Open Science in Action: Inaugural Symposium | The Neuro – McGill University

“To speed up discovery and impact health, we must transform our approach to science. Innovations in biomedical science and big data technology have brought hope, and are powered by a new way of doing science: Open Science. This is the concept of freely sharing research data and materials, and removing barriers to collaboration.   

We welcome you to engage and exchange around Open Science in action at The Neuro and beyond.

Meet and learn from national and international experts on intellectual property protocols, ethics, patient consent and engagement, pharma, neuroinformatics, and more!     

The symposium will be moderated by Susan Usher, Director of the Health Innovation Forum. Our keynote speakers include John Wilbanks (Sage Bionetworks), Dario Taraborelli (Chan Zuckerberg Initiative), Russ Poldrack (Stanford Center for Reproducible Neuroscience), and Brian Wallach (I am ALS).  We are also pleased to welcome Alain Schuhl (French National Centre for Scientific Research) and Suzana Petanceska (National Institute on Aging). The symposium will close with the Wilder Penfield Lecture, delivered by Susan M. Fitzpatrick, President of the James S. McDonnell Foundation.     …”

OECD Workshop on the Revision of the Recommendation concerning access to research data from public funding | Mercè Crosas

“Two presentations to the OECD workshop on the Revision of the Recommendation concerning access to research data from public funding at part of the two following panels: 1) Use cases of enhanced access to software, algorithms, and workflows; 2) Use cases of access to sensitive data for research puposes….”

2019 Award Winner — World Data System: Trusted Data Services for Global Science

“Libby [Liggins] is part of the Steering Committee for the Genomics Observatory Metadatabase (GEOME), purpose-built to capture the metadata associated with biological samples and genomic sequences and conforming to current international standards for biodiversity and genomic data. Libby is also a core member of the Diversity of the Indo-Pacific Network (DIPnet) that seeks to advance biodiversity science in the world’s largest biogeographic region through international collaboration. DIPnet members have developed the largest, curated, georeferenced population genetic/genomic database in the world, and forms the core of GEOME….

Through collaboration with Local Contexts and Te Mana Rauranga (the M?ori Data Sovereignty Network), the Ira Moana Project and GEOME are now beta-testing the capacity for researchers to add a Traditional Knowledge Notice (TK Notice) and new Biocultural Labels as metadata. TK Notices signal that there are accompanying indigenous rights that need further attention for any responsible and equitable future use of the data. Biocultural Labels further allow the addition of provenance information and community expectations for future use based on Indigenous Data Sovereignty principles—including CARE (Collective Benefit, Authority to Control, Responsibility, Ethics) Principles launched by the Global Indigenous Data Alliance—thereby enabling indigenous stewardship and persistent recognition of indigenous rights within an international framework of Nagoya compliance. The implementation of a TK Notice and Biocultural Labels using GEOME’s infrastructure is a first for a biological resource and for genetic data, establishing new ethical standards in this research community.”

Improving Health Care with Publicly Reported Data

“But do people use that information to make choices?  Does it change where they get their care? There is little evidence that this is the case.  While the study mentioned earlier showed hospitals respond to this such data, that same study showed that consumers and purchasers of healthcare rarely search out the information and do not understand or trust it.  It had a small, although increasing, impact on their decision making.  According to another study, there is little evidence that patients use publicly reported data to make a choice.  There are several reasons that the authors of the study felt this was the case.   Among those reasons were that consumers didn’t believe they had choice because of their insurance provider, consumers couldn’t understand the quality data (the reports are poorly designed), and that consumers don’t trust the information provided….”

SASBDB: Towards automatically curated and validated repository for biological scattering data – Kikhney – – Protein Science – Wiley Online Library

Abstract:  Small?angle scattering (SAS) of X?rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small?angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user?relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.

bjoern.brembs.blog » Scholarship has bigger fish to fry than access

” For the last 6-7 years, paying for subscriptions has ceased to be necessary for access. One sign of the changing times is the support that initiatives such as DEAL, Bibsam etc. have: two years without subscriptions to Elsevier and what do you hear out of, e.g., Germany? Crickets! Nothing! Of course, it would be silly to conclude that in these two years nobody in Germany has read any Elsevier articles. The reason for the silence and the continued support for DEAL is that we now can access anything we want without subscriptions….

With the realization that EOSC; Plan S, DEAL, etc. are actually working on different aspects of the same issue, the problem to be solved is no longer that scholars publish in toll-access journals, but that institutions haven’t come up with a more attractive alternative. If individuals are not to blame, than there is no reason to mandate them to do anything differently. Instead, institutions should be mandated to stop funding journals via subscriptions or APCs and instead invest the money into a modern, more cost-effective infrastructure for text, data and code. Obviously, in this specificity, this is nearly impossible to mandate in most countries. However, there is a mandate that comes very close. It has been dubbed “Plan I” (for infrastructure). In brief, it entails a three step procedure:

Build on already available standards and guidelines to establish a certification process for a sustainable scholarly infrastructure
Funders require institutional certification before reviewing grant applications
Institutions use subscription funds to implement infrastructure for certification….”

Two Competing Visions for Research Data Sharing – The Scholarly Kitchen

“In recent years, mechanisms for sharing and preserving research data have grown considerably. But the landscape is crowded with a number of divergent models for data sharing. And because these divergent approaches to research data sharing are poorly distinguished in much of the discourse, it can be a confusing landscape. Some are driven by the needs of science, some by business strategy. Today, I propose that two fundamentally competing visions are emerging for sharing research data….”

The Big Data Challenge – Recommendations by Mercè Crosas – Big Data Value

“Currently, Mercè’s team is in the process of implementing datatags for datasets in the Harvard Dataverse repository. This has been a big task due to legal compliance issues, security requirements and the conditions set by various data agreements. These datasets often contain sensitive information about individuals and therefore safeguards need to be put in place to protect these individuals. Policies on data sharing play a critical role in balancing the benefits and risks. The average citizen wants privacy and safety of his data but has little time for data governance. As the amount of data driven products is only expected to increase, so is the demand of citizens for privacy management. It is important to map the data beforehand because the manner in which relevant regulation is to be attached to the data is dependent on the data itself. When regulation changes, the datatags will have to be adopted as well, for instance by providing an updated version of the tag. For these purposes, they teamed up with lawyers helping them with the verification of the datatags. More recently, Mercè has been involved with the OpenDP project as one of the co-PIs, an open-source platform for differential privacy libraries. This work would allow to mine and analyze sensitive datasets while preserving their privacy and never been accessed directly by the researchers. Dataverse, DataTags, and OpenDP will together provide a privacy-preserving platform for sharing and analyzing sensitive data….”