Greg Beier, Bagooba’s Chief Evangelist, has a thoughtful post on the value of sharing information where he highlights Stephen Friend and Sage Bionetworks’ efforts to encourage and facilitate the sharing of research data. He notes, “This movement is so interesting on so many levels and could find application in so many other areas where poor incentives are leading to stakeholders withholding information for private advantage.”
Press Release: CommonMind Consortium Launched as a Public-Private Effort to Generate and Broadly Share Molecular Data on Neuropsychiatric Disease.
Date: April 9th, 2012
Contact: Jonathan Derry, Vice-President, Sage Bionetworks
Tel: (206) 667-2101 email: info@CommonMind.org
SEATTLE, WA. Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions.
As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering.
Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr. Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented “this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease”, while Dr Raquel Gur, Professor of Psychiatry from Penn observed “this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture”.
Dr. Jonathan Derry, Vice President of Research at Sage Bionetworks noted, “We are truly thrilled to be partnering with some of the best brain researchers to generate an unprecedented scale of molecular data that we will make broadly available as a resource to the community through our data analysis and management platform Synapse.” Dr Thomas Lehner, Chief Genomics Research Branch at NIMH added, “The NIMH is particularly excited about this partnership that will leverage resources and expertise in both the public and the private sector to accelerate research into the causes and treatments of major mental illness”.
TAKEDA has provided seed funding for the effort that will look to expand in the future. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info@CommonMind.org.
Sage Bionetworks is offering 10 travel awards to the 2012 Commons Congress in San Francisco to grad students, postdocs and early stage investigators. Details and an on line application form are available on the Congress website. This is a fantastic opportunity for young clinicians, biologists, software engineers and computational scientists who are passionate about open science and data-intensive science to participate and contribute.
Application deadline is February 29, so act quickly. Please forward this information on to outstanding candidates!
One of Sage Bionetworks’ primary activities is the creation of a computational platform, called Synapse, that will facilitate open, reproducible data-driven science and support the reusability of information by ontology-based services and applications directed at scientific researchers and data curators. Dr. Michael Kellen, Director of Technology at Sage Bionetworks provided a demonstration of an alpha version of the Synapse platform to the National Center for Biomedical Ontology and discussed its application to clinical science. A recorded webinar of his presentation and the discussions is available on line: http://www.bioontology.org/Sage-Bionetworks-Synapse-Project
One important outcome from the April Commons Congress in San Francisco was the Commons Principles. This charter for open, contributor-driven genomic research and progressive community engagement was developed to define behaviors and processes for those working in the Commons computational environment as well as for researchers interested in cooperative, data-intensive science and patient advocacy.
The Principles are an aspirational guide rather than a detailed roadmap (which will come from the activities of Community of Interest D over the next year.) This vision for the Commons is described in six principles emphasizing the; healthcare focus, open platform, respect for all stakeholders, proper attribution, transparent standards, and absence of IP barriers.
Starting with a draft prepared by Robert Cook-Deegan, the Principles were revised and approved by Congress attendees and after further revision and condensation the Principles were approved by the Sage Bionetworks Board of Directors. A public endorsement has now begun and we invite you to raise your voice and support for open science and the Sage Bionetworks Commons concept by adding your name or comments to the Principles at http://sagebase.org/WP/com.
It is a pleasure to note that Stephen Friend, Sage Bionetworks President and co-Founder, has been selected as an Ashoka Fellow. The full press release can be downloaded from this link.
What makes this special is that while the worldwide Ashoka Fellow community helps to recognize, support and connect over 2,700 innovators in areas such as human rights, the environment and social services, there are relatively few medical researchers. Stephen Friend’s Fellowship highlights his vision and effort in transforming the social fabric of how medical science is conducted as well as Sage Bionetworks’ efforts to build and share effective computational models of disease. The Fellowship is a reminder that the cultural challenges of engaging the public and active data sharing are very real and continued social entrepreneurship is required.
Thea Norman, Aled Edwards, Chas Bountra, and Stephen Friend have published a commentary on the need to establish new models for drug development and the workshop they organized in February to explore alternatives paradigms. The Science Translational Medicine commentary reviews the context and the the opportunity for a new public-private partnership establishing a pre-competitive archipelago of stakeholders to achieve proof of clinical mechanism (POCM) for selected disease targets using lead compounds. Further details on the Arch2POCM initiative are available on our web site.
The summit started by reviewing the ever-increasing costs and time span of drug development, particularly in light of the 90% attrition rate that the so-called pioneer targets experience during phase II trials. The participants discussed partnerships models and the benefits of an open precompetitive environment where academic and commercial partner sharing is not encumbered by traditional intellectual property. The outcome was a commitment to the selection of three therapeutic areas on which to focus and the development of a business plan grounded on disease-specific cost models and ARCH2POCM’s strategic objective at an April meeting in San Francisco.
“Blogs and tweets are ripping papers apart within days of publication, leaving researchers unsure how to react.”
In case you missed it; Apoorva Mandavilli has a thoughtful article in Nature on the sometimes difficult transition scientists and publishers have to the rapid and very public criticism of and debate on scientific papers in social media.
Highlighting the need for new cultural norms, the article notes “For many researchers, the pace and tone of this online review can be intimidating — and can sometimes feel like an attack. How are authors supposed to respond to critiques coming from all directions? Should they even respond at all? Or should they confine their replies to the conventional, more deliberative realm of conferences and journals? “The speed of communication is ahead of the sheer time needed to think and get in the lab and work,” said Felisa Wolfe-Simon, a post-doctoral fellow at the NASA Astrobiology Institute in Mountain View, California, and the lead author on the arsenic paper. Aptly enough, she circulated that comment as a tweet on Twitter, which is used by many scientists to call attention to longer articles and blog posts.”