Textmining: My years negotiating with Elsevier

This post – which is long, but necessary – recounts my attempts to obtain permission to text-mine content published in Elsevier’s journals. (If you wish to trust my account the simple answer is – I have got nowhere and I am increasingly worried about Elsevier’s Sciverse as a monopolistic walled garden. If you don’t trust this judgement read the details). What matters is that the publishers are presenting themselves as “extremely helpful and responsive to request for textmining” – my experience is the opposite and I have said so to Efke Smit of the STM publishers’ assoc. In particular I believe that Elsevier made me and the chemical community a public promise 2 years ago and they have failed to honour it.

Although it is about chemistry it is immediately understandable by non-scientists. It is immediately relevant to my concerns about the collaboration between the University of Manchester and Elsevier but has much wider implications for scientific text-mining in general. New readers should read recent blogs posts here including http://blogs.ch.cam.ac.uk/pmr/2011/11/25/the-scandal-of-publisher-forbidden-textmining-the-vision-denied/ which explains what scientific textmining can cover and should also read forthcoming posts and comments.

I shall frequently use “we” to mean the group I created in Cambridge and extended virtual coworkers. I am not normally a self-promotionist, but it is important to realise that in the following history “we” are the leading group in chemical textmining, objectively confirmed by the ACS Skolnik award. “we” deserve a modicum of respect in this.

I start from common practice, logic, and legal facts. My basic premises are:

• I have the fundamental and absolute right to extract factual data from the literature and republish it as Open content. “facts cannot be copyrighted” (though collections can). It has been common practice over two or more centuries for scientists to abstract factual data from the literature to which they have access (either by subscription or through public libraries). There are huge compilations of facts. A typical example is the NIST webbook; please look at http://webbook.nist.gov/cgi/cbook.cgi?ID=C64175&Units=SI&Mask=1#Thermo-Gas. This is a typical page (of probably >> 100,000) carefully abstracted from the literature by humans. It is legal, it is valuable and it is essential.
• We have developed technology to automate this process. I argue logically that what a human can do, so can a machine. Logic has no force in business or in court and I am forbidden to deploy my technology it by restrictive publisher contracts (see previous posts). So what is a perfectly natural extension of human practice to machines is forbidden for no reason other than the protection of business interests. It has no logical basis.
• I wish to mine factual data from Elsevier journals, specifically “Tetrahedron” and “Tetrahedron Letters”. I shall refer to these jointly as “Tetrahedron”. The factual content in these journals is created by academics and effectively 100% of this factual content is published verbatim without editorial correction. Authors are required to sign over their rights to Elsevier (and even if there may be exceptions they are tortuous in the extreme and most authors simply sign). Elsevier staff refer to this as “Elsevier content”. I shall always quote this phrase as otherwise it implies legitimacy which I dispute – I do not believe it is legally possible to sign over factual data to a monopolist third party. But it has never been challenged in court.
• Everything I do is Open. I have no hidden secrets in my emails and anyone is welcome to write to the University of Cambridge under FOI and request any of all my emails with Elsevier. I personally cannot publish them many of them because they contain the phrase: The information is intended to be for the exclusive use of the intended addressee(s).  If you are not an intended recipient, be aware that any disclosure, copying, distribution, or use of the contents of this message is strictly prohibited.” However I suspect an FOI request would overrule this.

I have corresponded verbally and by email with several employees of Elsevier. I have done this through my natural contacts as Elsevier provide no central place for me to discuss the questions. I shall anonymise some of the Elsevier employees. If they feel their position has been misrepresented they are welcome to post a comment here and it will be reported in full. If they send an email I reserve the right to publish it Openly.

The simple facts (which can partly be substantiated by FOI on my emails but are stated without them are):

• About 5 years ago I wrote to all five editors of Tetrahedron and also the Elsevier office about the possibility of enhancing Tetrahedron content through text-mining. I did not receive a single reply
• Two years ago there was a textmining meeting at Manchester, organized by NaCTeM and UKOLN (http://www.nactem.ac.uk/tm-ukoln.php). At that meeting Rafael Sidi, Vice-President Product Management, Elsevier presented “Open Up” (30 mins). [He is the named Elsevier contact in the NaCTeM / Elsevier contract]. He gave no abstract and I do not have his slides. From a contemporaneous blog (http://namesproject.wordpress.com/2009/10/ ) “Rafael Sidi of Elsevier (who got through an eye-boggling 180 slides in 30 minutes!) emphasised the importance of openness in encouraging innovation”. With no other record I paraphrase the subsequent discussion between him and me (and I would be grateful for any eyewitness accounts or recordings). If Rafael Sidi wishes to give his account, he is welcome to use this blog.

Essentially Rafael Sidi enthusiastically stated that we should adopt open principles for scientific content and mashup everything with everything. I then asked him if I could textmine Tetrahedron and mashup the content Openly. He said I could. I then publicly said I would follow this up. I have taken this as a public commitment by Sidi (who was representing Elsevier very clearly) that factual content in Tetrahedron could be mined without further permission.

• I then followed it up with mails and phone calls to Sidi. Suffice to report that all the drive can from me and that after six months I had made no progress. I then tried another tack with Elsevier contact. After another 6 months no progress. I then raised this in 2010-10 with a member of Elsevier staff involved with the Beyond the PDF initiative http://sites.google.com/site/beyondthepdf/ . Although not directly concerned with chemistry she took up the case (and I personally thank her efforts) and thought she had made progress (a) by getting Elsevier to draw up a contract allowing me to textmine Tetrahedron and (b) relaying this to David Tempest (Deputy Director “Universal Access”, Elsevier) who is “currently reviewing policies” and “we have finalised our policy and guidelines I would be happy to discuss this further with you.” [That was 9 months ago and I have heard nothing].

The contract is public, apparently available to anyone to negotiate (though there are no rights – all decisions are made by Elsevier). I was told:

You can mine 5 years of Tetrahedron, and will be helped to do so by Frankfurt. You can talk to them about formats.  There are two conditions:

1) You agree with the SciVerse developer’s agreement – on http://developer.sciverse.com/start this is http://developer.sciverse.com/developeragreement – this also means you are not allowed to provide access to the Tetrahedron content (no surprise)

2) You can send us a description of the project you are working on, specifically describing the entities you are interested in mining, and the way in which you will use them.

To summarise:

• Elsevier decide whether I can mine “their” content. I have no right. I can only beg.
• All my results belong to Elsevier and I cannot publish them. Specifically:

3.1.3 the Developer has not used robots, spiders or any other device which could retrieve or

index portions of the Elsevier website, the Elsevier content or the APIs for any unauthorized

purpose, and Developer conforms to all ethical use guidelines as published on the Elsevier

website;

So I cannot search their site except as they permit

3.1.4 the Developer acknowledges that all right, title and interest in and to the Elsevier content,

and any derivative works based upon the Elsevier content, remain with Elsevier and its

suppliers, except as expressly set forth in this Agreement, and that the unauthorized

redistribution of the Elsevier content is not permitted;

“And any derivative works” means that everything I do – chemical structures, spectral data – everything BELONGS TO ELSEVIER. Note the phrase “Elsevier content”. The whole agreement is based on the concept that Sciverse (their platform for publishing “Elsevier content”) is being developed as a walled garden where no-one has rights other than Elsevier.

Well I have only taken 18 months to get to that position. I might be able to negotiate something slightly better if I take another 2 or three years.

And, in any case, I am not begging for permission to do a project. I am asking for my right. Both implied by current practice and also started by Rafael Sidi.

[Incidentally It will be interesting to see if the University of Manchester has signed up to

And that’s where the matter rests. No progress…

But no, I received a request from Elsevier asking if they can use my software. (Why? Because our group is a/the leading one in chemical information extraction). I can’t reproduce it as it’s confidential and I have therefore omitted names , but here is my reply (copied to all the people in Elsevier including Rafael Sidi):

Dear Mr. Murray-Rust,

With great interest I have read your description of the OSCAR 4 chemical entity recognizer. We (redacted) would like to evaluate OSCAR for use in our entity recognizer system and compare it to other analysers.

Because OSCAR is Open Source you may do this without permission.

A few months ago, I have done some comparisons with other annotators and can only say that OSCAR compares quite favourably and is easily deployed – that is to say, if it runs as a Java server.

I assume these comparisons are confidential to Elsevier

This type of functionality is included in the the OSCAR 3 implementation and is really easy to access because no coding layers are required to go between our code and yours – just an http webrequest.

We are using .Net for all our development so a web interface would be real nice. I gather from the article posted (OSCAR4: a flexible architecture for

chemical text-mining) that there are several wrappers around by several users – is there any chance that there is a .Net or HTTP wrapper that we might use? A short-cut in Java to build one ourselves?

I understand this to be a request for free consultancy. Unfortunately we have run out of free consultancy at present.

Do you have any advice here?

Normally I would reply in a positive light to anyone asking polite questions, but I have had two years of unfulfilled promises from Elsevier so I am will engage on one condition – that Elsevier honour the public promise that Rafael Sidi made two years ago.

Mr Sidi stated in public that I could have permission to use OSCAR on chemical reactions published in Elsevier journals (Tetrahedron, Tett Letters, etc.) and to make the results publicly Open. Over that last two years I have tried to get action on this (see copied people). The  closest I got was an agreement which I would have to sign saying that all my work would belong exclusively to Elsevier and that I would not be able to publish any of it. (The current agreement that my library has signed for subscriptions to Elsevier is that all text-mining is explicitly and strictly forbidden). Not surprisingly I did not sign this.

By Elsevier making a public promise I assumed I would be able to do research in this field and publish all the results. In fact Elsevier has effectively held back my work for this period and looks to continue to do it. I regard Elsevier as the biggest obstacle to the academic deployment of textmining at present.

The work that you are asking me to help you with will be an Elsevier monopoly with restrictive redistribution conditions and I am not keen on supporting monopolies. If you can arrange for Elsevier to honour their promise I will be prepared to explore a business arrangement though I am making no promises at present.

Thank you very much,

I am sorry this mail is written in a less than friendly tone but I can not at present donate time to an organisation which works against the direction of my research and academia in general. If Elsevier agrees that scientific content can be textmined without permission and redistributed (as it should be if it is to be useful) then you will have helped to make progress.

I have copied in your colleagues who have been involved in the correspondence over the last two years.

[Name redacted]

I am currently treating your request as confidential as it says so but I do not necessarily regard my reply as such. You will understand that I need a reply

Needless to say I have received no reply. You may regard my reply as rude, but it is the product of broken promises from Elsevier, delays, etc. So, Rafael Sidi, if you are reading this blog I would appreciate a reply and the uncontrolled permission to mine and publish data from Tetrahedron.

Because I shall forward your response (or the lack of one) to the UK government who will use your reply as an example of whether the publishers are helpful to those wanting to textmine the literature.

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The latest articles from BMC Public Health, published between 19-Nov-2011 and 26-Nov-2011For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.Study protocolHome-based exercise and support programme for people with dementia and their caregivers:

???????? ??????? ?????…

?????? ????? ????? ????? ??????? ????? ???? ????????? 90 ???, ?????? ????? ??????? ?????? ????????? 50 ?????? ????? ??? ???????????? ???? ????? ???????????? ??????????? ????? ????? ????? ???? ?????? ???? ??????!

?????? ????? ??????? ????? ??????? ??????? ???????? ???? ????? ???????? ????????? ?????? ??????? ???????? ??? ???????? ???????????!

??????? ?????, ?????????, ????????? ??????? ????????? ??? ????????? ????????

• Springer – 1842 ??? ?????? ??????????????
• Nature – 1869 ??? ?????? ??????????????
• Elsevier – 1880 ??? ?????? ??????????????

3-? ???????? ????????????? ????? ????? ????? ???????????? ?????????? ?????????? ??????? ???? ?????? Prejevalsky-??? ??????, ??????? 1871-73 ??? ?????? ????? ???????? ???? Nature-??? Scientific American ???????? “Rainless Districts—Freaks of the Weather” ????? ????????? ???????? ??? ??????? ?????? 1869 ??? ??????? ???????? ???????? ?????? ?????? ?????? ???????? ???? ????? ????? ?????? ?????? ????? ?????????? ?????? ????????? ??????. ?????? ??????? ??? ???????? ???? ???? ????? ???? ???? ?????.
http://bit.ly/vJ8rJa

N. Prejevalsky-??? ??????? ?????? ????????? ???????? ?????????:

• E. Delmar Morgan, “Prejevalsky’s Journeys and Discoveries in Central Asia,” Proceedings of the Royal Geographical Society and Monthly Record of Geography, New Monthly Series, Vol.9, No.4.(Apr.,1887), pp.213-232
• N. Prejevalsky, E. Delmar Morgan trans., Mongolia: The Tangut Country and the Solitudes of Northern Tibet, (London: Sampson Low, Masrston, Searle, & Rivington, 1876)

20-? ????? ???? ???
Roy Chapman Andrews Mo????, ???? M??????? ??????? ?????? ?????????? ??????? ??????? ???????? ??????? ????? ?????????? ????????? ?? ?????????????? ?????????? ???????? ????? ?????? ???????? ????? ????? ??????? ??????? ???????? ???????????? ?????? ???? ????? ????????.

Roy Chapman Andrews-??? ?????????? ???????? ????????????:

• American Museum of Natural History. (1916). Third Central Asiatic Expedition administrative records,.
• Andrews, R. (1921). Across Mongolian plains a naturalist’s account of China’s “great northwest”, by Roy Chapman Andrews … photographs by Yvette Borup Andrews … New York?;London: D. Appleton and company.
• Andrews, R. (1926). On the trail of ancient man?: a narrative of the field work of the Central Asiatic Expeditions. New York: Putnam.
• Andrews, R. (1953). All about dinosaurs. New York: Random House.
• Andrews, R. (n.d.). Across Mongolian plains.
• Green, F. (1930). Roy Chapman Andrews?: dragon hunter (1st ed.). New York: Putnam.

Roy Chapman Andrews-??? ??????? ???????? Springer-??? Die Naturwissenschaften ????????

• Mongolia the New World. (1928).Die Naturwissenschaften, 16, 243-244. doi:10.1007/BF01504885

???????? ????? ????? ?????? ?????? ??? ???? ????????? ?????? ?????? ??? ??? ????????? ???????????? ?????? ???????? ????? ?????? ??????? 1978 ???

· Purvé, O., Zham’yansan, Y., Malikov, V. M., & Baldan, T. (1978). Flavonoids of Hippophaë rhamnoides growing in Mongolia. Chemistry of Natural Compounds, 14, 341-342. doi:10.1007/BF00713341

???????? ??????????.

????????? ????? ????? ????? ??????????? ???????? ?????? ????? ????? ???????? ???????? ??? ??????? ?????? ?????, ???????? ???????? ?????????? ??????????? ????? ?????? ?????? ?????? ?????????????? ????????? ?? ?? ?????? ?????? ?????? ????????? ????????????? ?????? ?????????? ????????? ??????? ??????? ???????? ?????? ??????? ??????? ????????.

“?? ?????? ???????? ????????? ????? ???????????? ?????? ??????? ?????? ????????? ?? ????? ??? ????????? ! – ????., ??? ?????????

?????? 2 ??? ????? ????? ??????????? ?????? ?????? ????????? 1878-1962 ??? ????? ????? ?????????? 1960-1977 ??? ??????? ?????????? ??? ????? ???????????? ??????? ?????????? ???? ????????? ??. ???: ?????????? ????? ?? ??????? ???????? ??????.

???????? ????? ????? ????? ???????????? ????? ????? ??????? ?????????? 1878-1962 ?????

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• (1878). “Mongolia and Siberia.” Nature 17(439): 435.

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• (1907). “PLAGUE AND THE “TARABAGAN” DISEASE IN MONGOLIA.” The Lancet 170(4397): 1630.

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• Osborn, H. F. (1922). “Discovery of cretaceous and older tertiary strata in mongolia.” Science 56(1446): 291-293.

1923 (3)

• (1923). “The fossil field in Mongolia.” Science 58(1496): 156-157.
• (1923). “Giant hornless rhinoceros from Mongolia.” Nature 112(2802): 67.
• Osborn, H. F. (1923). “Ancient fauna of Mongolia discovered by the third asiatic expedition of the American Museum of Natural History.” Science 57(1487): 729-732.

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• Gregory, W. K. and G. G. Simpson (1926). “Cretaceous mammal skulls from Mongolia.” Nature 118(2976): 698-699.

1928 (1)

• (1928). “Mongolia the New World.” Die Naturwissenschaften 16(14): 243-244.

1929 (1)

• (1929). “Zoological exploration of Mongolia.” Nature 123(3099): 475.

1933 (1)

• (1933). “Distribution of birds of the Russian Altai and northwest Mongolia.” Nature 131(3311): 551.

1936 (1)

• Voelker, C. H. (1936). “Amelioration of dyslogia mongolia.” Journal of Abnormal and Social Psychology 31(3): 266-270.

1938 (1)

• Kislovsky, D. (1938). “The domestic animals of mongolia: A review.” Journal of Heredity 29(1): 27-32.

1952 (3)

• Aberle, D. F. (1952). “Arctic hysteria and latah in Mongolia.” Transactions of the New York Academy of Sciences 14(7): 291-297.
• Flerov, K. K. (1952). “New Dinocerata from Mongolia.” Novye Dinocerata iz Mongolii. 86(5): 1029-1032.
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• Vandeishin, I. (1956). “Surgical treatment of patients with acute and chronic appendicitis in Mongolia.” Khirurgicheskaia pomoshch’ bol’nym s ostrym i khronicheskim appenditsitom v Mongolii. 32(2): 55-56.

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• Kovaleva, R. V. (1958). “Certain characteristics of Pasteurella pestis strains isolated in Mongolia from Microtus brandti and from other rodents.” O nekotorykh osobennostiakh shtammov Pasteurella pestis, vydelennykh v Mongolii ot polevok Brandta i drugikh gryzunov. 29(8): 30-36.

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• Beer, A., P.-Y. Ho, et al. (1961). “An 8th-century meridian line: I-Hsing’s chain of gnomons and the pre-history of the metric system.” Vistas in Astronomy 4(C): 3-28.

1962 (1)

• Khoo, B. C. (1962). “The Mongolian fold (Plica Mongolia).” Singapore medical journal 3: 132-136.

???????? ???????? ??????????? ?????? ????? ???????????? ??????? 1960-1977 ???????:

1960 (1)

• Nagibin, G. B. (1960). “Innovators and inventors of the leading factories.” Glass and Ceramics 14(2): 66-69.

1970 (2)

• Anzon, E. V., I. Y. Chasnikov, et al. (1970). “Coherent production of particles by 60 GeV/c pions on emulsion nuclei.” Physics Letters B 31(4): 241-245.
• Anzon, E. V., I. Y. Chasnikov, et al. (1970). “General characteristics of ?–nucleon interactions at 60 GeV/c obtained in nuclear emulsion.” Physics Letters B 31(4): 237-240.

1972 (2)

• Antonova, M. G., E. G. Boos, et al. (1972). “Coherent production of particles by 67 GeV/c protons on emulsion nuclei.” Physics Letters B 39(2): 285-288.
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• Abdurakhmanov, E., A. Basina, et al. (1974). “Correlations in particle production in pion-proton interactions at 40 GeV/c.” Nuclear Physics, Section B 74(1): 1-11.
• Balea, O., V. Boldea, et al. (1974). “Inclusive ?-p??+ anything and ?-12C??+ anything reactions at 40 GeV/c.” Nuclear Physics, Section B 83(3): 365-376.
• Balea, O., V. Boldea, et al. (1974). “Neutral strange particle production in ?- p, ?- n and ?- C interactions at 40 GeV/c.” Nuclear Physics, Section B 79(1): 57-69.
• Bondarev, G. I. and T. Lamzhav (1974). “Vitamin C provision of children in Mongolia (Russian).” Voprosy Psikhologii 33(2): 53-56.
• Chultem, T. and N. A. Yakovkin (1974). “Stationary equations of hydrogen excitation and ionization in prominences.” Solar Physics 34(1): 133-150.
• Dolgor, P. and L. Zhigzhidsuren (1974). “Combined laparoscopy in diseases of the hepatobiliary system (Russian).” Khirurgiya 50(1): 80-82.
• Shagdarsuren, T. and E. Bodkhyy (1974). “Some results of surgical treatment of cardiovascular diseases in Mongolia (Russian).” EKSPER.KHIR.ANESTESIOL. 19(1): 27-29.
• Zedew, N., Z. Dorsh, et al. (1974). “Results of ectoparasite control of livestock in Mongolia.” ERGEBNISSE DER EKTOPARASITENBEKAMPFUNG IN TIERBESTANDEN DER MVR 29(p): 667-670.

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• Dashzeveg, D. (1975). “New primitive therian from the early Cretaceous of Mongolia.” Nature 256(5516): 402-403.
• Demid, G. (1975). “Rate of congenital dislocations of the hip among the child population in the Mongolian People’s Republic (Russian).” Ortopediya Travmatologiya i Protezirovanie No. 5: 26-29.

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• Gun Aazav, T. and A. K. Kukuskin (1976). “Investigation of two photosystem interaction by fluorescence method (Russian).” Studia Biophysica 60(3): 223-231.
• Mishigdorzh, B. (1976). “Experience with setting up of bronchological service at an antituberculous establishment in the Mongolian People’s Republic (Russian).” Problemy Tuberkuleza 54(4): 11-13.
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• Naidan, D. and I. I. Sapezhinskii (1977). “Photochemiluminescence of tryptophan containing peptides and proteins on photo-oxidation-VI. Kinetic patterns of eosin-sensitized photochemiluminescence of solutions of human serum albumin.” BIOPHYSICS 22(4): 590-594.
• Naydan, D. and I. I. Sapezhinsky (1977). “Photochemoluminescence of tryptophan-containing peptides and proteins during photooxidation. VI. Kinetics of eosin-sensitized photochemoluminescence of human serum albumin solutions.” Biofizika 22(4): 571-575.
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The latest articles from Journal of Occupational Medicine and Toxicology, published between 11-Nov-2011 and 25-Nov-2011For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.ResearchReduced inclination of cervical spine in a novel notebook screen

Stepping down as Moderator of American Scientist Open Access Forum

In September 2011 the AmSci Open Access Forum went into its 14th year. I think I have been moderating the Forum long enough, and so I’m stepping down as moderator, effective the end of December.

Subscribers will vote on whether to continue the AmSci Forum or whether the other two OA Forums (SOAF and BOAI) are now sufficient to air views on OA.

I will of course remain active in OA and will be posting to the existing Forums (and AmSci, if it continues) and/or the OA Archivangelism blog whenever the spirit moves or the occasion calls!

Textmining: NaCTeM and Elsevier team up; I am worried

A bit over two weeks ago the following appeared on DCC-associates: http://www.mail-archive.com/dcc-associates@lists.ed.ac.uk/msg00618.html

Mon, 07 Nov 2011 09:16:34 -0800

This press release may be of interest to list members.


University enters collaboration to develop text mining applications


07 Nov 2011


http://www.manchester.ac.uk/aboutus/news/display/?id=7627




The University of Manchester has joined forces with Elsevier, a leading


provider of scientific, technical and medical information products and


services, to develop new applications for text mining, a crucial research tool.


The primary goal of text mining is to extract new information such as named


entities, relations hidden in text and to enable scientists to systematically


and efficiently discover, collect, interpret and curate knowledge required for


research.


The collaborative team will develop applications for SciVerse Applications,


which provides opportunities for researchers to collaborate with developers in


creating and promoting new applications that improve research workflows.


The University's National Centre for Text Mining (NaCTeM), the first


publicly-funded text mining centre in the world, will work with Elsevier's


Application Marketplace and Developer Network team on the project.


Text mining extracts semantic metadata such as terms, relationships and events,


which enable more pertinent search. NaCTeM provides a number of text mining


services, tools and resources for leading corporations and government agencies


that enhance search and discovery.


Sophia Ananiadou, Professor in the University's School of Computer Science and


Director of the National Centre for Text Mining, said: "Text mining supports


new knowledge discovery and hypothesis generation.


"Elsevier's SciVerse platform will enable access to sophisticated text mining


techniques and content that can deliver more pertinent, focused search results."


"NaCTeM has developed a number of innovative, semantic-based and time-saving


text mining tools for various organizations," said Rafael Sidi, Vice President


Product Management, Applications Marketplace and Developer Network, Elsevier.


"We are excited to work with the NaCTeM team to bring this expertise to the


research community."


Now I have worked with NaCTeM, and actually held a JISC grant (ChETA) in which NaCTeM were collaborators and which resulted in both useful work, published articles and Open Source software. The immediate response to the news was from Simon Fenton-Jones

Let me see if I got this right.


"Elsevier, a leading provider of scientific, technical and medical


information products and services", at a cost which increases much faster


than inflation, to libraries who can't organize their researchers to back up


a copy of their journal articles so they can be aggregated, is to have their


platform, Sciverse, made more attractive, by the public purse by a simple


text mining tool which they could build on a shoestring.


Sciverse Applications, in return, will take advantage of this public


largesse to charge more for the journals which should/could have been


compiled by public digital curators in the first instance.


Hmmm. So this is progress.


Hey. It's not my money!


[PMR: I think it’s “not his money” because he writes from Australia, but he will still suffer]

PMR: I agree with this analysis. I posted an initial response (http://www.mail-archive.com/dcc-associates@lists.ed.ac.uk/msg00621.html )

No – it’s worse. I have been expressly and consistently asking Elsevier for

permission to text-mine factual data form their (sorry OUR) papers. They

have prevaricated and fudged and the current situation is:

“you can sign a text-mining licence which forbids you to publish any

results and handsover all results to Elsevier”

I shall not let this drop – I am very happy to collect allies. Basically I

am forbidden to deploy my text-mining tools on Elsevier content.

P.

I shall elaborate on this. I was about to write more, because I completely agree about the use of public money and the lack of benefit to the community. However I have been making enquiries and it appears that public funding for NaCTeM is being run down – effectively they are becoming a “normal” department of the university – with less (or no) “national” role.

However the implications of this deal are deeply worrying – because it further impoverishes our rights in the public arena and I will explain further later. I’d like to know exactly what NaCTeM and the University of Manchester are giving to Elsevier and what they are getting out of it.

This post will give them a public chance – in the comments section, please – to make their position clear.

The scandal of publisher-forbidden textmining: The vision denied

This is the first post of probably several in my concern about textmining. You do NOT have to be a scientist to understand the point with total clarity. This topic is one of the most important I have written about this year. We are at a critical point where unless we take action our scholarly rights will be further eroded. What I write here is designed to be submitted to the UK government as evidence if required. I am going to argue that the science and technology of textmining is systematically restricted by scholarly publishers to the serious detriment of the utilisation of publicly funded research.

What is textmining?

The natural process of reporting science often involves text as well as tables. Here is an example from chemistry (please do not switch off – you do not need to know any chemistry.) I’ll refer to it as a “preparation” as it recounts how the scientist(s) made a chemical compound.

To a solution of 3-bromobenzophenone (1.00 g, 4 mmol) in MeOH (15 mL) was added sodium borohydride (0.3 mL, 8 mmol) portionwise at rt and the suspension was stirred at rt for 1-24 h. The reaction was diluted slowly with water and extracted with CH2Cl2. The organic layer was washed successively with water, brine, dried over Na2SO4, and concentrated to give the title compound as oil (0.8 g, 79%), which was used in the next reaction without further purification. MS (ESI, pos. ion) m/z: 247.1 (M-OH).

The point is that this is a purely factual report of an experiment. No opinion, no subjectivity. A simple, necessary account of the work done. Indeed if this were not included it would be difficult to work out what had been done and whether it had been done correctly. A student who got this wrong in their thesis would be asked to redo the experiment.

This is tedious for a human to read. However during the C20 there have been large industries based on humans reading this and reporting the results. Two of the best known abstracters are the ACS’s Chemical Abstracts and Beilstein’s database (now owned by Elsevier). These abstracting services have been essential for chemistry – to know what has been done and how to repeat it (much chemistry involves repeating previous experiments to make material for further synthesis , testing etc.).

Over the years our group has developed technology to read and “understand” language like this. Credit to Joe Townsend, Fraser Norton, Chris Waudby, Sam Adams, Peter Corbett, Lezan Hawizy, Nico Adams, David Jessop, Daniel Lowe. Their work has resulted in an Open Source toolkit (OSCAR4, OPSIN, ChemicalTagger) which is widely used in academia and industry (including publishers). So we can run ChemicalTagger over this text and get:

EVERY word in this has been interpreted. The colours show the “meaning” of the various phrases. But there is more. Daniel Lowe has developed OPSIN which works out (from a 500-page rulebook from IUPAC) what the compounds are. So he has been able to construct a complete semantic reaction:

If you are a chemist I hope you are amazed. This is a complete balanced chemical reaction with every detail accurately extracted. The fate of every atom in the reaction has been worked out. If you are not a chemist, try to be amazed by the technology which can read “English prose” and turn it into diagrams. This is the power of textmining.

There are probably about 10 million such preparations reported in the scholarly literature. There is an overwhelming value in using textmining to extract the reactions. In Richard Whitby’s Dial-a-molecule project (EPSRC) the UK chemistry community identified the critical need to text-mine the literature.

So why don’t we?

Is it too costly to deploy?

No.

Will it cause undue load on pubklisher servers.

No, if we behave in a responsible manner.

Does it break confidentiality?

No – all the material is “in the public domain” (i.e. there are no secrets)

Is it irresponsible to let “ordinary people” do this/

No.

Then let’s start!

NO!!!!

BECAUSE THE PUBLISHERS EXPRESSLY FORBID US TO DO TEXTMINING

But Universities pay about 5-10 Billion USD per year as subscriptions for journals. Surely this gives us the right to textmine the content we subscribe to.

NO, NO, NO.

Here is part of the contract that Universities sign with Elsevier (I think CDL is California Digital Library but Cambridge’s is similar) see http://lists.okfn.org/pipermail/open-science/2011-April/000724.html for more resources

 The CDL/ Elsevier contract includes [@ "Schedule 1.2(a)


 General Terms and Conditions  "RESTRICTIONS ON USAGE OF THE LICENSED PRODUCTS/ INTELLECTUAL PROPERTY RIGHTS" GTC1]


"Subscriber shall not use spider or web-crawling or other software programs, routines, robots or other mechanized devices to continuously and automatically search and index any content accessed online under this Agreement. "


What does that mean?

NO-TEXTMING. No INDEXING. NO ROBOTS. No NOTHING.

Whyever did the library sign this?

I have NO IDEA. It’s one of the worst abrogations of our rights I have seen.

Did the libraries not flag this up as a serious problem?

If they did I can find no record.

So the only thing they negotiated on was price? Right?

Appears so. After all 10 Billion USD is pretty cheap to read the literature that we scientists have written. [sarcasm].

So YOU are forbidden to deploy your state-of-the art technology?

PMR: That’s right. Basically the publishers have destroyed the value of my research. (I exclude CC-BY publishers but not the usual major lot).

What would happen if you actually did try to textmine it.

They would cut the whole University off within a second.

Come on, you’re exaggerating.

Nope – it’s happened twice. And I wasn’t breaking the contract – they just thought I was “stealing content”.

Don’t they ask you to find out if there is a problem?

No. Suspicion of theft. Readers are Guilty until proven innocent. That’s publisher morality. And remember that we have GIVEN them this content. If I wished to datamine my own chemistry papers I wouldn’t be allowed to.

But surely the publishers are responsive to reasonable requests?

That’s the line they are pushing. I will give my own experience in the next post.

You will have to find out.

Meanwhile you are going to send this to the government, right?

Right. The UK has commissioned a report on this. Prof Hargreaves. http://www.ipo.gov.uk/ipreview-finalreport.pdf

And it thinks we should have unrestricted textmining?

Certainly for science technical and medical.

So what do the publishers say?

They think it’s over the top. After all they have always been incredibly helpful and responsive to academics. So there isn’t a real problem. See http://www.techdirt.com/articles/20111115/02315716776/uk-publishers-moan-about-content-minings-possible-problems-dismiss-other-countries-actual-experience.shtml

Nonetheless, the UK Publishers Association, which describes its “core service” as “representation and lobbying, around copyright, rights and other matters relevant to our members, who represent roughly 80 per cent of the industry by turnover”, is unhappy. Here’s Richard Mollet, the Association’s CEO, explaining why it is against the idea of such a text-mining exception:

If publishers lost the ability to manage access to allow content mining, three things would happen. First, the platforms would collapse under the technological weight of crawler-bots. Some technical specialists liken the effects to a denial-of-service attack; others say it would be analogous to a broadband connection being diminished by competing use. Those who are already working in partnership on data mining routinely ask searchers to “throttle back” at certain times to prevent such overloads from occurring. Such requests would be impossible to make if no-one had to ask permission in the first place.

They’ve got a point, haven’t they?

PMR This is appalling disinformation. This is ONLY the content that is behind the publisher’s paywalls. If there were any technical problems they would know where they come from and could arrange a solution.

Then there is the commercial risk. It is all very well allowing a researcher to access and copy content to mine if they are, indeed, a researcher. But what if they are not? What if their intention is to copy the work for a directly competing-use; what if they have the intention of copying the work and then infringing the copyright in it? Sure they will still be breaking the law, but how do you chase after someone if you don’t know who, or where, they are? The current system of managed access allows the bona fides of miners to be checked out. An exception would make such checks impossible.

[“managed access” == total ban]

If you don’t immediately see this is a spurious argument, then read the techndirt article. The ideal situation for publishers is if no-one reads the literature. Then it’s easy to control. This is, after all PUBLISHING (although Orwell would have loved the idea of modern publishing being to destroy communication).

Which leads to the third risk. Britain would be placing itself at a competitive disadvantage in the European & global marketplace if it were the only country to provide such an exception (oh, except the Japanese and some Nordic countries). Why run the risk of publishing in the UK, which opens its data up to any Tom, Dick & Harry, not to mention the attendant technical and commercial risks, if there are other countries which take a more responsible attitude.

So PMR doing cutting-edge research puts Britain at a competitive disadvantage. I’d better pack up.

But not before I have given my own account of what we are missing and the collaboration that the publishers have shown me.

Latest Article Alert from BMC Infectious Diseases

The latest articles from BMC Infectious Diseases, published between 25-Oct-2011 and 24-Nov-2011For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.CommentaryCMV retinitis in China and SE Asia: the way forwardHeiden D, Saranchuk PBMC Infectious

Latest Article Alert from BMC Medical Research Methodology

The latest articles from BMC Medical Research Methodology, published between 25-Oct-2011 and 24-Nov-2011For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.ReviewSelection of the appropriate method for the assessment of insulin resistanceBorai A,

60% of Journals Allow Immediate Archiving of Peer-Reviewed Articles – but it gets much much better…

The database improvements we made to SHERPA/RoMEO in August 2011 have enabled us to generate new statistics on the number of journals that permit self-archiving. We presented a provisional pie chart of journals broken down by RoMEO Colour at Open Repositories 2011. This is updated in the following chart, which uses a snapshot of the RoMEO Journals database taken on the 15th November 2011.

An alternative way of viewing this data is to look at how many of the versions of articles that academics prefer most can be archived, as in the following chart:

Like RoMEO Colours, this chart is based on strong open access, where there are no embargoes or restrictions that prevent immediate self-archiving. As with the colour chart, this shows that 60% of  journals allow the final peer-reviewed version of an article to be archived immediately, with a further 27% permitting the submitted version (pre-print) to be archived immediately.

Only 13% of journals do not allow immediate archiving, but moving away from the ideal of immediate open access, the situation changes once any embargo periods have expired. This is shown in the following chart:

This chart takes account of embargoes of any length. The most common embargo period is 12 months, followed by 6 months, and then 24 months. A few embargoes are longer, the maximum recorded in RoMEO now being 5 years.

Embargo (months) Percent Relative Frequency
3 1% |
6 17% |||||||||||||||||
12 47% |||||||||||||||||||||||||||||||||||||||||||||||
18 4% ||||
24 28% ||||||||||||||||||||||||||||
36 1% |
60 1% |

Expiring embargos clearly improve the situation regarding archiving, but additional restrictions may still remain. For instance, it may be necessary to obtain permission to archive from the publisher, a fee might have to be paid, or archiving may only be available to authors whose work is paid for by certain specific funders. These restrictions may therefore make archiving impractical. However, if these restrictions can be complied with, the archiving situation improves still further, as shown in our final chart:

This chart shows that a remarkable 94% of journals allow archiving of peer-reviewed articles after any embargo period has expired and any addional restrictions have been complied with. Indeed, for nearly a quarter of journals, the publisher’s version/PDF itself can be archived. Just 1% of journals only permit the pre-peer review submitted version to be archived. This leaves only 5% of journals that do not permit self-archiving of some form or another.

On the date the data for these charts was compiled (15th Nov.2011), the RoMEO Journals database held about 19,000 titles. Unfortunately, assigning journals to policies is not an exact process, due to the vagueness of some publishers’ policies and the fact that some publishing houses do work for societies and other third parties whose own open access policies may take precedence. It is therefore difficult to gauge the precision of these figures, but we guestimate that they are accurate to within 2%. The charts do not take into account journals that are not covered by RoMEO’s own database, but we expect that the relative proportions would be similar.

Peter Millington