Monday, April 04, 2011

What scientists really want from digital publishing.

This section of the conference allowed librarians and publishers to hear directly from scientific researchers; first up is Philip Bourne from University of San Diego who is a computational biologist among other things (e.g. open access advocate).

Bourne starts by explaining his big hope for scientists’ relationship with publishers in the future:

“as a scientist I want an interaction with a publisher that does not begin when the scientific process ends but begins at the beginning of the scientific process itself”

The current situation is:

  • 1. Ideas
  • 2. Experiments
  • 3. Data gathering
  • 4. Conclusions - it’s at this stage that the publisher comes in

But why couldn't the publisher come in at the data stage? They could help store it for our group. Or even earlier, at the ideation stage: The moment I jot down a few ideas, the publisher could control access to that information and then at some point down the line when the access is opened up – that’s when it becomes ‘published’.

There are movements in that direction. For example in Elsevier’s ScienceDirect (and some others too) you can click on a figure/image and move it around and manipulate it – the application is integrated on the platform because a publisher and a data provider has cooperated. But this is just the beginning; when you click on the diagram in the article, you’re getting some data back but it’s generic and it might not be organised in the way that you want. It’s generic – the figure is being viewed separately from the article text and related data – now you have to figure out what that metadata means to the article. So this is a good step but it’s not capturing all of the knowledge that you might want. It needs more cooperation, more open and interactive apps. And it needs:

  • Integrated rich media that improves comprehension, viewable in different ways. A video of an experiment actually being done, delivered to me alongside the text from the article.
  • The ability to review and interact with data on the mobile platform. Should have apps not just to read but also interact with data.
  • Mashups with content from other articles and data, must be at the point of capture, not post- anything.
  • Semantic linking of data that can lead to new knowledge discovery. To find all references to that piece of data – that data itself is probably not cited – would like to know how the actual data is being used discover relationships that other people have found between your data and other sets of data.

So Bourne wants publishers to become more involved with his work as – he confesses – some of the work is less than organised. He thinks scientists need help with management of data in general, and specifically:

  • · Project management. They use e.g. basecamp for project management but email folders are primary – this in an unhealthy ‘hub and spoke’ situation
  • · Content management. It’s a mess with content stored all over such as on slides, posters, lab notebooks etc.
  • · Manage negative data. They generate way more negative data than positive – Negative data is important. But you can’t find it – it stays hidden. This needs to change.
  • · Software. All the software they create is open source but when the grad student that wrote it leaves, it’s lost.


Bourne’s ‘Beyond The PDF’ workshop has generated discussion and ideas. He says “the notion of a journal is just dead – sorry. The concept of a journal is lost to me; its components and objects and data are what I think about. Research articles are useful but the components could be seen as a nanopublication.”

We need more:

  • · Semantic tagging of PDFs and beyond
  • · Citation ontologies
  • · Scholarly html – to write these workflows
  • · Authoring tools

Microsoft are looking at some of these things already and Bourn’es group has written plugins for Word – e.g. as you type you auto-check various ontologies that may suggest you change a common name to a standard name. You can tag that at the point of authoring.

All of this is not yet a huge success but it’s coming. Right now there is not much incentive but if publishers can help fast-track the development of these applications then authors will start using them. There’s no use talking about it but it’s only on researchers’ radar when they see science done in a way where this process has made a difference. For example Bourne’s group is running a test to look at spinal muscular atrophy (designated by the NIH as treatable). They will coalesce a set of disparate tools, engage the publishers (Elsevier have opened up ths), in order to address a specific problem that could change lives.

If this works then that would get the kind of attention that scientists would take notice. Only when they see thus process succeeding will they start adopting it. The tipping point will come when the tenure ‘reward system’ starts to change for the next generation, the way science is researched will improve.


Anonymous Anonymous said...

So much can be done with scientific journals through digital publishing. I am intrigued by the proposition of publishers working with scientists at the ideation and data gathering phases. Being involved that early in the process provides opportunities to publish data in ways that were not possible before. The best product is going to come about when there is a true partnership and collaboration between the science provider and the publisher at the right time. The right digital publisher can ensure all data is presented engagingly using video, audio, external linking for sources, and other tools of the trade.
Eric Freese
Aptara, Inc.

8:19 pm  
Anonymous Digital Publishing Specialist said...

Publishing journals on experiments and studies is a convenient way for scientists to present their ideas and develop them. Thank you for this post.

9:40 am  

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