Finding equipoise: CEPI revises its equitable access policy – ScienceDirect

“Both the original policy and the revised one recommended that CEPI not take ownership in IP, particularly with regard to patents….

Awardees may choose to obtain intellectual property rights (such as patents or copyrights) for inventions, research materials, data bases and the like developed using funding from CEPI. If they seek such intellectual property protection, it will be at their own cost and they must promptly notify CEPI….

CEPI has committed to “Open Access” for project data, requiring that any final manuscripts of the research results must be publicly available and published in accordance with globally accepted standards, in particular the principles of “Plan S” (https://www.scienceeurope.org/wp-content/uploads/2018/09/Plan_S.pdf), an initiative developed by Science Europe regarding open access publishing.
CEPI has committed to “Open Data” for project data….”

Addgene: COVID-19 Resources

“The global research community is moving quicky to expand the knowledge and understanding of COVID-19 and related coronaviruses. To assist with this effort Addgene will maintain this plasmid collection page, which outlines various plasmids available and those coming soon. Additionally, we have linked to collections of open-access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists….”

 

Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials | Applied and Environmental Microbiology

Abstract:  In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies. These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues. Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized. This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers. Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

 

The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system | Genetics in Medicine

Abstract:  Purpose:

Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.

Methods

Three of the nation’s leading children’s hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model.

Results

Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype–phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications.

Conclusions

The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system | Genetics in Medicine

Abstract:  Purpose:

Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.

Methods

Three of the nation’s leading children’s hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model.

Results

Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype–phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications.

Conclusions

The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

The advantages of UK Biobank’s open access strategy for health research – Conroy – – Journal of Internal Medicine – Wiley Online Library

Abstract:  Ready access to health research studies is becoming more important as researchers, and their funders, seek to maximise the opportunities for scientific innovation and health improvements. Large?scale population?based prospective studies are particularly useful for multidisciplinary research into the causes, treatment and prevention of many different diseases. UK Biobank has been established as an open?access resource for public health research, with the intention of making the data as widely available as possible in an equitable and transparent manner. Access to UK Biobank’s unique breadth of phenotypic and genetic data has attracted researchers worldwide from across academia and industry. As a consequence, it has enabled scientists to perform world?leading collaborative research. Moreover, open access to an already deeply characterized cohort has encouraged both public and private sector investment in further enhancements to make UK Biobank an unparalleled resource for public health research and an exemplar for the development of open access approaches for other studies.

Graphene as an open-source material | TechCrunch

Graphene is fundamentally different from software in that it is a physical resource. Since the material’s discovery, quantity has been a serious issue, preventing the material from seeing widespread use. Natural reserves of graphene are few and far between, and while scientists have discovered ways of producing graphene, the methods have proved unscalable.

In addition, graphene would need a way to be experimented with by the average user. For those who don’t have the same equipment researchers do, how can they go about tinkering with graphene? In order for graphene to become an open-source material, a solution for these two problems must be found….

The solutions may be closer at hand than you might think….”

Depositing and reporting of reagents: Accelerating open and reproducible science. | The Official PLOS Blog

Centralized depositing of materials advances science in so many ways. It saves authors the time and burden of shipping requested materials. Researchers who request from repositories save time by not having to recreate reagents or wait months or years to receive samples. Many scientists have been on the receiving end of a request that was filled by an incorrect or degraded sample, which further delays research. Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research….

By encouraging authors to deposit materials at the time of publication, journals will help accelerate research through timely distribution and accurate identification of reagents. Biological repositories exist to serve the scientific community. Take Addgene’s involvement in the explosive advancement of CRISPR research. Since 2012, over 8,400 CRISPR plasmids have been deposited and Addgene has distributed over 144,000 CRISPR plasmids worldwide, enabling researchers to share, modify, and improve this game-changing molecular tool. It is a prime example of the positive impact that biological repositories are making on research….”

Governance of a global genetic resource commons for non-commercial research: A case-study of the DNA barcode commons

Abstract:  Life sciences research that uses genetic resources is increasingly collaborative and global, yet collective action remains a significant barrier to the creation and management of shared research resources. These resources include sequence data and associated metadata, and biological samples, and can be understood as a type of knowledge commons. Collective action by stakeholders to create and use knowledge commons for research has potential benefits for all involved, including minimizing costs and sharing risks, but there are gaps in our understanding of how institutional arrangements may promote such collective action in the context of global genetic resources. We address this research gap by examining the attributes of an exemplar global knowledge commons: The DNA barcode commons. DNA barcodes are short, standardized gene regions that can be used to inexpensively identify unknown specimens, and proponents have led international efforts to make DNA barcodes a standard species identification tool. Our research examined if and how attributes of the DNA barcode commons, including governance of DNA barcode resources and management of infrastructure, facilitate global participation in DNA barcoding efforts. Our data sources included key informant interviews, organizational documents, scientific outputs of the DNA barcoding community, and DNA barcode record submissions. Our research suggested that the goal of creating a globally inclusive DNA barcode commons is partially impeded by the assumption that scientific norms and expectations held by researchers in high income countries are universal. We found scientific norms are informed by a complex history of resource misappropriation and mistrust between stakeholders. DNA barcode organizations can mitigate the challenges caused by its global membership through creating more inclusive governance structures, developing norms for the community are specific to the context of DNA barcoding, and through increasing awareness and knowledge of pertinent legal frameworks.

ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks

Abstract:  Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.