petermr's blog

A Scientist and the Web


Text-mining the scholarly literature: towards a set of universal Principles; Update and strategy

For some years I have seen the primary literature as an enormous untapped resource of scholarly information. We humans are very good at some aspects of “reading the literature” but there are many areas where machines are better and should be used. These include scale (hundreds of thousands of manuscripts), checking, validation, transformation (e.g. scientific units), deduction (many papers have implicit semantics), aggregation of knowledge, and much more. We are now reaching the time when the technology of “text-mining” is mature enough to deploy and, for example, my group and I have developed among the best tools in the world for mining chemistry. I am now expanding that to other fields which I will describe in later posts.

In general the readers of the scholarly literature (who may include the #scholarlypoor) have been seriously frustrated by the restrictions imposed by publishers and universally agreed by librarians. Most subscriptions to most major journals have terms forbidding readers to mine/crawl/index/extract etc. This is not a consequence of copyright – it is an additional restriction imposed by published and apparently automatically assented to by academic purchasing systems (mainly libraries). This automatic assent has done scholarship a grave disservice, so I give the library community a chance to correct the historical record:

Has any library ever publicly challenged the terms of use [on mining] set by publishers? I haven’t seen any. But I’d be grateful to know public cases, and what happened. My current view is that publishers set conditions and that libraries accept them verbatim, which, unfortunately, means that they don’t have a track record of fighting for text-mining or other freedoms.

Moving on, the UK Hargreaves report has recommended removing these restrictions (which are not legally required) and also modifying copyright law. My grapevine suggests there is a high probability that significant changes will be made and that “text-mining” will become widely available without requiring explicit permission. We should prepare for this, and any responsible publisher and library/purchaser should be preparing for this.

A month ago I and colleagues in OKF submitted cases to the Hargreaves process. As part of that I asked 6 major publishers whether I could “text-mine” their journals. Naomi Lillie of OKF is summarising the results and I will keep you in suspense till then. It’s fair to say some were helpful, some were not and some were fuzzy (for whatever motivation).

A number of publishers said we should discuss it with the library. There is no need for this. I and my group can text mine material by myself – in one week Daniel Lowe extracted 500,000 chemical reactions from the US Patent Office without needing any help. Nick Day has built PubCrawler and extracted 200,000 crystal structures from supplemental information without any help. The only thing I need is:

  • An assurance I won’t be sued for behaving like a responsible scholar
  • An assurance that my institution won’t get cut off for (my) responsible behaviour

In case anyone in the publishing or library communities doesn’t understand what “responsible” means, it means:

  • I do not intend deliberately to re-publish the publishers manuscripts (“the PDF”) in bulk without valid scholarly reason.

I am a responsible scholar. I conform to health and safety. I obey the law of the UK. I do not steal. I can justify the expenditures on my grants. I attempt to value and promote human equality in my scholarship. I try to give credit where it is due. Responsible scholarship is a fundamental principle which I believe applies to almost all readers of the scholarly literature. Occasionally I and others fail – there are ample mechanisms for addressing these without forbidding textmining.

So this post asserts my absolute right as a subscriber to the scholarly literature to carry out textmining and to disseminate the results to anyone. I do not need any other permissions.

A number of details follow which I’ll address in later posts.

At present, therefore, a group of us – under the aegis of the Open Knowledge Foundation – is drafting a set of principles for textmining. They include:

We shall come up with a manifesto/set-of-principles. This will be a statement of our rights and our responsibilities. It is not a negotiation, anymore than Tom Paine or the Founding fathers negotiated in the construction of their declarations. Or, more recently, the BBB declarations of Open Access. Those declaration are priceless – it’s just a pity that there are not enough who believe in them enough to push for their universal acceptance. We shall not make the same mistake with the principles of textmining.


Leave a Reply