In case anyone has doubts, this is a continuing stream of (un)consciousness arising from my earlier Dogpatch thoughts about innovation and STM. And, of course, in my enthusiasm for the new, I neglected some of the “slightly older but just as valid” new. Thanks everyone for reminding me of this. We shall go there anon, but I wanted to start at the STM Association dinner the night before the events described in my last blog. There I had the pleasure of sitting next to Rhonda Oliver, now running publishing at the Royal College of Nursing, but doing so after leaving Portland Press, where she was CEO. And it was Portland Press, a distinguished but not yet world dominant player in biochemistry publishing, that I first learnt of really interesting forays ito the world of semantic-based publishing. Here is what I wrote about them in this blog last year:

“Particularly noteworthy was a talk by Professor Terri Attwood and Dr Steve Pettifer from the University of Manchester (how good to see a biochemistry informatician and a computer scientist sharing the same platform!). They spoke about Utopia Documents, a next generation document reader developed for the Biochemical Journal which identifies features in PDFs and semantically annotates them, seamlessly connecting documents to online data. All of a sudden we are emerging onto the semantic web stage with very practical and pragmatic demonstrations of the virtues of Linked Data. The message was very clear: go home and mark-up everything you have, for no one now knows what content will need to link to what in a web of increasing linkage universality and complexity. At the very least every one who considers themselves a publisher, and especially a science publisher, should read the review article by Attwood, Pettifer and their colleagues in Biochemical Journal (Calling International Rescue: Knowledge Lost in the Literature and information Landslide Incidentally, they cite Amos Bairoch and his reflections on Annotation in Nature Precedings ( and this is hugely useful if you can generalize from the problems of biocuration to the chaos that each of us faces in our own domains.”

And the reference to Steve Pettifer recalled to mind my old friend Jan Velterop, once agent-provocateur in Springer’s thrust into OA (how grateful they should be to him now, given that his work drew them alongside BMC, and thus to real growth in this year of OA and eBooks compensating for negative trends elsewhere). Dr Pettifer advises Utopia Documents  (, who have been developing in parallel to Labiva and Mendeley in the workflow space for PDFs. Each is different, though they have common attributes. The fact that there are now three environments in this space is a strength for all of them. Isolated good ideas rarely work out. Constantly re-iterated solutions “invented” separately in several places shows a sector responding to the same calls from many customers – “Help me out of here – I am losing control!”.

Utopia Documents is also running a public trial on Elsevier’s SciVerse environment. This is critical, and prompts a question: if Nature and Elsevier see this, why doesn’t everyone else? And I think this may be in part because we have been confusing the workflow utility of PDF handling with the strange world of scientific networking. In one of the many frank and helpful comments made by Annette Thomas in the interview I referred to earlier this week, she remarked that much of what Nature had done to “create” networking between scientists had shown very modest results. She said that while scientists showed a modest appetite for networking via news and blog comments, she thought that Nature Networks did not succeed because they lacked the immediacy and involvement of workflow tools, and it was more likely that in this context real contact between self-formed interest groups would take place. Here she seems to be moving closer to the Mendeley ( position, but with a qualification. She clearly feels that you build the utilities first, and then see how interest groups develop their own dynamic using the shared information created by the toolset. Crowd-sourcing a la Mendeley is good, but self determination may be better.

Thinking about Portland Press and Jan Velterop also took me back to Jan’s company, Academic Concept Knowledge Ltd (AQnowledge – The semantic search environment created here is now embedded in Utopia Documents. But this is not what strikes me most emphatically about Jan’s work in recent years. Here is a hugely experienced academic research publisher who is not format bound and can think beyond the book, the journal, and even the article. Integrating, with its 300,000 antibodies and related products for concept matching shows that he and his team are creating a small player with an eye for data and for what research workflow really entails. By putting together all of the laboratory supply sources and the raft of descriptive material that they generate AQnowledge may be doing more for using article stores as a live element in workflow than any of their peers. Yet it has taken a company like BioRAFT  ( to push this home with compliance information, demonstrating once again that we are in the sectoral tools age of workflow, unable as yet to envisage the full desktop of tools and utilities, or the way they link together, or indeed the Electronic Lab Manual to which they in all probability lead.

Finally, STM now has major players – think of MarkLogic, TEMIS and SilverChair to name but three – quite capable of deploying the technology to drive towards the Big Data vision which I referenced in my previous piece. So, with all of this in the wings, why do the publishers still want to pursue the parochial and eschew the visionary?


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2 Comments so far

  1. dworlock on October 14, 2011 10:54

    Is self commenting permitted ? Shortly after writing this , I noticed that I had missed the story on Protein Interactions on the Elsevier SciVerse site . This shows clearly how intensely they too “get” the data interaction . Here is the link :

  2. David Worlock | Developing digital strategies for the information marketplace | Supporting the migration of information providers and content players into the networked services world of the future. on June 13, 2012 21:06

    […] science articles , and I wrote about it under the heading ” I Can See So Clearly Now “( ) in October 2011. Then I tucked it into the semantic publishing cubbyhole , until warned by one of […]