Context is something we’ve been thinking a lot about at ScienceOpen recently. It comes from the Latin ‘con’ and ‘texere’ (to form ‘contextus’), which means ‘weave together’. The implications for science are fairly obvious: modern research is about weaving together different strands of information, thought, and data to place your results into the context of existing research. This is the reason why we have introductory and discussion sections at the intra-article level.
But what about context at a higher level?
Context can defined as: “The circumstances that form the setting for an event, statement, or idea, and in terms of which it can be fully understood.” Simple follow on questions might be then, what is the context of a research article? How do we define that context? How do we build on that to do science more efficiently? The whole point for the existence of research articles is that they can be understood by as broad an audience as possible so that their re-use is maximised.
There are many things that impinge upon the context of research. Paywalls, secretive and exclusive peer review, lack of discovery, lack of inter-operability, lack of accessibility. The list is practically endless, and a general by-product of a failure for traditional scholarly publishing models to embrace a Web-based era.
ScienceOpen Collections are thematic groups of research articles that transcend journals and publishers to transform how we collate and build upon scientific knowledge.
What are Collections
The modern research environment is a hyper-dimensional space with a vast quantity of outputs that are impossible to manually manage. You can think of research like a giant Rubik’s cube: you have different ‘colours’ of research that you have to mix and match and play around with to discover how the different sections fit together to become something useful.
We view Collections as the individual faces of a Rubik’s cube. They draw from the vast, and often messy, pool of published research to provide an additional layer of context and clarity. They represent a new way for researchers to filter the published record to discover and curate content that is directly relevant to them, irrespective of who published it or what journal it appears in.
Advantages of Collections
Perhaps the main advantage of Collections to researchers is that they are independent of journals or publishers and their branding criteria. Researchers are undoubtedly the best-placed to assess what research is relevant to themselves and their communities. As such, we see Collections as the natural continuing transformation of the concept of the modern journal, acting in almost full cycle to return them to their basic principles.
The advantage of using Collections is that they provide researchers with the power to filter and select from the published record and create what is in essence a highly-specialised virtual journal. This means that Collections are not pre-selective, but instead comprise papers discriminated only by a single criterion: research that is relevant to your peers, and also deemed relevant by them.
Filtering for Collections occurs at different levels depending on scope or complexity of research. For example, Collections can be designed to focus on different research topics, lab groups or research groups, communities, or even departments or institutions. Collections can also be created for specific conferences and include posters from these, published on ScienceOpen. Youdefine the scope and the selection criteria.
Two days ago, the World Health Organisation declared that the threat of the Zika virus disease in Latin America and the Caribbean constituted a Public Health Emergency of International Concern.
The decision was based on the outbreak of clusters of microcephaly and Guillian-Barré syndrome, which are devastating cases of congenital malformation and neurological complications. While a direct causal relationship has yet to be formally stated, the correlation between Zika infection during pregnancy and microcephaly is strongly correlated.
At ScienceOpen, we believe that rapid publication serves the communication of research, and aim to have submitted papers published online within 24-48 hours. For articles relating to the Zika outbreak, we are waiving the usual submission charge, and any published articles will be integrated into our pre-existing research collection on the Zika virus. Articles will receive top priority, and therefore be almost immediately available to the research community, medical professionals, and the wider public. We encourage submission of all articles relating to the virus. Please directly contact Stephanie Dawson for submissions and related enquiries.
There is clearly a need to co-ordinate international efforts, including those of the research community, to investigate and understand the Zika virus better. At ScienceOpen, we want to play our part in facilitating the communication of any such research, and the speedy protection of those at risk. We are happy to join other open access publishers such as F1000 Research and PLOS Current Outbreaks (both of which which publish very rapidly) who have similarly declared that all research published with them on the Zika virus can be published free of charge.
I wrote this post on the plane back from my trip to Shanghai after a multiple day delay that (looking on the bright side) allowed me to see some of the sights courtesy of Hainan Airways!
I was invited to speak at the 3rd International Academic Publishing Forum on August 19th. Organized by the Shanghai Jiao Tong University press, the event brought together nearly 60 Chinese University Presses and representatives from some Western academic publishers – Elsevier, Wiley, Springer, Sage, Brill and ScienceOpen –to discuss what we can learn from one another.
My most powerful impression was the high value China places on knowledge. Mr. Shulin Wu, Vice-Chairman of the Publishers Association of China said in his in his keynote speech that the government regards “knowledge production to be as important as mining or oil”. And China is set to surpass both the US and the EU in spending on research and development by 2020. Communicating this knowledge, therefore, also has a high priority and falls mainly to the university presses. Their main short-term goals expressed over the two days were internationalization and digitalization of their content, with language seen as the main hurdle. Certainly all had a plan for going global.
But some publishers, including myself, were already thinking beyond internationalization and digitalization to the next step in academic publishing. Jason Wu hit the nail on the head by describing Wiley’s process of transformation “from publishing business to global provider of knowledge and learning services.” Solutions for researchers must be digital, global, mobile, interdisciplinary (Bryan Davies of Elsevier quoted a study that found 44% of researchers look for information outside of their own field). And Open Access is a good place to start.
The Open Access business model for journal publishing is perfect for Chinese publishers who have until now been dependent on cooperation with Western publishers to get their authors heard. Chinese scientists who do world-class research can publish in “world-class” journals such as Science or Nature, but publishers here were asking the hard question of themselves – why are so few of those world-class journals published in China? While Open Access cannot itself address the problem of reputation, it can insure that research can be read immediately and globally, without a team of sales representatives on every continent. As essentially non-profit entities with a mission to communicate China’s research successes to the world they are uniquely situated. With access to so much outstanding research, I sincerely hope that Chinese publishers will embrace this opportunity.
Taking the Shanghai subway I can attest that young Chinese are constantly networking on their mobile devices. A scientific networking and research platform like ScienceOpen in China would have a good chance to catch the imagination of young scientists. But time will tell how open this generation will be allowed to be. During my stay the Chinese government shut down up to 50 online news websites and nearly 400 Weibo and WeChat accounts for spreading “rumours” of the recent chemical explosion which took 129 lives. Twitter, Facebook, Google and many other sites were blocked during my visit, which left me feeling rather cut off from the rest of the world.
It was a crazy week – from the crowds and flashing neon of Shanghai to the peaceful magnificence of the Great Wall. I came away with a sense of the huge potential in China and the feeling that China needs Open Access and the Open Access movement needs China.
Every year in May, I attend the Charité Entrepreneurship Summit, a unique event for international medical entrepreneurs and life science innovators organized by the Charité Foundation in Berlin. This ‘think-tank’ meeting connects sparkling ideas with pragmatic reality and facilitates a ‘one-of-a-kind’ scene for ‘let’s innovate and implement’ biomedical professionals and entrepreneurs from all over the world. This year, I had a special opportunity to meet and conduct an interview with Dr. Anula Jayasuriya, a wonderful personality and a talented scientist, physician, and investor. While contacting and talking with Anula Jayasuriya, I realized that she represents an amazing role model for every young scientist-entrepreneur. Here is some of food for thought from our conversation on entrepreneurship in medical sciences and open science.
Q1: The NIH has been one of the biggest forces behind the push towards increasing access to scientific information, but we are just at the beginning of the open science movement – open data being the next big hurdle. Do you see potential for an impact on the US health care system?
AJ: I think the NIH initiatives are very exciting, and open data will make a huge difference in the whole US health care system – but it will take time. At the end of the day, the NIH doesn’t make drugs, right? So we have to contend with industry. I wonder how it’s going to play out for pharma and biotech? Their business model is centered on protecting their innovations with IP and making money from products during the exclusivity period.
The moral imperative to share drug development data is that such information would greatly benefit patients and society. Let’s speculate that three big pharma companies working on development of the same category of drugs in their pipelines would be willing to share their failure results. This would be very important in preventing adverse reactions and health-related complications in patients. Perhaps these companies could form an industry consortium where every company was required to share their drug development failure data. There are many hurdles to be overcome before this can be a reality. For example, the first to fail is likely to benefit others but not itself. Money saved by averting future failures maybe eclipsed by lost revenues and compromised IP, etc. Pharma has to see an economic incentive to share data. Perhaps there could be an attractive market for acquiring failure information? In any case, there would need to be a dramatic transformation and innovation around the existing IP-based “winner-take-all” industry business model.
Pharma has to see an economic incentive to share data
Q2: Do you believe that patient access to the clinical trial data and mandated data sharing will create a climate that could accelerate drug development and translational science research?
AJ: I believe that the biggest motivator and catalyst in this process of sharing clinical trial information will be the patient. We are entering a very exciting era of patient engagement. Going forward, I see patients playing active roles in clinical trials. As patient participation is essential to clinical drug development patients have the power to make the change. The passive patient is likely to become a memory of the past. Already today there is a US Government funded institute called PCORI (Patient Centered Outcomes Research Institute) that is making grants to investigators who engage patients in clinical trial design. I see patients challenging Pharma, Biotech and Regulators to adapt to a world where patients are active decision makers alongside industry and regulators. The FDA today is caught in the middle of a rapidly transforming ethos. All stakeholders will need to adapt to a new equilibrium. Let me give you some examples. In 1993, I was working for Roche pharmaceuticals. This was during the early days of the HIV outbreak where there was an urgent need to develop new drugs to fight the devastating epidemic. Patient advocacy groups had a huge impact on getting pharma companies to work together and also influenced the FDA to act quickly and really make a difference (read more about Act Up). I saw first-hand how powerful the cooperative approach was. By the way, physicians were very pleased to see collaborations, which led to effective treatment and greatly benefited patients. But that was one narrow case in the past.
Today, I see changes taking place across several diseases, especially in fighting cancer and rare diseases. Patients, together with their families, are building tight communities to share and disseminate knowledge about their diseases. In the USA, there is a popular movement called “hacking your body”. This is a different kind of open innovation – the innovations are ones that have been “opened”/discovered by patients. The drive is coming from patients and their families. Now, patients are playing active roles, often going around regulatory barriers and industry specifications and advocating for themselves. As a physician, I am immensely pleased to see engaged patients. There are likely to be some hiccups and missteps along the way but I think that in the long run it will lead to accelerated drug development and, most importantly, better patient outcomes.
I believe that the biggest motivator and catalyst in this process of sharing clinical trial information will be the patient… This is a different kind of open innovation – the innovations are ones that have been “opened”/discovered by patients.
In the US, patients are entitled to free access to their medical records. If patients who participated in clinical trials were also entitled to access to their clinical trial records and were able to communicate with co-participants in the same trial I think they could “hack” the trial, by comparing adverse events and outcomes. And they are likely to share these aggregated data openly even if industry does not. I see patients, their families and society as the key actors in improving their health care.
There are two important ways to improve and accelerate drug development: understanding the science behind drug failures, and developing a process of sharing information openly within trial participant and disease the communities through the internet.
It is very encouraging that the NCI (the National Cancer Institute (NCI), part of the US National Institutes of Health) has successfully mediated a unique public-private partnership called the lung map trial, a multi-pharma collaboration in lung cancer. Five pharmaceutical companies (Amgen, Genentech, Pfizer, AstraZeneca, and AstraZeneca’s global biologics R&D arm, MedImmune) and Foundation Medicine (a cancer tumor genome analytics company) will collaborate to provide the treatment that is best suited to the individual patient – delivering personalized care. Patients need to enroll only in a single trial to access drugs developed by five different pharma companies. This is a groundbreaking development – real progress.
In addition, there are many digital health start-up companies whose business models are based on selling anonymized clinical trial data. (Of course, there are several ethical, privacy and compliance considerations to be addressed, but let’s just put them aside for now.) The promise of “Big Data Analytics” as it applies to health care is that the aggregation of these data will lead to better outcome for patients. I am optimistic!
There are two important ways to improve and accelerate drug development: understanding the science behind drug failures, and developing a process of sharing information openly within trial participant and disease the communities through the internet.
Q3: Do you think that big data, open science, and a worldwide network could in the future precisely tailor therapies to each patient’s individual requirement?
AJ: Precision medicine is the holy grail of health care. Tailoring cancer therapies makes a big difference in treatment outcomes today – cancer is the “low hanging fruit” due to easy access to the genomic analyses of tumors. Ultimately, delivering precision medicine relies on aggregating and analyzing data on a large number of areas: genomics, metabolomics, RNA, proteomics, behavior, environmental exposures, social and cultural milieus, etc. – this is a VERY big data play. I think the delivery of precision medicine will happen incrementally, in stages – with ever increasing degrees of precision as our understanding of the various contributing areas increase. Open science and data sharing are essential to generating the best data inputs from a multitude of sources to create a big data repository that serves as the basis for analytics.
Open innovation enables us to create products from a platform (repository) of information, which is freely available to everybody. For instance, having unrestricted access to scientific literature enables a company to develop their own algorithms for novel prognostic and diagnostic genomic screens – they could, for example, figure out which patients are sensitive/resistant to various drugs. Algorithms “learn” — the more patient data tested, the more an algorithm is refined and hence clinically informative. If, however, a company develops a screening or diagnostic test and patents it, thus excluding its use by others, it is no longer “open”.
The case of Myriad Genetics Inc. is interesting. They recently lost a lawsuit contesting the exclusivity of their BRCA test for breast cancer. The company used patient sequence information to develop and patent their screening test. Myriad claimed that they had exclusive rights to patients’ sequence information and to the test they derived from it. For several years Myriad was able to build a very profitable business by excluding others from duplicating their test, even though the actual sequence information the company used belonged to patients (http://www.the-scientist.com/?articles.view/articleNo/36076/title/Gene-Patents-Decision–Everybody-Wins/). Myriad’s claims were overturned and patent law is the US changed such that naturally occurring sequences can no longer be patented. I am in favor of this outcome as it greatly benefits patients who can now access BRACA tests from several companies at a much lower price.
I am excited about the concept of open innovation because it is a major step toward improving patient care. That being said, in a capitalist society, this has to be tempered by providing sufficient incentives to industry (on whom we are dependent unless we innovate a new model) to produce drugs, diagnostics, etc. I am confident that the “new normal” will result in better health care for society and the ability of industry to adapt and innovate novel and more productive business models.
I thank Dr. Anula Jayasuriya for the fascinating insights into the world of drug discovery and the role open innovation can play.
Across the street from the venerable University of Toronto, at the intersection of College Street and Elizabeth Street in downtown Toronto, you will find the heart of Toronto’s commercialization activity across the sciences: MaRS Innovation.
If you share the values of Marc Andreessen, the American entrepreneur, investor and software developer who revolutionized a very small part of San Francisco to become the world famous Silicon Valley, you will appreciate learning about the contemporary Canadian version of biomedical Silicon Valley. MaRS Innovation was founded in 2008 and began operations in 2009 to turn Toronto’s leading research and sciences into successful start-up companies and license deals.
I really love this part of Toronto. I used to tackle my research on zebrafish heart development on the 11th floor of the MaRS building’s East Tower (MaRS Innovation’s offices occupy part of the 4th floor on the West Tower). So, I am no stranger to Toronto’s life sciences scene. But the story of how MaRS Innovation landed in Toronto and found its home is worth sharing.
Prior to the 8th Charité Entrepreneurship summit in Berlin, Germany, I spoke to Dr. Raphael Hofstein, president and CEO of MaRS Innovation about his vision for open access and open innovation models. Here is what he had to say.
Q1: What is MaRS Innovation: an innovation hub, a medical and health care technology accelerator/incubator or all of that together?
RH: We are the outcome of the Government of Canada’s fairly tenacious campaign to close the gap between Canada’s highly-qualified scientific research and its commercialization success. So, we really try to help start-ups bridge the “valley of death” and we do that in a very distinct way. Particularly, every new exciting research idea coming out of the 15 institutions in and around the Toronto area is disclosed to MaRS Innovation. As the agency of these 15 member institutions, we have to select the ideas with the best chances of successful commercialization in the shortest possible time. That is essentially what MaRS Innovation is: a research and innovation pipeline.
Every year, scientific organizations disclose between two and 15 intended projects; we select approximately 15 per cent of what we see. Since 2009, we have seen about 1500 ideas, which we successfully converted under our management into over 100 technologies. Some of them turned into start-up companies, or options/licenses to a third-party or private sector entity. Other inventions are blended or packaged together and to be more appealing to the market.
Q2: How do you see a role of open access and open innovation processes in life sciences?
RH: To highlight open innovation models in life sciences, I would like to emphasize that there are different understandings of this process. So, I need to specify an invisible margin where life sciences research should be open, and where interaction with business should not be transparent. Personally, I am for open access and open data sharing, which should benefit scientists, medical doctors, and entrepreneurs, especially at the initial stage of discovery. Later on, the research becomes industry-driven and requires a proper investment from the private sector, including big pharma and life sciences industry. Let me give you one most recent example.
Due to a successful partnership with Quebec-based Consortium for Drug Discovery (CQDM), MaRS Innovation founded a company named Encycle Therapeutics, a University of Toronto biotechnology start-up. Interestingly, being a start-up venture, Encycle has two sub-divisions. One addresses the basic essence of all CQDM activities and represents an open innovation part; using the chemistry of peptides to develop an approach to synthesizing small, drug-like macrocycles. Encycle is creating a library of cyclic peptides, called nacellins, which are small macrocycles or cyclic peptidomimetics. This library is completely open and freely available to every pharma outlet who is interested in testing or developing orally bioavailable modulators of proteins, including small-cell permeable systems. That approach fits well positioned into a concept of open access. The other Encycle subdivision is commercially focused and working with industry partners to create proprietary technologies.
Another example is the adoption of embryonic stem cell lines for medical repair. Such cell lines should serve as a foundation for the further development of cell-based technologies and the public should have free access to it. As soon as it concerns further derivation and differentiation of stem cell lines for specific medical indications, it becomes part of proprietary ownership to the developer/investor since it requires a substantial investment into research and development. That part should be closed for public use.
As we can see, a major issue of open innovation remains on where we have to draw a borderline between the public and private use. In terms of the drug discovery process, I believe it could be at phase 1 stage of clinical development.
In Toronto, we have a very strong advocate of open access and open innovation, Dr. Aled Edwards. Aled Edwards leads the Structural Genomics Consortium (SGC), a private-public open collaborative network of researchers from the University of Toronto, the University of Oxford, UK and the State University of Campinas (Unicamp) in Brazil working together with nine global pharmaceutical companies and several research funding agencies. This is a unique, first open science international institution that offers completely free access and use of research results focused on unrestricted drug discoveries. I think it is a great example of open innovation in practice. However, in later stages, clinical development requires appropriate investments and, in reality, cannot be supported through open access. Therefore, I see managing this process as the technologies develop as quite challenging in its practical realities.
Q3: Do you think that big data, open science, and a worldwide network could in the future precisely tailor therapies to each patient’s individual requirements?
RH: I am a big proponent of big data. I think an open innovation model in big data science may play a greater role. At MaRS Innovation, we engage with IBM and several venture capital groups working on harnessing big data for medical purposes. Also, pharma companies expressed strong interest in having access to medical records which represent a high-value ‘big data treasure’ within our member institutions. However up to now, it has not been easy to fulfil our dreams of turning big data into a big practical opportunity. It is obviously a work in progress! Finally, it is my expectation that mining through big data collections of patient medical records (contingent on strict patient privacy!) will significantly accelerate the development of precision medicine (aka personal medicine). The global medical community should be prepared to address the trend.
About 24 years after its launch the arXiv preprint server hits 1 million articles on 29 December. The site reached that terrific target after administrators returned from holidays and updated the server with manuscripts submitted after business hours on Christmas Eve, Richard van Norden said in his report in Nature. Impressively more and more papers were posted as preprints from year to year, starting from a few hundred in the early nineties, when Paul Ginsparg initiated the arXiv site, to about 10,000 per months meanwhile.
“Kudos to Paul Ginsparg and the arXiv team for this achievement.” (Peter Suber, 2014)
Since more than two decades particularly physicists, mathematicians, and computer scientists were used to upload their manuscripts to arXiv to share their results with peers as a preprint prior to the submission to a standard scholarly journal. When I was working as a physicists myself, I also regularly used arXiv.org as a resource to browse and access the most recent findings of my colleagues. And I definitely know that I had been not the only guy who started his work in the morning in this way. The advantage of the arXiv to publicly share recent results of scholarly research has been quite obvious: only a few hours or days after a competing group had finished their draft to summarize their findings, researchers were able to read them without any delay and without any restrictions for access. Possibly this has been also one aspect which contributed to that story of success which now results in one million posts on arXiv. As an another result, most publishers meanwhile accept submissions from arXiv.
Preprint-posts on the arXiv are not peer-reviewed because managing and controlling of that filtering process had been the monopoly of scholarly journals for decades. Nevertheless one may ask if we do need something outside the ArXiv? I discussed this question in a blog almost a year ago, based on the perspective of physicists and their attitude to foster Open Access. This question, or more generally the basic idea to combine a well-established preprint server, as the ArXiv, with something to enable and moderate the scientific discourse as a substitute of the classical peer-review process was raised some years ago by Field’s medalist Timothy Gowers. In 2011 Gowers asked in one of his blog posts how we might get to a new model of (scientific) publishing, however focused, but principally not limited, to mathematics. His visionary thoughts had been motivated by an earlier post by Michael Nielsen. Gowers suggested “something like a cross between the arXiv, a social networking site, Amazon book reviews, and Mathoverflow”. In a very systematic way, he further developed his smart idea, or his gedankenexperiment as a physicist would call it, as an “ideal world” towards future scholarly communication. The proposed (non-existing) website should be an extension of the arXiv, or simply a separate website with links to articles which were hosted at arXiv.
“If we didn’t have journals, then what might we have instead?” (Timothy Gowers, 2011)
Here we are: The scientific community which had been used to regularly post and access recent findings on the arXiv would then be invited to comment, rate, and discuss new posts. I personally like that concept which is straightforward and based on the experiences and the behavior of researchers over two decades. Despite the fact that the latter oberservation is true mostly for researchers from physics, mathematics and computational sciences it could be adopted in principal to all disciplines of scholarly research. Amazingly, I read Timothy Gowers’s excellent blog some time after it had been published when I had already developed the concept for ScienceOpen in 2013. Nevertheless, his visionary considerations to develop a new model for scholarly publishing and the following, very intensive discussion of these ideas within the community strongly supported me to continue developing a new website which fosters not only Open Access, but also consists of a community-based concept to evaluate scientific results in an open and transparent manner. I am confident that future workflows for publishing and quality assessment in science will be based on these principles.
Let’s see if ScienceOpen can further contribute to this vision in 2015! Have a great start into the new year!
David Black is Secretary General of the International Council for Science (ICSU) and Professor of Organic Chemistry at the University of New South Wales, Australia. An advocate of Open Access for scientific data in his role at ICSU, Professor Black is a proponent of the initiatives of ICSU and ICSU-affiliate groups, such as the Committee on Freedom and Responsibility in the Conduct of Science (CFRS), the ICSU-World Data System (ICSU-WDS), the International Council for Scientific and Technical Information (ICSTI), the ICSU’s Strategic Coordinating Committee on Information and Data (SCCID), Continue reading “ScienceOpen Interview with David Black, Secretary General, International Council for Science.”
Over the last few days I attended the Spring Meeting of the German Physical Society (DPG) in Berlin. Physicists are considered sometime as a very special species among scientists, and not only because the characters introduced in the “Big Bang Theory” sitcom. Physicists developed the World Wide Web in the late eighties which became the starting point for all internet activities today. In 1991 Paul Ginsparg started to post preprints of research articles in a repository at Los Alamos National Laboratory which is known as “arXiv” ( www.arXiv.org ) which now consists of more than Continue reading “Open Access in Physics: Do we need something outside the arXiv?”
2014: The year is off to a good start for the Open Access movement. In the US, Congress passed legislation to require that all research funded by public funding bodies be freely accessibly, at least in the author’s final version and with a 12 month embargo after publication. (Peter Suber has a good summary of the legislation in his blog: http://goo.gl/Pmlkg1 ) Will this continue a trend started by the National Institute of Health and its public access database PubMedCentral (PMC –http://www.ncbi.nlm.nih.gov/pmc ) to increasingly direct readers to the pre-typeset version of an article? Phil Davis of the Continue reading “2014 – A good year for Open Access publishing?”