How much does it cost to buy all my scientific articles?
Disregarding the slight difference in exchange rate between the current Euro and USD the answer is around 1’200 USD/Euros. That is the amount of money I would have to pay to download all the scientific articles I have been involved in, – if I did not have access to a university library with subscription. I have signed off the copyright to many articles to a long string of publishers, Elsevier, Wiley, IEEE, Springer, etc., and I no longer control the publication.
I have added a good number of my articles to Wikidata including the price for each article. The SPARQL-based Wikidata Query Service is able to generate a table with the price information, see here. The total sum is also available after a slight modication of the SPARQL query.
The Wikidata Query Service can also generate plots, for instance, of the price per page as a function of the publication date (choose “Graph builder” under “Display”). In the plot below the unit (currency) is mixed USD and Euro. (there seem to be an issue with the shapes in the legend)
Something like 3 to 4 USD/Euros per page seems to what an eyesight averaging comes to.
Among the most expensive articles are the ones from the journal Neuroinformatics published by Springer: 43.69 Euros for each article. Wiley articles cost 38 USD and the Elsevier articles around 36 USD. The Association for Computing Machinery sells their articles for only 15 USD. A bargain.
It may be difficult to find the price of the articles. Science claims that “Science research is available free with registration one year after initial publication.” However, I was not able to get to the full text for The Real Power of Artificial Markets on the Science website. On one page you can stubble onto this: “ ” and that is what I put into Wikidata. The article is fairly short so this price makes it the priciest article per page.
I ought to write something discerning about the state of scientific publishing. However, I will instead redirect you to a recent blog post by Tal Yarkoni.
Recently Lambert Heller wrote an overview piece on websites for scholarly profile pages: “What will the scholarly profile page of the future look like? Provision of metadata is enabling experimentation“. There he tabularized the features of the various online sites having scholarly profile pages. These sites include (with links to my entries): ORCID, ResearchGate, Mendeley, Pure and VIVO (don’t know these two), Google Scholar and Impactstory. One site missing from the equation is Wikidata. It can produce scholarly profile pages too. The default Wikidata editing interface may not present the data in a nice way – Magnus Manske’s Reasonator – better, but very much of the functionality is there to make a scholarly profile page.
In terms of the features listed by Heller, I will here list the possible utilization of Wikidata:
- Portrait picture: The P18 property can record Wikimedia Commons image related to a researcher. For instance, you can see a nice photo of neuroimaging professor Russ Poldrack.
- Researchers alternative names: This is possible with the alias functionality in Wikidata. Poldrack is presently recorded with the canonical label “Russell A. Poldrack” and the alternative names “Russell A Poldrack”, “R. A. Poldrack”, “Russ Poldrack” and “R A Poldrack”. It is straightforward to add more variations
- IDs/profiles in other systems: There are absolutely loads of these links in Wikidata. To name a few deep linking posibilities: Twitter, Google Scholar, VIAF, ISNI, ORCID, ResearchGate, GitHub and Scopus. Wikidata is very strong in interlinking databases.
- Papers and similar: Papers are presented as items in Wikidata and these items can link to the author via P50. The reverse link is possible with a SPARQL query. Futhermore, on the researcher’s items it is possible to list main works with the appropriate property. Full texts can be linked with the P953 property. PDF of papers with an appropriate compatible license can be uploaded to Wikimedia Commons and/or included in Wikisource.
- Uncommon research product: I am not sure what this is, but the developer of software services is recorded in Wikidata. For instance, for the neuroinformatics database OpenfMRI it is specified that Poldrack is the creator. Backlinks are possible with SPARQL queries.
- Grants, third party funding. Well there is a sponsor property but how it should be utilized for researchers is not clear. With the property, you can specify that paper or research project were funded by an entity. For the paper The Center for Integrated Molecular Brain Imaging (Cimbi) database you can see that it is funded by the Lundbeck Foundation and Rigshospitalet.
- Current institution: Yes. Employer and affiliation property is there for you. You can see an example of an incomplete list of people affiliated with research sections at my department, DTU Compute, here, – automagically generated by the Magnus Manske’s Listeria tool.
- Former employers, education etc.: Yes. There is a property for employer and for affiliation and for education. With qualifiers you can specify the dates of employment.
- Self assigned keywords: Well, as a Wikidata contributor you can create new items and you can use these items for specifying field of work of to label you paper with main theme.
- Concept from controlled vocabulary: Whether Wikidata is a controlled vocabulary is up for discussion. Wikidata items can be linked to controlled vocabularies, e.g., Dewey’s, so there you can get some controlness. For instance, the concept “engineer” in Wikidata is linked the BNCF, NDL, GND, ROME, LCNAF, BNF and FAST.
- Social graph of followers/friends: No, that is really not possible on Wikidata.
- Social graph of coauthors: Yes, that is possible. With Jonas Kress’ work on D3 enabling graph rendering you got on-the-fly graph rendering in the Wikidata Query Service. You can see my coauthor graph here (it is wobbly at the moment, there is some D3 parameter that need a tweak).
- Citation/attention metadata from platform itself: No, I don’t think so. You can get page view data from somewhere on the Wikimedia sites. You can also count the number of citations on-the-fly, – to an author, to a paper, etc.
- Citation/attention metadata from other sources: No, not really.
- Comprehensive search to match/include own papers: Well, perhaps not. Or perhaps. Magnus Manske’s sourcemd and quickstatement tools allow you to copy-paste a PMID or DOI in a form field press two buttons to grap bibliographic information from PubMed and a DOI source. One-click full paper upload is not well-supported, – to my knowledge. Perhaps Daniel Mietchen knows something about this.
- Forums, Q&A, etc.: Well, yes and no. You can use the discussion pages on Wikidata, but these pages are perhaps mostly for discussion of editing, rather than the content of the described item. Perhaps Wikiversity could be used.
- Deposit own papers: You can upload appropriately licensed papers to Wikimedia Commons or perhaps Wikisource. Then you can link them from Wikidata.
- Research administration tools: No.
- Reuse of data from outside the service: You better believe! Although Wikidata is there to be used, a mass download from the Wikidata Query Service can run into timeout problems. To navigate the structure of individual Wikidata item, you need programming skills, – at least for the moment. If you are really desperate you can download the Wikidata dump and Blazegraph and try to setup your own SPARQL server.
In a letter to the Danish newspaper Politiken a group of young researchers, Anders Søgaard, Rebecca Adler-Nissen, Steffen Dalsgaard, Vibe Gedsø Frøkjær, Kristin Veel, Sune Lehmann and Kresten Lindorff-Larsen wrote against letting business get too much influence on the universities. Among their arguments was one example with the Pinski-Narin paper:
“A good example on basic research, which has made a huge economical difference, is Gabriel Pinski’s and Francis Narin’s article about citation analysis from 1976. That article made the PageRank algorithm possible, which still is used in Google Search. According to some statistics Google Search can account for 2 percent of the BNP of the world, all because of research in how researchers cites each others article” (translated from Danish)
The specific paper is Citation influence for journal aggregates of scientific publications: theory, with application to the literature of physics published in ‘Information Processing & Management’. In this paper the two researchers set up a citation matrix corresponding to a graph where the nodes are “publishing entities” such as “journals, institutions, individuals, fields of research, geographical subdivisions or levels of research methodology”. They perform an eigenvalue computation to find the ‘influence’ of the publishing entities. The method is demonstrated on the citation network between physics journals.
Is Pinsk-Narin basic research and did it influence Brin and Page for PageRank?
Interestingly, the two researchers are not university researchers. Pinski and Narin worked in the company “Computer Horizons, Inc” as President and Research Advisor according to the information in the article, being support by the National Science Foundation.
The Pinski-Narin paper is cited by Jon Kleinberg in his Hubs, authorities, and communities paper from December 1999. Pinski-Narin is also cited by Kleinberg’s Authoritative Sources in a Hyperlinked Environment that was published as an IBM research report in May 1997, i.e., a company report.
Brin’s and Page’s famous article The anatomy of a large-scale hypertextual Web search engine (made while they were students at Stanford University) has no mentioning of Pinski and Narin. So were they not aware of it? Initially I thought so.
However, Brin’s and Page’s paper cite Kleinberg’s ‘Authoritative Sources in a Hyperlinked Environment’ which has information about Pinski-Narin, so if Brin and Page read Kleinberg’s paper they must have known about Pinski-Narin, – at least in the latter part of 1997.
The Brin-Page paper is from the Seventh International World Wide Web Conference which was held in April 1998 with submission deadline in December 1997. The tracing of PageRank leads further back to Lawrence Page’s patent US 6285999 with filing date in January 1998 and a priority date in January 1997. This patent has a citation to Pinski-Narin. It is not clear when the citation was added to the patent. I suppose it could be somewhere between during the writing process leading up to the priority date in 1997 and the publication date in 2001. I have not been able to find information about whether the Pinski-Narin influenced Page to PageRank, but in late 1997 they must have been aware of the paper, so it is not at all unlikely that they were inspired from it. However, as an argument for keeping business out of universities the PageRank/Pinski-Narin issue seems a poor example because Pinski-Narin came from a company.
The entire field of scientometrics has depended quite heavily on data from the Science Citation Index (SCI), – a data from the company ‘Institute of Scientific Information’. Indeed, the Pinski-Narin paper used data from SCI. Still the scientometrics field is dominated by commercial interests. Thomson-Reuter now owns SCI, Elsevier has Scopus and Google Google Scholar. Also note that CiteSeer/ResearchIndex was developed, not by a university, but by the American research branch of the Japanese company NEC. And in turn (according to Wikipedia) SCI was “heavily influenced” by the non-academic Shepard’s Citations.
Interestingly, Massimo Franceschet has written on the history of PageRank: “PageRank: Standing on the shoulders of giants” and tracing it back to Wassily W. Leontief in 1941. Wikipedia’s PageRank article also mentions Yanhong Li‘s work Toward a qualitative search engine and US 5920859. At the time Li worked for a company “GARI Software/IDD Information Services” and later cofounded Baidu.
It may be worth to note the lack of references in the Pinski-Narin paper. It has no citation to, e.g., Leo Katz’ 1953 paper or Leontief. Perhaps they were unaware of the research in the other areas?
Although PageRank can be said to depend on university-based basic research such as German-speaking matematicians Oskar Perron, Ferdinand Georg Frobenius and Richard von Mises the work in the Computer Horizons company is not an example of university-based basic research.
One final note: Though some academics may see PageRank as an example of a basic numerical research yielding a company of great economic value, I see it as only a component in the Google success. The application of low-cost Linux computers together with a non-intrusive quick-responding interface may well explain more of the success. Linux, inspired by academic MINIX, is mostly an non-academic endeavor.
Yesterday (i.e., 13 April 2011 Danish time, 12 April 2011 American time) I blogged a bit about Poul Thorsen. Now today (i.e., 14 April 2011 Danish time, 13 April 2011 American time) the newest development is a Reuters message sent from Atlanta stating that Thorsen “has been indicted by a federal grand jury in Atlanta” and US authorities are seeking to extradite him from Denmark.There has still been strangely little written about this case in Denmark, — and nothing about the new development. In December 2010 science journalist Jens Ramskov wrote a bit about Poul Thorsen being co-author on the scientific article Parental infertility and cerebral palsy in children even though the University of Aarhus had declared:
Aarhus University will not be able to collaborate with Poul Thorsen in the future. To the extent that other parties collaborating with Aarhus University wish to draw on Poul Thorsen’s expertise, Aarhus University will only accept such collaboration if it has the purpose of securing data or protecting the interests of participating researchers and funding agencies”
Most of the information in Denmark is from a single article in Information by freelancer Sanne Maja Funch published in March 2010. Journalist Ulla Danielsen has also written about the lack of Danish media attention to the case which moneywise seems to be bigger than the Milena Penkowa case. Danielsen has written a few English articles to Age of Autism, — seemingly an anti-vaccine blog as far as I can determine.
(Typo correction: 14 April 2011)
In Denmark we have the hilarious case of the neuroscientist Milena Penkowa from the University of Copenhagen which involves embezzlement, forgery, the head of the university, allegation of scientific misconduct, personal ties to the former Minister of Science, to an employee of the Ministry of Science, inappropriate use of research funds, change of a Danish law because of anonymous questions, a documentary movie, personal ties to the documentary movie maker, and so on. I have a previous blog post on the case from February 2011.
Now we have a new case. That of Poul Thorsen. Like Penkowa he is/was an industrious researcher and he headed a large research group: North Atlantic Neuro-epidemiology Alliances (NANEA) at the University of Aarhus. I am trying to find heads and tails on this story and begun the Danish version of the Wikipedia article on Poul Thorsen. If you compared with the corresponding article on Milena Penkowa you will see that it is much smaller.
- Poul Thorsen gained large grants from the US Center of Disease Control to NANEA: almost 8 million American Dollars in 2000 and a renewal on over 8 millions in 2007. These are a very large sums. Apparently, he is suspected for falsifying documents from the US Center of Disease Control so University of Aarhus paid him 2 million US Dollars (believing that money to cover it would come). The university discovered this in the spring 2009. See Information.
- It is unclear who had the responsibility for administering the money. According to Ulla Danielsen the Danish Agency for Science, Technology and Innovation was the administrator until the University of Aarhus took over the administration in November 2009. If the university has paid Poul Thorsen before that date it seems that the agency has not done its job well.
- On his center in Aarhus Thorsen apparently employed a person that received a special salary support from the state. However Poul Thorsen adds some extra money on top and that is not legal, according to Information.
- NANEA is under the University of Aarhus and Thorsen was employed there. However, he has also been employed at the Emory University and this double employment was not approved by the University of Aarhus. See Information.
- In the Danish media there has been much less written about Poul Thorsen compared to Milena Penkowa. Penkowa has been keen on interviews before and after her fall from the throne, so the press has lots of interesting citations and photos and videos with her, see one here. For Thorsen there seems to be very few images (one?). I guess the difference in good picture material might be the reason for the discrepancy in press coverage. The case of Thorsen also has little juicy sex. In the case of Penkowa there was speculations around the Minister of Science and the head of the University. Though these speculations are very likely unfounded they nevertheless fueled the story that ran almost each day in February and part of March.
- Poul Thorsen has done research in autism and vaccine, see Thimerosal and the occurrence of autism: negative ecological evidence from Danish population-based data. Since Andrew Wakefield this area has been a minefield, where some contend that (mercury-containing) vaccination is harmful and causes autism. There are groups that are anxious about the issue. Age of Autism seems to be one. One blogger refers to this as “the anti-vaccine propaganda blog of Generation Rescue“. Age of Autism has not failed to write critical articles about Poul Thorsen. Even one of the Kennedys has written critically about the issue in Huffington Post.
- I think the issues around Poul Thorsen moneywise calls his scientific integrity into question. I haven’t heard much of this issue.
- Poul Thorsen has fairly few first author articles from recent years. The first author is usually the one with the hands in the data — and that has the possibility to falsify data. Thorsen is not first author on the Thimerosal/autism article. The collegue and medical doctor Kresten Meldgaard Madsen says that Thorsen could not change or compromise the data.
- According to Ulla Danielsen Poul Thorsen is charged with tax evation and the case is planned to begin 13 April 2011 (as I am writing this is today). There is a list for court cases in Aarhus. Among them is a case beginning 9:30 with the lawyer Jan Schneider. This might be the one. As far as I understand the court room was packed when Penkowa went to trial. I am not sure Poul Thorsen will attract as many, but we might hear more in the afternoon if any journalist attends.
Accusations of fraud – both real and researcher fraud – target high-profile Danish glossy neuroscientist Milena Penkowa from the University of Copenhagen. It has been frontpage news in Denmark for some time now. Want an English introduction to the case as it stood in the beginning of January 2011 then read the Nature News article Nature News. Since then the case has grown. Now the central damaging allegation is that she falsified documents stating that a Spanish company was involved in an experiment with many hundreds of rats.
I have tried to aggregate the different sources on the Danish Wikipedia page about Milena Penkowa. I have not yet managed to assemble all the material. During the writing I stumbled on some “loose ends” and subjective thoughts about the case (I must warn you though. I have a conflict of interest: I am from the Technical University of Denmark – a competing university in Copenhagen. I also know some of the professors that just before yule sent a letter with a request for an investigation):
- An element of the Milena Penkowa case cannot be discussed in public because of “legalities”. Journalists and researchers generally know the details of that case but are prohibited from mentioning them in public. Information seekers that want to find out about it may either need to seek a person in-the-know or do a bit of triangulation with an Internet search enginge. Hmmm… Aren’t the Danish variation of free speech, The Ytringsfrihed, having a problem here?
- Some have questioned her overall scientific contribution. If you pubmed Penkowa you’ll see she has first-authored 33 PubMed papers and the total listing counts 98 PubMed papers. Most of her research seems to revolve around the protein metallothionein. The blog entry from Morten Garly Andersen states that “Penkowas first big article, which came in 2000 in the scientific magazine Glia has her coauthor, the Spanish Professor Juan Hildalgo, now retracted.” That statement seems not to be true: “Strongly compromised inflammatory response to brain injury in interleukin-6-deficient mice” is from 1999 and is with 114 citation her most cited article on Google Scolar. As far as I know this has not been retracted. As far as I can determine her Google Scholar h-index is 32. That is quite much compared to her young age. Quite impressive I would say. On the other hand among her first authored papers I find no journal I can recognize as a high-impact journal. From a medical researcher one would have expected at least one article in, e.g., The Journal of Neuroscience. So we may not be talking about ground-breaking science. She has two patents, but I am not presently aware of any application of these patents. Correction 22 August 2011: Here I am definitely wrong: She has an article in Journal of Neuroscience called CNS wound healing is severely depressed in metallothionein I- and II-deficient mice!
- Penkowa has claimed that she was under contractual obligations with a company. But can a researcher sign such a contract without the university approving it? Has the university approved such a contract? Has the university investigated whether such a contract exists?
- One commentator noted that Helge Sander exited as Minister of Science one month prior to Penkowa’s suspension from the university. Is that a coincidence?
- In the begining of January Chairman of the Board of the University of Copenhagen found that “Penkowa’s research is already being treated by the relevant authority, The Danish Committees on Scientific Dishonesty (DCSD)”. I presume he no longer will accept his own statement as the university has involved the police in the investigation?
- The university has reported Penkowa for falsifying documents. Even if the allegation is correct it is probably the case that the police cannot do anything about it because too many years have passed. The alleged falsification have supposedly taken place back in 2003. A document falsification allegation case that expired has recently happened for a Danish businessman with a high-profile politician wife. In that case the Danish police simply rejected the case.
- Fraud? What fraud? The university has reported Penkowa to the police for fraud (real fraud – not science fraud). But to commit fraud you need to gain value from it. If the allegation is correct what she gained is not clear. One “gain” was to avoid being dragged through a scientific dishonesty process, but is that a “gain” in the sense of that paragraph of the law? Has the university lost any money on that? It is probably not the case that she gained her degree based on the documents – she simply left out the problematic study from the disertation. So fraud? What fraud?
- Her collaborator fra Barcelona has said little. Penkowa has two papers in Glia from 2000: Impaired inflammatory response and increased oxidative stress and neurodegeneration after brain injury in interleukin-6-deficient mice and Metallothionein I+II expression and their role in experimental autoimmune encephalomyelitis (as far as I can see the contested table is Table 1 with 784 rats. The method section reads “Female Lewis rats, weighing 180-200 g, were obtained from the animal facilities of the Panum Institute in Copenhagen”). I find his name on both papers. Has he anything to say? If Copenhagen researchers find it strange that over 700 rats have been used in a study, why does this Spanish collaborator and co-author not find that strange? Now, hold on! Hold on! On the 8th February 2011 he actually came forward: According to Danish news the Spanish collaborator has asked the editor of “Glia” to retract the article. So it clarifies that aspect. Then February 9th Danish news paper BT got a strong statement from the Spanish researcher saying he is not a second in doubt that she has lied about the rats and he used words such as “not a friendly person”, evil and demanding.
- If Penkowa writes “Female Lewis rats, weighing 180-200 g, were obtained from the animal facilities of the Panum Institute in Copenhagen” in her paper then why was the university satisfied with Penkowa’s explanation that part of the rat study was performed in Spain?
- IMK Almene Fond has supported Penkowa with 5.6 million kroner (around 1 million American dollars). They have demanded (some of) the money paid back. According to Politiken the foundation accepted to pay salaries (that had been paid), but not travel expenses and restaurant bills, bills to laywers and expenses for patent application as well as office funitures, cloths, (office?) rental, hardware and software etc. Now a foundation can put any kind of restriction on the use
of its donated money. But its seems strange that a foundation given such a large grant does not support travel expenses and restaurant bills in connection with research. In standard research grants you usually get money to exactly that: Money to travel to scientific conferences, money to pay for hotel and food while you outside the country to the conferences, money to pay for food in you home country if you have lunch or dinner with foreign scientific visitors or internal scientific meetings within the group. Has the university paid money back to the foundation just to be on good terms with them for prospect of future grants? That might be a good strategy, but is that legal? The question may be answered as our national financial auditor Henrik Otbo now will examine this aspect
- Milena Penkowa received the EliteForsk prize. It is unclear who promoted her. Ralf Hemmingsen ok’ed it even though he must have known about the suspicions against Penkowa. Minister of Science Helge Sander has personal ties to Penkowa. Has there been a direct or indirect pressure from Sander on the people in the nomination committee? Who can investigate a former minister? Surely not the university.
- Penkowa stated in a letter that she had been to a funeral following a traffic accident involving her mother and sister. At the later party at the university her mother showed up. Did any one at the university remember the letter? Did they write it off as a white lie composed by a stressful person?
- Ralf Hemmingsen has apologized for the treatment the three members of the Penkowa’s original 2001-2003 doctoral committee got. However, it still an open question if committee members did a reasonable scientific job. Prominent Nordic neuroscientists Per Andersen and Anders Björklund critized the work of the committee. So where does that leave us? Was the work of the committee not good enough? Did Andersen and Björklund not get enough material or time to evaluate. Is Andersen and Björklund’s criticism unfounded? Should we have an investigation of the investigation of the investigation?
- Committee members said in 2011 they investigated the possibility of submitting Penkowa to the Danish Committees on Scientific Dishonesty back in the early 00s but were adviced not to do so as it could be regarded as a breach of confidentiality. Apparently the members reluctance to call in DCSD put Ralf Hemmingsen in a catch-22 and was the reason he called in the investigation with Andersen and Björklund. Is the claim of the committee members really true? Shouldn’t such members be allowed to submited to DCSD?
- Some have critized that Ralf Hemmingsen for not involving Andersen and Björklund in the investigation about the 784 rats. But is that critique fair? The investigation would involve looking through bureaucratic documents (bills, invoices, lab reports) and really not scientific material. Do the critics think that busy widely known neuroscientists Andersen and Björklund should spend their valuable time looking into such things?
- Penkowa’s latest statement from February 12th says the following: “That company has of course existed, like the persons, that at that time was involved and performed the experiment, also existed. The university called the company to get it confirmed. The one, Weekendavisen has called in 2010, is in all likelihood not the same person”. So either the newspaper Weekendavisen and the Spanish lawyer the University of Copenhagen employed for investigating the whereabouts of the existing or nonexisting Spanish company have made a major blunder or Penkowa has now shown a considerable strained relationship with reality.
Care for a bit more science gossip? Here is some in Danish provided by
Nu er jeg så gammel, at jeg husker en sag for omkring 40 år siden, hvor en kvik og dejlig dame blev “båret frem” til en medicinsk doktorgrad af ældre “velgørere” på Københavns Universitet. Bagefter var der nogle unge forskere, som pillede doktorgraden fra hinanden – med en hel del røde ører til følge. De unge læger blev i øvrigt bagefter blacklistet som hævn, så vidt jeg ved. Det kunne man gøre dengang.
Photo: A Mazda MX-5 roadster. A photo by Mauricio Marchant from Wikimedia Commons with license CC-by-sa. Penkowa has a similar car and has been photographed in it a couple of times.
(Typo fix: 14. February 2011)
(Factual correction: 22. August 2011: I was wrong to state that she has not an article in a high-impact journal. The article CNS wound healing is severely depressed in metallothionein I- and II-deficient mice from 1999 published in The Journal of Neuroscience is what I would call a high-impact journal.)