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A Scientist and the Web


ODOSOS and an article on OA

Egon reminds us of the importance of the intensity of purpose that we need in the Blue Obelisk. (ODOSOS is our mantra: Open Data, Open Source, Open Standards). I won’t add very much new to that but I’ll also add and contrast OA.

I value ODOSOS very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly. It was not until the alchemists started to properly write down procedures that it, as a science, took off. Now, with chemoinformatics in mind, we have the opportunity to write down our procedures in high detail.I keep wondering what the state of drug research would be, if the previous generation of chemoinformaticians would have valued ODOSOS as much as I do. Now, with a close relative being diagnosed last week with a form of cancer with low five-year survival rates, I can not get more angry about those who want to make (unreasonable) money by selling scientific research. A 1M bonus is unreasonable. I can have 10 post-docs work on chemoinformatics research for the same period; I can have them work on drug design for various kinds of cancer.Therefore, I will continue to use every opportunity to convince people of ODOSOS, and will continue to develop new methods to improve accurate exchange of scientific data and experimental results. I will help people where I can to distribute open data, even if the whole project is not 100% ODOSOS. For example, the Chemistry Development Kit is open source itself (LGPL) which does allow embedding into proprietary software. This does not mean that I will contribute to the proprietary software, and actually am proud not having done so in the last 10 years.

I will continue to advice people how to make their work more ODOSOS, even if they cannot make the full transition. I will also continue to make sure that all my scientific results are ODOSOS, as there is no other kind of science. To set a good example, and, hopefully, to lead the way.

This is why I am a proud member of the Blue Obelisk.

PMR: I have had exactly these thoughts today and I’d like to ask for some literature help.

I have been invited to write an article on Open Data for a closed access journal, Serials Review – Elsevier which has a special issue every so often (ca. 4 years) on Open Access. I normally accept such invitations (assuming it’s on something I want to write on) and this one is important …

Serials Review (v.30, no.4, 2004) was a focus issue on Open Access. It remains one of the most heavily downloaded issues and articles even now. Open Access remains a “hot topic” and fundamental discussion in scholarly communication.

I’m not sure who has also accepted but the invitees are well known in the area.
I have taken my subject “Open Data in Science”. I intend to make exactly the case that Egon has made, that Closed anything usually disadvantages the human race.

In the Blue Obelisk we did not include Open Access, because it wasn’t – and isn’t – central to our activities. We are – I suspect – largely in favour but are forced to publish in Closed access journals because the the conservatism of chemists. We make our protests regularly and ritually – the technical editors know us well for the requests to mount stuff here, add addenda there, etc.

So I started through the disciplines – astronomy is open, chemistry is closed, biology is open. And I thought – if the bioscientists had been as selfish as the chemists we wouldn’t have genomes, we wouldn’t know how HIV works, we wouldn’t have the ribosome structure, we wouldn’t understand amyloid. Back in the mid 1990′s there was a movement to patent ESTs (bits of the the genome). I’d be grateful for chapter and verse but essentially Craig Venter wanted to patent these (I know patents are yet another concern) but in 1995 the pharma company Merck donated all its ESTs to the public good. This was typical of the concern of locking up IP.

I’m not sure when journals started to permit and then to require that authors publish their protein and nucleic sequences – I remember late 1980′s. But it’s now mandatory. Earlier the pioneers of bioinformatics , e.g.

*Needleman SB, Wunsch CD. (1970). A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48:443-453.

but also Bill Pearson (who’s here in Cambridge for a year and I met last week), Russell Doolittle, David Lipman, and Margaret Dayhoff (called the “founder of bioinformatics” by Lipman). They showed that the mechanical comparison of sequences was an incredibly powerful tool in understanding the function of proteins and genes, of modelling evolutionary processes, including viral mutations. This technique (and many variants) is at the heart of modern molecular bioscience.


That is why I and Egon feel so angry when information is less than Open. Without Open information people die. So does our planet.
The technology is here. If we wished we could make every new piece of chemistry Open within a year. How much value would that be in finding new chemistry to use in the service of humanity.

[PS. I'd be grateful for any pointers as to how bioinformatics became free. Are there any lessons there for trying to change the chemists' mindset?]

One Response to “ODOSOS and an article on OA”

  1. baoilleach says:

    Here’s my take on it: I think it essentially started before there was any money in it. And since the main tools were free *and* better (due to a head start) there never was any way to make money.

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