petermr's blog

Essential action from Peter Suber’s blog:
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In my last post (Nature: How much content can our robots access?) I asked general questions about what data, if any, in a scientific article publishers would not allow humans and robots to use without permission. So, as an example, I’m asking Nature what parts of a data-rich article can be re-used automatically.
The model I have is that our robots can access electronic publications, extract data, and re-use it. Ideally we would like XML, but text and PDF can give good (though not perfect) results. Nature has recently brought out “Protocols”, which publishes recipes. I think this is a great idea – not enough credit is given to the actual work laboratory done in many subjects. So I give some snapshots (claiming fair use as the paper is freely readable and I haven’t taken the whole) show what our robots can do, and ask what I am permitted to do:
That’s the abstract. I expect it’s on Pubmed, so perhaps my robots can mine it for chemicals?
YES/NO?

This is one of the molecules mentioned in the paper (there are 10-20). This is the normal way of communicating the structure of a molecule, but it’s also an image. My robots can download it and interpret the structure. But technically it’s an image. Are the robots allowed to download and extract the molecular data without permission:
YES/NO
So then the protocol shows what actually happens in the reaction, and notes that there is a critical patch of colour:

Here the only way of communicating the FACT of the reaction colour is to show an image. This isn’t a creative work of art (though there are good photos and bad ones) but is an ESSENTIAL part of the record. There are now systems which could be trained to browse the Internet and return all flasks which contain a greenish liquid. Can we download and analyse images of experimental results:
YES/NO:
And here is the spectral data.

Can my robots download this and turn it into semantic data.?
And in doing so this is the sort of thing that OSCAR can produce. It’s taken part of the text and identified all the compounds (and worked out the atomic connectivity – see “furan” at the right).

All of this is enormously valuable. If we are allowed to do it we can answer questions like “what reactions involve furans, or pyrroles, use Sodium ammonia, and undergo a light green colour”.
But it will only happen if publishers let us have access to their data without any barrier – no written permissions, no hangup over scientific photographs and images.
I’ve put Timo on the spot, but I trust him to be clear. That will make it easier when asking the other publishers later.

In this blog ( Copyrighted Data: replies [1], Wiley and eMolecules: unacceptable; an explanation would be welcome –[2] , and elsewhere we have been discussing the “copyright” of factual information, or “data”. In [2] I ask a major publisher whether copyright applies to some or all of the factual scientific record they publish. So far I have had no reply. Here I ask another, Nature, who – at least through Timo Hannay – have been very helpful in discussing aspects of publication (most other publishers have been silent).
The issue arises in “supplemental data” or “supporting information” which is the factual record of the experiment – increasingly required as proof of correctness. Some major publishers (Royal Soc Chemistry, Int. Union of Crystallography, Nature) do not claim copyright over this; others such as American Chemical Society and Angewandte Chemie (Wiley) appear to do so, though I haven’t had a definitive public statement from either.
Our vision for the future is that a large part of published scientific data could be made directly machine-understandable, if the publishers collaborate in this. This would mean that we would have semantic knowledge accessible through engines such as Google, Metaweb, OpenLink, etc. We have built technology (OSCAR) that can extract 80% of the chemistry from scientific publications and it could index the whole literature in a few days using systems such as Condor. I heard yesterday of an image recognition system which can scan Flicker for photos of “family of four”, “red flower”, “cat and dog”, for example (feature recognition, not tagging). It looks straightforward to ask for papers which contain images of “gel”, “protein surface (GRASP)”, “aligned sequences”, “dose response curve”, “chemical formulae” etc. These are sufficiently stereotyped that I am sure this is possible – and even if it isn’t we should try.
But many publishers will simply forbid us to do this. Wiley claims graphs are their copyright. I expect they do this for gels, protein images, etc. If I ask I expect the average publisher will say you have to apply separately for permission for every image. This, of course, is impossible for a robot – we want to index a million images in a day.
The information itself is not copyright. If I sit down with a keyboard I can retype all the factual information into abstracts, collections, etc. But only the stuff that can be entered on a keyboard. Not images. Not graphs. Those I have to disassemble into words or numbers, which – in the C21 is grotesque.
So I am going to ask Nature what I can do and what I can’t. What my robots can do and what the can’t. If the answer is not “YES” to a question it is “NO” – there can be no “middle ground” for robots. If you don’t know then the answer is NO. If I have to ask for permission the answer is NO.
As background I want to praise Timo and colleagues for their support for us over the years – they have funded a summer student, and also given us an XML corpus for our SciBorg project (on which they also advise). They understand the vision.
This is already a long post, so the details and questions will be in the next one.
I’ll be using the new – and I think exciting and valuable – Nature Protocols as an example – in particular http://www.nature.com/nprot/journal/v2/n8/full/nprot.2007.245.html
which I think is currently Freely Accessible though not (in my language  and BBB) full Open Access.

As readers will know I have written Open letters to publishers with whom I have a connection about their connection with PRISM. I am pleased to report that I have a clear response from CUP, the University’s press. Interestingly – and I shall comment on this in later posts – my normal email didn’t get through (as I think this may not be uncommon). Stephen Bourne of CUP writes:

I heard about PRISM launch for the first time last week, from which you will understand that Cambridge University Press has in no way been involved in,  or consulted on, the PRISM initiative.
PRISM’s message is over-simplistic and ill-judged, with the unwelcome consequence of creating tension between the publishing community and the proponents of Open Access. While there will inevitably be some differences in philosophy between those two communities, we believe that there will always be a place for alternative forms of publishing, and that we can and should co-exist. With that objective in mind, Cambridge University Press has long been constructively engaged in Open Access issues, the Cambridge Open Option (http://www.journals.cambridge.org/action/forAuthors?page=open# ) being an example of one of the forms of publishing we offer. We will continue to be open to discussions on this matter.
Yours sincerely,
Stephen Bourne

PMR: Thank you,  Stephen, for a very clear statement.