will faithfully execute the office of president of the United States that I will faithfully execute the office of president of the United States and will to the best of my ability and will to the best of my ability preserve protect and defend the Constitution of the United States preserve protect and defend the Constitution of the United States. So help me God. So help me God. Congratulations.

It didn't pick up the separate speakers, but other than that it was a perfect transcription of a somewhat noisy audio clip, which moves it to the top of the list of the one's I've looked at so far.

You'll get 15 minutes of free transcription when you sign up (and as far as I can tell, you could use this w/o having a license for NVivo), though you DO have to enter a credit card to get an account. You can access the tool from within NVivo, on the Create tab:

Or from the website of your account, which is what I did. You just browse to your audio file and hit "upload". NVivo claims transcription occurs at 2x speed, so this should've only taken 20-seconds to transcribe. In my case it was just going and going, so I refreshed my browser after two minutes and it was all done, so that may be a little bug, or more likely something with my browser.

Cost of the service is on a per/hour basis, as follows:

I honestly have no idea if that's a fair price, but it certainly seems like it is. If you needed quality transcription I suspect you could pay a lot more. A major bonus is that this service covers 28 different languages! Feel free to try out one you know and let me know if the quality is still this high. Oh, I chose "English - North American" when I tried the Bush file.

Pretty nifty overall, I think.

Tweet Archive from Designing Libraries 2018

The 7th edition of the Designing Libraries conference just wrapped up here at the U of Calgary, and I thought it'd be fun to capture the tweets using the hashtag #designinglibraries, so here you go:

Here's the full archive (457 tweets as of posting)

Here's a dashboard summary view

Here's a nifty view that allows for easy searching and filtering. (only one tweet even mentioned the weather!)

All this brought to you by the awesome TAGS project.

Update: Here's an article from our campus newspaper: Calgary 'head of the list' of library cities around the world.

A fascinating article about replication in psychology

The Atlantic recently posted a fascinating article looking at the problem of reproducibility in the field of psychology: Online Bettors Can Sniff Out Weak Psychology Studies
So why can't the journals that publish them? Ed Yong breaks down

the new results from the Social Sciences Replication Project, in which 24 researchers attempted to replicate social-science studies published between 2010 and 2015 in Nature and Science—the world’s top two scientific journals. The replicators ran much bigger versions of the original studies, recruiting around five times as many volunteers as before. They did all their work in the open, and ran their plans past the teams behind the original experiments. And ultimately, they could only reproduce the results of 13 out of 21 studies—62 percent.

I've seen lots of dismal numbers like that before in other fields, but what I found fascinating was that in addition to their attempts to reproduce these studies, the SSRP team also ran "a "prediction market", a stock exchange in which volunteers could buy or sell “shares” in the 21 studies, based on how reproducible they seemed." And it turns out these 206 volunteers predicted overall that the 21 studies would replicate 63% of the time!

That's just freaky-close! I want to be in on one of these prediction markets, and I want to see how these would play out in other academic disciplines. Off to learn more!

Some thoughts on citations in the 21st Century

Colleagues at work pointed to this long read on Medium: Open Access Knowledge: Digital Style Guide. In it, Patrick Dunleavy makes the case that, whenever possible, academic citations should point to "free" online versions of resources rather than the archaic "dead tree" version seemingly favoured by traditional style guides. He also argues that in addition to "real" open access repositories, if the material is available on ResearchGate, Academia.edu or Mendeley, go ahead and throw in a link. The idea is that whatever gets the material into the hands of the reader is what should be included in the citation (or alternate citation, which he suggests adding). Fair enough, but why not go ahead and include some sort of link to SciHub too? :-)

One of the other arguments he makes is to drop the practice of abbreviating author names and journal titles in the citation, and I wholeheartedly agree. Why, then, does he suggest abbreviations to describe the type of access? ([OAg] [PW] [LEV] [Non$] etc.) Spell those suckers out too! If you're going to stick with them though, why not substitute the $ for PW - I think it's clearer.

The second interesting citation-related post comes from Jon Udell, who suggests How to improve Wikipedia citations with Hypothesis direct links. Hypothes.is is sort of like a URL-shortening service, but with the ability to annotate text as well. Hey wait a minute, Hypothes.is could be used to perfectly solve the issues mentioned in points 9 and 10 of Dunleavy's post! Seriously, click this link!

I love it when stuff like this mashes up. I'm now off to make sure Patrick and Jon know about each other!

Some tweaks at Google Scholar

Somehow I wasn't subscribed to the Google Scholar blog already, and missed last week's announcement that they'd made some tweaks to the interface of Google Scholar. Today though I was presented with a big link under the search box to the post on their blog touting Better ways of getting around. I've gotta say I found their screenshot pretty confusing. In a nutshell, they've moved things like Alerts and Metrics to the hamburger menu which appears to the left of the words "Google Scholar" on all the results pages.

Looks nice!

Free access to the Rights, Action, and Social Responsibility Collection from de Gruyter

Until the end of 2017, de Gruyter is offering free access to its Rights, Action, and Social Responsibility ebook Collection for "all students and faculty". You do have to register, and it appears that when I did so, I did so for my entire University! I had expected an email with a username and login, but got a notice several days later (as did at least one other colleague) that "Your institution now has online access to all the titles in our Rights, Action, and Social Responsibility collection until December 31, 2017." It appears to be IP-based, but I didn't give them any info other than my institution name, so YMMV. Content is available only chapter-by-chapter as PDF documents.

Public debates surrounding immigration policy, climate change, international relations, and constitutional and human rights are currently at the forefront of our national discourse. Critical reasoning, supported through academic research, is needed.

As a result, De Gruyter, along with our partner presses, is making freely available books and journal articles across nine topical areas for all students and faculty. Broadening access to this scholarship enables more people to address these issues in an informed manner: it helps us combat false news sources, to consider the nature of truth and ethics, and to understand the struggles of all members of society.

We can engage in these important debates intelligently and confidently using credible sources. To provide free access for your library please register here.

Steve Fallon, Director of Publishing Partnerships
Boston, MA

Definitely some timely topics available:

Factiva filters for Fake News Phenomenon

Thanks to a tip from my colleague Dani I learned that Factiva has recently added a filter for fake news. Like many things with Factiva (IMHO), it's not terribly intuitive to find, so here are the steps. You can either add this as a filter to a  search you've already run, or just use it to see what all is out (in) there.

From the main search page choose Subject, then Political/General News, and finally, Fake News Phenomenon. If you simply click on the blue arrow to the right and then run the search you'll see all there is on the subject within Factiva. According to the scope note, it looks like this category was added on March 14, 2017.

 

 

 

 

Hydrator is my new favourite tool to hydrate tweet-ids (aka so many tools!)

Update - April 18, 2023: From the developer: Twitter's changes to their API which greatly reduce the amount of read-only access means that the Hydrator is no longer a useful application. The application keys, which functioned for the last 7 years, have been rescinded by Twitter.

For the past couple of weeks I've been helping a student gather a collection of historical tweets, based on specific hashtags. You may be aware that Twitter's search API limits searches to only the past week or so, which sucks for those doing historical research. I'm still on the hunt for a tool that would allow me to easily gather older tweets, so please let me know if you have one!  I tried Octoparse and Import.io, but neither ended up being reliable for this purpose.

At this point I reached out to Ed Summers, creator of the awesome command-line tool twarc, who suggested I try scraping with Webrecorder.io (protip, use the autoscroll button at the top). Webrecorder.io did a pretty decent job of capturing my historical search, but it took a fair amount of work. It seemed to bog down a bit after a while, so I ended up chunking my searches into 2-3 days, necessitating running the scrape about a dozen times to capture the entire event. And then I was knee-deep in learning about WARC files. I was unable to find a tool that I could make work that would allow me to extract either the full tweets, or the tweet-ids from the WARC files, so simply having the entire search results at my disposal still didn't help me. 

Then I did what I should've done first. I searched to see if anyone had posted an archive of the tweets my student was looking for. And someone had. If ever you're doing social media research around crisis situations, you'll want to know about CrisisLex.org.

So now we almost had what we needed. But, Twitter also says that if you've collected a pile of tweets, you can't post them for someone else to download, you can only post a file of the tweet-ids. Ed again has some good thoughts on this rule. This is why I needed to "hydrate" the tweet-ids contained in the CrisisLex files in order to get the actual details of the original tweets.

twarc does this, but somehow I screwed up my extraction of the tweet-ids from the .csv provided by CrisisLex and it didn't seem to be working correctly for me. So I went crying back to Ed to see if he knew what I was doing wrong, and he showed me a screen shot of a tool he used to prove that it was all working for him.

And the screen shot seemed to show some sort of graphical user interface!

Hey, if I can find a "program" to do something so I don't have to do it in the command line, I am one happy camper! Turned out he was using Hydrator, which works on OS X, Windows and LINUX. You feed it a file of tweet-ids and it spits out a JSON file AND a CSV file of the actual tweets. Golden. My student is tickled and I can move on to something new, but with a wicked new tool at my disposal. I owe you several drinks, Ed!

Update: April 8, 2020 - see this post for tips on prepping a dataset to work within Hydrator.

First run on autoEdit 2, open source transcription tool

Having had this tab opened for what seems like forever, I finally got around to running some tests of autoEdit 2, an open-source automatic transcription tool (automatically creates a text file from a given audio or video file). This tool only runs on the Mac, and there are two flavours, if you will. One, Gentle STT, runs completely on your local machine and costs nothing to do transcriptions, but it's not the best at it. If you have very clean audio you can probably get by with this, but I found it pretty sketchy. The second makes use of IBM Watson's Bluemix service, and for me was both faster and much more accurate. With Bluemix you get 16 hours of transcription free per month, but anything more than that will cost $0.02/minute, which is still pretty darn reasonable, IMHO.

One of the things that slowed me down was a lack of troubleshooting documentation. The software itself is pretty straightforward and easy to use, but the first step of plugging in your Bluemix API key is a bit sparse. I put in the wrong credentials, and autoEdit took them without complaint, and pretended to work on the transcription for a long time before I decided it wasn't really doing anything. I couldn't find anywhere to re-enter credentials, so I ended up uninstalling and reinstalling the program.

I'll see if I can contribute to the documentation, but for now, once you've got your free Bluemix account, you want to scroll to the bottom right of the main account page and click on the Create button.

On the next screen, choose the 2nd "tab", "Service Credentials", and then View Credentials. That's where you'll find your API username and password. Be sure to enter them in the correct order within autoEdit; the username, at least in my case, was much longer, and is presented 2nd on the Bluemix page :-/

That's all from me. It does work quite well, and if you need to create a written transcript from a video or audio file, I think this is a pretty darn good way to go!

Archive of tweets from Semantic Web in Libraries (swib) 2016

As I did last year, I have captured all the tweets from this year's Semantic Web in Libraries conference using the TAGS tool for Google Sheets. As of this posting there are 630 tweets with the hashtag #SWIB, 573 of them unique. Last year had 1,736 tweets! with 1,633 of them unique. 

Here's the archive for 2016. Have fun!

Alberta Open Data Developments

Yesterday was a pretty good day for Open Data in Alberta. First, the City of Calgary went live with a Socrata version of their Open Data portal. Previously they had been running on some sort of Microsoft SharePoint (my guess) site, and it was not a particularly pretty or useful thing. Really looking forward to working with their data in this new format, and with sweet APIs.

Second up, the announcement of Open Data Areas Alberta (ODAA). From their landing page:

Open Data Areas Alberta (ODAA) is a new undertaking being spearheaded by Alberta Data Partnerships to put extensive data in the hands of those who can use it. Datasets from six key rural areas across Alberta is available for no cost to inspired entrepreneurs, SMEs and creative problem solvers. These will include earth observation, remote sensing, geospatial data, environmental data, and social and economic datasets from private industry and government.

Those six areas include Beaver Hills, Fox Creek, Taber, Fort McMurray, RMH Sylvan and Utikuma Lake. It's good, current (for the most part) data, too! Want 17GB of orthophotos of the Fort McMurray Oilsands? Here you go. Wonder why Taber grows such great corn? Maybe the Agricultural Regions of Alberta Soil Information Database (AGRASID) will tell the tale.