Archive for the ‘future of publishing’ Category

QOTD: Scholarly communication online, circa 1996

December 2nd, 2015

Here is a glimpse into scholarly communication 20 years ago, from a paper about Alzforum, the Alzheimer Research Forum website. “In July of 1996, the website made its debut at the International Conference on Alzheimer’s Disease and Related Disorders in Osaka, Japan.”1

Having established a foothold in cyberspace, the challenge for Alzforum was and continues to be to define new types of scientific publishing that take advantage of the speed and wide distribution of the Web and to curate and add value to information available from other public sources. This is a perennial challenge, thanks to the rapid advances in biomedical resources on the Web.

This uphill struggle, however, seems less strenuous when we compare the current situation with the “old days.” Recall that in 1996, PubMed did not exist! (PubMed was launched in June of 1997.) Medical institutions had access to Medline, but in order for Alzforum to produce its Papers of the Week listings, the editor had to ask the Countway Medical Library at Harvard Medical School to provide weekly text files listing newly indexed AD papers. The Alzforum hired a curator to paraphrase each abstract so that this information could be posted without violating journal copyrights. These documents were manually edited, sent out in a weekly email to the advisors for comments, and compiled into a static HTML page. Looking back, we can see that the entire process seems as antiquated as the hand-copying of manuscripts in the Middle Ages.

(emphasis mine)

From pages 459-460 of “Alzheimer Research Forum: a knowledge base and e-community for AD research”2

  1. page 458, Kinoshita, June, and Gabrielle Strobel. “Alzheimer Research Forum: a knowledge base and e-community for AD research.” in Alzheimer: 100 Years and Beyond, Mathias Jucker, Konrad Beyreuther, Christian Haass, Roger M. Nitsch, Yves Christen, eds. Berlin Heidelberg:Springer-Verlag, 2006: 457-463. []
  2. Kinoshita, June, and Gabrielle Strobel. “Alzheimer Research Forum: a knowledge base and e-community for AD research.” in Alzheimer: 100 Years and Beyond, Mathias Jucker, Konrad Beyreuther, Christian Haass, Roger M. Nitsch, Yves Christen, eds. Berlin Heidelberg:Springer-Verlag, 2006: 457-463. []

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Rating the evidence, citation by citation?

September 4th, 2014

Publishers from HighWire Press are experimenting with a plugin called SocialCite. This is intended to rate the evidence, citation by citation. Like this:

SocialCite at PNAS, HighWire Press from

SocialCite at PNAS, HighWire Press from

So far a few publishers (including PNAS) have implemented it as a pilot. Apparently the Journal of Bone and Joint Surgery is apparently leading this effort, I’d be really interested in speaking with them further:

Find out more about SocialCite from their website or the slidedeck from their debut at the HighwirePress meeting.

I’m *very* curious to hear what peopel think of this — it really surprised me.

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Altmetrics can help surface quality content: Jason Priem on the Decoupled Journal as the achievable future of scholarly communication

November 4th, 2012

Jason Priem has a wonderful slidedeck on how to smoothly transition from today’s practices in scientific communication to the future. Here is my reading of the argument given in Jason’s slides:

Communicating science is a central and essential part of doing science, and we have always used the best technology available.
Yet currently, there are several problems with journals, the primary form of scholarly communication.

Journal publication is

  • Slow
  • Closed
  • Hard to innovate
  • and has

  • Restrictive format: function follows form
  • Inconsistent quality control

These problems are fixable, if we realize that journals serve four traditional functions:

  1. Registration
  2. Archiving
  3. Dissemination
  4. Certification

By decoupling these functions, into an a la carte publishing menu, we can fix the scholarly communication system. Decoupled scholarly outlets already exist. Jason mentions some outlets (I would say these mainly serve registration functions, maybe also dissemination ones):

  • ArXiv
  • Math Overflow
  • SSRN
  • Faculty of 1000 Research
  • the blag-o-sphere

Jason doesn’t mention here — but we could add to this list — systems for data publishing, e-science workflow, and open notebook science; these may fulfil registration and archiving functions. Also, among existing archiving systems, we could add the journal archiving functions of LOCKSS is the main player I’m familiar with.

To help with the certification functions, we have altmetrics tools like Impact Story (Jason’s Sloan Founded project with Heather Piwowar).

Jason’s argument well worth reading in full; it’s a well-articulated argument for decoupling journal functions, with some detailed descriptions of altmetrics. The core argument is very solid, and of wide interest: Unlike previous articulations for “pre-publication peer review”, this argument will make sense to everyone who believes in big data, I think. There are other formats: video of the talk1 and a draft article called “Decoupling the scholarly journal”2.

Briefly noted in some of my earlier tweets.

  1. Thanks to Siegfriend Handschuh, who suggested the video of Jason giving this talk at Purdue. []
  2. by Jason Priem and Bradley M. Hemminger, under review for the Frontiers in Computational Neuroscience special issue “Beyond open access: visions for open evaluation of scientific papers by post-publication peer review” []

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Error reporting: it’s easier in Kindle

May 9th, 2012

One thing I can say about Kindle: error reporting is easier.

You report problems in context, by selecting the offending text. No need to explain where - just what the problem is.

Feedback receipt is confirmed, along with the next steps for how it will be used.

By contrast, to report problems to academic publishers, you often must fill out an elaborate form (e.g. Springer or Elsevier). Digging up contact information often requires going to another page (e.g. ACM.). Some make you *both* go to another page to leave feedback and then fill out a form (e.g. EBSCO). Do any academic publishers keep the context of what journal article or book chapter you’re reporting a problem with? (If so, I’ve never noticed!)

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Commercial Altmetric Explorer aimed at publishers

May 7th, 2012

Altmetrics is hitting its stride: 30 months after the Altmetrics manifesto1, there are 6 tools listed. This is great news!

I tried out the beta of a new commercial tool, The Altmetric Explorer, from They are building on the success and ideas of the academic and non-profit community (but not formally associated with The Altmetric Explorer gives overviews of articles and journals by the social media mentions. You can filter by publisher, journal, subject, source, etc. Altmetric Explore has a closed beta, but you can try the basic functionality on articles with their open tool, the PLoS Impact explorer.

"The default view shows the articles mentioned most frequently in all sources, from all journals. Various filters are available.

Rolling over the donut shows which sources (Twitter, blogs, ...) an article was mentioned in.

Sparklines can be used to compare journals.

A 'people' tab lets you look at individual messages. Rolling over the photo or avatar shows the poster's profile. seems largely aimed at publishers2. This may add promotional noise, not unlike coercive citation, if it is used as an evaluation metric as they suggest:3

Want to see which journals have improved their profile in social media or with a particular news outlet?

Their API is currently free for non-commercial use. are crawling Twitter since July 2011 and focusing on papers with PubMed, arXiv, and DOI identifiers. They also get data from Facebook, Google+, and blogs, but they don’t disclose how. (I assume that blogs using ResearchBlogging code are crawled, for instance.)

  1. J. Priem, D. Taraborelli, P. Groth, C. Neylon (2010), Altmetrics: A manifesto, (v.1.0), 26 October 2010. []
  2. “Altmetric sustains itself by selling more detailed data and analysis tools to publishers, institutions and academic societies.”, says the bookmarklet page, to explain why that is free []
  3. ‘This quote from an editor as a condition for publication highlights the problem: “you cite Leukemia [once in 42 references]. Consequently, we kindly ask you to add references of articles published in Leukemia to your present article”’-from the abstract of Science. 2012 Feb 3;335(6068):542-3. Scientific publications. Coercive citation in academic publishing. Wilhite AW, Fong EA. summary on Science Daily. []

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Support EPUB!

November 7th, 2011

EPUB is just HTML + CSS in a tasty ZIP package. Let’s have more of it!

That’s the message of this 3 minute spiel I gave David Weinberger when he interviewed me at LOD-LAM back in June. Resulting video is on YouTube and below.

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The Legacy of Michael S. Hart

September 16th, 2011

ship sinking into a whirlpool near the Lone Tower

Sometimes people are important to you not for who they are, but for what they do. Michael S. Hart, the founder of Project Gutenberg, is one such person. While I never met him, Michael’s work has definitely impacted my life: The last book I finished1, like most of my fiction reading over the past 3 years, was a public domain ebook. I love the illustrations.

KENBAK-1 from 1971

The first personal computer: KENBAK-1 (1971)

In 1971, the idea of pleasure reading on screens must have been novel. The personal computer had just been invented; a KENBAK-1 would set you back $750 — equivalent to $4200 in 2011 dollars2.

Xerox Sigma V-SDS mainframe

Xerox Sigma V-SDS mainframe

Project Gutenberg’s first text — the U.S. Declaration of Independence — was keyed into a mainframe, about one month after Unix was first released34. That mainframe, a Xerox Sigma V, was one of the first 15 computers on the Internet (well, technically, ARPANET)5. Project Gutenberg is an echo of the generosity of some UIUC sysadmins: The first digital library began a gift back to the world in appreciation of access to that computer.

Thanks, Michael.

Originally via @muttinmall

  1. The Book of Dragons, by Edith Nesbit: highly recommended, especially if you like silly explanations or fairy tales with morals. []
  2. CPI Inflation Calculator []
  3. Computer history timeline 1960-1980 []
  4. Project Gutenberg Digital Library Seeks To Spur Literacy:
    Library hopes to offer 1 million electronic books in 100 languages
    , 2007-07-20, Jeffrey Thomas []
  5. Amazingly, this predated NCSA. You can see the building–Thomas Siebel–hosting the node thanks to a UIUC Communication Technology and Society class assignment []

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They really know how to throw a party in Chicago…

September 14th, 2011

This is my kind of performance art, from this year’s Printer’s Ball. Got pictures, anybody?

Busted Books: The Great Soaking. Performance by Davis Schneiderman. Attendees are invited to use a artisan-constructed dunk tank to soak either a book or a Kindle—depending upon the dunker’s feelings regarding the printed word and e-readers. With this simple choice, this physical act, readers can finally stop theorizing about the future of the book and do something about it.

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Understanding Wikipedia through the evolution of a single page

August 26th, 2011

“The only constant is change.” – Heraclitis

How well do you know Wikipedia? Get to know it a little better by looking at how your favorite article changes over time. To inspire you, here are two examples.

Jon Udell’s screencast about ‘Heavy Metal Umlaut’ is a classic, looking back (in 2005) at the first two years of that article. It points out the accumulation of information, vandalism (and its swift reversion), formatting changes, and issues around the verifiability of facts.

In a recent article for the Awl1, Emily Morris sifts through 2,303 edits of ‘Lolita’ to pull out nitpicking revision comments, interesting diffs, and statistics.

  1. The Awl is *woefully* distracting. I urge you not to follow any links. (Thanks a lot Louis!) []

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Reading Ontologically?

July 24th, 2011

What are the right ontologies for reading? And what kind of ontology support would let books recombine themselves, on the fly, in novel ways?

Today keyword searches within books and book collections is commonplace, highlighting a word in your ebook reader can bring up a definition, and dictionaries grab recent examples of word use from microblogs.1 But can’t we do more? But what kind of synthesis do we need (and what is possible) for supporting readers of literature, classics, and humanities texts?

Current approaches seem to aim at analysis (e.g. getting an overview of the literary works of a period with “distant reading”/”macroanalysis”) and at creating flexible critical editions (e.g. structural, sometimes overlapping markup, as in TEI-based editions and projects like Wendell Piez’ Sonneteer2.) I would call these “sensemaking” approaches rather than tools for reading.

I was intrigued by the Bible Ontology3 because of their tagline: “ever wanted to read and study the Bible Ontologically?” Yet I don’t really know what they mean by reading ontologically4.

Of course, they have recorded various pieces of data. For instance, for Rebekah, we see her children, siblings, birthplace, book and chapters she figures in, etc.:

Rebekah, from

They offer a SPARQL endpoint, so you can query. For instance, to find all the married women6 (live query result):

PREFIX bop: <>
select ?s ?o where {?s bop:isWifeOf ?o }

Intense and long-term work has gone into Bible concordances, scholarship, etc., so it seems like a great use case for “reading ontologically”. With theologians and others looking at the site, using the SPARQL endpoint, etc., perhaps someone will be able to tell me what that means!

  1. In 2003, Gregory Crane wrote that “Already the books in a digital library are beginning to read one another and to confer among themselves before creating a new synthetic document for review by their human readers.” When I first read it in 2006, that article seemed incredibly visionary to me. Yet these commonplace “syntheses” no longer seem extraordinary to me. []
  2. currently offline, but brilliant; do check back, meanwhile see also his Digital Humanities 2010 talk notes []
  3. It’s a bit disingenuous to advertise their work as an ontology: in fact they have applied the ontology, rather than just creating it. []
  4. even though I’ve given a talk about supporting reading with ontologies! []
  5. The most meaningful of their terms is the bop:isRelatedInEvent, perhaps since these events, like Isaac_blesses_Jacob, would require more analysis to discern. []
  6. Gender is not recorded so we can’t (yet) ask for all the women overall, though I’ve just asked about this. []

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