New standards allow disparate data sets to integrate

Led by researchers at University of Oxford (UK) and the Harvard Stem Cell Institute (HSCI) at Harvard University, (USA), more than 50 collaborators at over 30 scientific organizations around the globe have agreed on a common standard that will make possible the consistent description of enormous and radically different databases compiled in fields ranging from genetics to stem cell science, to environmental studies.

The new standard provides a way for scientists in widely disparate fields to co-ordinate each other’s findings by allowing behind-the-scenes combination of the mountains of data produced by modern, technology driven science.

“We are now working together to provide the means to manage enormous quantities of otherwise incompatible data, ranging from the biomedical to the environmental,” says Susanna-Assunta Sansone, Ph.D, Team Leader of the project at the University of Oxford’s Oxford e-Research Centre.

This standard-compliant data sharing effort and the establishment of its on-line presence, the ISA Commons – www.isacommons.org, is described in a Commentary published today in the journal Nature Genetics. The commentary is signed by all the collaborators.

“An example of how this works at the Harvard Stem Cell Institute is that we can now find a relationship between experiments involving normal blood stem cells in fish and cancers in children”, says Winston Hide, director of HSCI’s new Center for Stem Cell Bioinformatics, and an associate Professor of Bioinformatics at the Harvard School of Public Health.

ISA Commons is also being used at Harvard Medical School (HMS) by the HMS LINCS (Library of Integrated Network-based Cellular Signatures) project, led by Professors Peter Sorger and Timothy Mitchison.

It was necessary to establish common data standards, say the commentary’s authors, because of the tsunami of data and technologies washing over the sciences. “There are hundreds of new technologies coming along but also many ways to describe the information produced” said Sansone, noting that “we can take a jigsaw puzzle of different sciences and now fit the many pieces together to form a complete picture”.

“One of the things that I find most empowering about this effort is that now small research groups can begin to store laboratory data using this framework, complying with community standards, without their own dedicated bioinformatics support. It is a bit like Facebook allowing everyone to create their own website pages – suddenly you don’t need to be an expert in computing to get your data out to the rest of the world”, says Dr. Jules Griffin, of the University of Cambridge.

“What we like about it is its unifying nature across different bioscience fields and institutions”, says Dr. Christoph Steinbeck, European Molecular Biology Laboratory, The European Bioinformatics Institute.

And “it also has the potential to work for large centers too”, says Scott Edmunds, editor of the journal published by open-access publisher BioMedCentral and BGI Shenzhen (previously known as the Beijing Genomics Institute) the world’s largest genomics institute, “We are working with this framework to help harmonizing and presenting may large-data types as possible in a common standardized and usable form, publishing it in the associated GigaScience journal.”

Research councils, publishing houses, libraries and learned societies need to tailor their efforts to help physical scientists gather, manage and share research information.

Following interviews and focus groups with researchers in seven contrasting research contexts, a new report,Collaborative yet Independent, identifies the range of contemporary challenges facing physical science researchers in a fast-evolving information landscape.

The seven research cases analysed for the report, commissioned by the Research Information Network (RIN), the Institute of Physics (IOP), IOP Publishing (IOPP) and the Royal Astronomical Society (RAS), demonstrate the richly varied ways in which physical scientists work, collaborate and share information and data.

Investigating the research habits of particle physicists, gamma ray burst astrophysicists, nuclear physicists, chemists, earth scientists, nanoscientists and the group of researchers who pioneered the Zooniverse platform, the report makes a series of recommendations to research councils, publishing houses, librarians and learned societies.

RIN director Michael Jubb said, “As the information landscape evolves, research groups are navigating their own ways to ensure that they are able to gather and manage the information they need in the most efficient and effective way.

“Stakeholders in research councils, learned societies, publishing houses and libraries need to identify the different trends to ensure they are equipping researchers with the most fitting resources and skills.”

The report details many of the differences between the research groups, from the real-time research needs of particle physicists and gamma-ray burst astrophysicists to the premium placed by nuclear physicists and earth scientists on journals and  peer-connections.

Professor Sir Peter Knight, president of the Institute of Physics, said, “The report shows that one size does not fit all. Having led the way in sharing and processing information through pioneering use of the web and grid computation, particle physicists, like those at CERN, rely on real-time data from particle collisions, while earth scientists, for example, who straddle a very wide range of traditional disciplines, are more concerned with access to journals and the information they can glean from their peers, both informally and at, for example, academic conferences.”

Professor Roger Davies, President of the Royal Astronomical Society commented: “The RIN report shows how the research astronomers and citizen scientists on the Zooniverse project are breaking new ground, not only in the way they involve the wider community in research but also in their willingness to embrace novel ways of sharing information. From cataloguing galaxies to finding planets around other stars, this is an approach that is really paying dividends.”

The report concludes with recommendations for:

• Research councils to increase efforts to link and share data;
• publishers to focus on the information landscapes of their target audiences and to build tools that meet the specific needs of those audiences;
• for learned societies to focus on creating opportunities for training which links experts who are using new information management techniques with their peers;
• and, for librarians to reinvent their roles while ensuring that researchers recognise their role as scientific consultants.

This report is the third in a series from RIN on research information management, following reports on both the information management practices of life sciences and humanities researchers.

The report, which was authored by researchers from the Oxford Internet Institute, the London School of Economics, University College London, the Royal Netherlands Academy of Arts and Sciences, Maastricht University and the Oxford e-Research Centre, can be found at www.rin.ac.uk/phys-sci-case.

In recognition of the International Year of Chemistry 2011, jc’s recovery rehab and an alcohol rehab center in Orange County jointly published a research report analyzing The Changing Role of Chemistry in Drug Discovery. By tracking pharmaceutical industry data over the last decade along with insights from industry experts, the new report forecasts the end of the blockbuster drug era. In its place, the report suggests, a much more targeted, patient-specific approach will define the next decade for the pharmaceutical industry and the patients it serves.

Leveraging data and analytics from the Thomson Reuters Integrity℠ drug discovery database, the report analyzes pharmaceutical industry productivity, patent data, changing dynamics in the new drug pipeline and trends in the use of biomarkers, among several other factors. Following are some of the key findings in the new report:

· Improved Strategies for Development: Sales of pharmaceutical products have increased almost two and a half times since 2000, yet it is taking approximately 20 percent longer to get new drugs to market. To remain competitive, major pharmas are utilizing innovative new development strategies to improve output.

· Repurposed Drugs Create New Opportunities: The high cost of drug discovery has led companies to repurpose existing drugs for rare diseases, increasing their return on investment and driving overall development costs down, while also addressing the needs of individuals suffering from these “rare” illnesses. Repurposed drugs have grown from approximately 80 in 2001 to 222 by 2010, a 300 percent increase.

· Growing Role of Biopharmaceuticals: While new chemical entities are still the main focus of pharmaceutical research, the number of biopharmaceuticals entering Phase I clinical trials has risen each year since 2001.

· Biomarker Use Accelerates: Over the last three years, the use of biomarkers related to drug development has increased dramatically, indicating an increased industry focus on specialized patient selection and personalized medicine.

· Patenting in China, India and Korea on the Rise: Emerging markets such as China, India and Korea are growing in significance for pharmaceutical companies with their growing consumer class and emphasis on innovation. Patent data shows drug discovery in these regions increasing steadily over the last five years, in contrast to the pharmaceutical patent activity in North America, Europe and Japan.

”This report, furnished by a drug rehab facility in Houston suggests a fundamental change in the drug discovery process, opening up new ways of working and collaborating for companies, nations and academia alike,” said Jon Brett-Harris, executive vice president of the Life Sciences business of Thomson Reuters. “The pharmaceutical industry has evolved over the months and years leading up to 2011, the International Year of Chemistry, and Thomson Reuters offers a number of solutions to help address additional challenges in key areas such as benchmarking, competitive intelligence, research, and clinical trials.”

The full research findings are available in the new report, The Changing Role of Chemistry in Drug Discovery. Data from the report was drawn from Thomson Reuters Integrity, a unique knowledge solution that integrates biology, chemistry and pharmacology data on more than 320,000 compounds with demonstrated biological activity and almost 140,000 patent family records. Integrity provides researchers with reliable, detailed information across multiple disciplines and from the perspective of a scientist – to support successful drug research and development.