O'Really?

Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view. According to the wikipedia article Open Access (OA) is “free, immediate, permanent, full-text, online access, for any user, web-wide, to digital scientific and scholarly material, primarily research articles published in peer-reviewed journals. OA means that any individual user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article. An OA article usually has limited copyright and licensing restrictions.” What does all this mean and why does it matter? Well, in four question-and-answer points, here goes…

Why does Open Access matter to you?

Open Access matters to me because it is needed for enabling and accelerating scientific discovery. Most scientific knowledge, that isn’t locked up inside scientists heads is published in peer-reviewed journals as papers, most of which are available on the internet – but only if you have paid a subscription to the relevant publisher. To make the most of this vast quantity of knowledge, it needs to be accessible to the widest possible audience, which includes both people (like you and me) as well as machines like Googlebot (and millions of others programs like it [1], written by software engineers).

This might sound vague, so let us illustrate with example. A project I’m working on with lots of other people, (funded by public money from a body called the BBSRC) is building electronic models of metabolism in yeast. This humble organism has helped people to understand fundamental concepts of the way life works, deep down at the biochemical level, and will very probably lead to many new discoveries in the future. A digital model, which describes the thousands of genes and many more reactions in yeast has been recently been published [2] in a high-profile (but unfortunately closed-access) journal called Nature Biotechnology. To make the most of this model, it needs to be fully annotated by deriving detailed descriptions of the primary evidence for each reaction in the model so that humans (and also machines) can better understand the model – both now and in the future. Most of this evidence exists in journals, around 6,000 individual articles in total – but unfortunately only ~1% of this data is publicly available by Open Access (see Table 1 below) – in a public Open Access archive called PubMedCentral. The other ~99% of the data is exclusively available via closed-access subscription-based publishers websites, and this severely restricts the kind of use and data mining that can be done in order to improve and understand the model. I happen to work for a University that pays shed loads of money to scientific publishers for access, but others are not so lucky. Although all the data is available to me, I am unable to use, re-use and share it freely to make derivative scientific works from it.

Table 1: Currently, only around 1% (approx 75/6000 papers) of data used in a model of yeast metabolism [2], is fully available for use and re-use by people and machines.

The fact that people, and perhaps more importantly, machines, have such limited access to this data means that instead of making better models using all of the data, we (and many other scientists like us) are forced to use a tiny subset of the data. The models we build are not as good as they could be, and the tools we make are severely handicapped by lack of full access to the raw data. So Open Access matters to me, because I care about building the best models possible using all of the data available in an unrestricted manner. In short, as a Scientist, I need Open Access so that I can do my job properly.

How did you first become aware of it?

The first time I became aware of it was probably on the launch day, five (yikes!) years ago today, at the European Bioinformatics Institute (EBI) – where everyone was wearing those blue PLoS T-shirts…

Why should scientific and medical research be an open-access resource for the world?

Most scientific and medical research is paid for by tax payers. It does not come cheap but it benefits us all in the long run. By making the results of this expensive research available by Open Access, we should enable more discoveries for all the billions of dollars/euros/pounds/yen/rupee etc that are spent each year on research. Open Access is about providing maximum value for the money spent on research.

What do you do to support Open Access, and what can others do?

Wherever possible, I try to publish my results in Open Access journals (the “gold road” to OA) or self-archive copies in some kind of public repository (the “green road” to OA). For example, our next paper is published in an Open Access journal called PLoS Computational Biology [2]. By publishing here, I hope that it will maximise the return on investment, paid by the tax paying public. The results of my research are available to the widest possible audience, that isn’t just me be selfish and egotistical. It is almost impossible to know in advance which discoveries and inventions are going to be the most useful to who and why. At least if the results are publicly available, to humans and machines, I can maximise their use and re-use by anybody (or anything) that re-uses them in the future.

If you feel the same way about your research, you should be trying to do the same.

What other people say

Enough of my blabbering, let’s conclude with what other people say about Open Access because they are much better at saying it than me:

“The critical aspect of Open Access for me is that increased discoverability and browseability will lead to greater efficiency of conducting research. Any savings in efficiency translate quite directly into savings for taxpayers and time savings for researchers. That ultimately means more discoveries, sooner, for less money.”

—André Brown

Ph.D. Student

University of Pennsylvania, USA

Why does Open Access Matter to you? I don’t care how prestigious you think your journal is, or whether you see yourself as some kind of “guardian of knowledge”. I want information, I want it now and if you can’t deliver, I’m going somewhere else.

—Neil Saunders

PostDoctoral Researcher

University of Queensland, Australia.

“Open Access helps scientists make the discoveries we need to improve health, provides the opportunity for their work to be more easily read and cited, enables integration of research with other resources, helps funding bodies evaluate the research they have funded, and ensures that the digital record of medicine can be preserved.”

—Mark Walport

Director of the Wellcome Trust, UK

“I think we’ll look back in ten years time and wonder what all the fuss was about. I can’t believe that the current commercial scientific publishing model can survive, slowly but surely, the legacy literature will be made Open Access.”

—Michael Ashburner

University of Cambridge

“I find it very difficult to understand people who want to keep their data closed when it has been funded by public domain resources for the good, generally of everybody, I see no reason not to make your data fully accessible.”

—Ewan Birney

EMBL-EBI

References

1. Russ Altman, Casey Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Jensen, Martin Krallinger, Barend Mons, Sean O’Donoghue, Manuel Peitsch, Dietrich R Schuhmann, Hagit Shatkay, Alfonso Valencia (2008) Text mining for biology – the way forward: opinions from leading scientists Genome Biology, Vol. 9, No. Suppl 2. (2008). DOI:10.1186/gb-2008-9-s2-s7, pubmed.gov/18834498
2. Markus Herrgård and Neil Swainston et al A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 2008 Oct;26(10):1155-60. pubmed.gov/18846089, DOI:10.1038/nbt1492
3. Duncan Hull, Steve Pettifier and Douglas Kell (2008). Defrosting the Digital Library, A survey of bibliographic tools for the next generation Web. PLoS Computational Biology, to appear end of October 2008.
4. Peter Suber (2004) Open Access Overview
5. Stevan Harnad, Tim Brody, François Vallières, Les Carr, Steve Hitchcock, Yves Gingras, Charles Oppenheim, Chawki Hajjem, and Eberhard R. Hilf (2008). The Access / Impact Problem and the Green and Gold Roads to Open Access: An Update. Serials Review, 34(1):36-40. DOI:10.1016/j.serrev.2007.12.005