Category Archives: oa.specimens

Finding equipoise: CEPI revises its equitable access policy – ScienceDirect

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“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

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“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

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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

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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

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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

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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

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“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

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“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

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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

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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.

Extending U.S. Biodiversity Collections to Promote Research and Education

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“Our national heritage of approximately one billion biodiversity specimens, once digitized, can be linked to emerging digital data sources to form an information-rich network for exploring earth’s biota across taxonomic, temporal and spatial scales. A workshop held 30 October – 1 November 2018 at Oak Spring Garden in Upperville, VA under the leadership of the Biodiversity Collections Network (BCoN) developed a strategy for the next decade to maximize the value of our collections resource for research and education. In their deliberations, participants drew heavily on recent literature as well as surveys, and meetings and workshops held over the past year with the primary stakeholder community of collections professionals, researchers, and educators.

Arising from these deliberations is a vision to focus future biodiversity infrastructure and digital resources on building a network of extended specimen data that encompasses the depth and breadth of biodiversity specimens and data held in U.S. collections institutions. The extended specimen network (ESN) includes the physical voucher specimen curated and housed in a collection and its associated genetic, phenotypic and environmental data (both physical and digital). These core data types, selected because they are key to answering driving research questions, include physical preparations such as tissue samples and their derivative products such as gene sequences or metagenomes, digitized media and annotations, and taxon- or locality-specific data such as occurrence observations, phylogenies and species distributions. Existing voucher specimens will be extended both manually and through new automated methods, and data will be linked through unique identifiers, taxon name and location across collections, across disciplines and to outside sources of data. As we continue our documentation of earth’s biota, new collections will be enhanced from the outset, i.e., accessioned with a full suite of data. We envision the ESN proposed here will be the gold standard for the structured cloud of integrated data associated with all vouchered specimens. These permanent specimen vouchers, in which genotypes and phenotypes link to a particular environment in time and space, comprise an irreplaceable resource for the millennia….”

Taking knowledge preservation to the next level: new partnership between protocols.io, Addgene, PLOS

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“Digital information carries a significant risk of disappearing, as one of the “fathers of the Internet” Vint Cerf has been

. This is particularly problematic for research communication as vanishing records undermine the reproducibility and integrity of science. We have taken this concern seriously at protocols.io from day one, constantly aiming for better ways to ensure stability, preservation, and visibility of the methods and knowledge shared on our platform. Digital archiving solutions have been the center of our focus; however, today we are excited to share with you our new physical preservation initiative, guaranteeing zero loss, long into the future. We are thrilled to be joined by the Addgene plasmid repository and the Public Library of Science (PLOS) in this initiative.

 
Of course, for many years we at protocols.io have had public APIs and PDF export of all protocols. In 2016, we became a

of CLOCKSS (the digital preservation archive for scholarly content, started by Stanford librarians in 1999), sending a PDF copy of every new protocol to them, the second it is made public. More recently, we introduced integration with Dropbox and GoogleDrive, to facilitate individual backups.

 
While all of our efforts are reasonable and ensure preservation and accessibility for decades, they are not infallible solutions in the long run. This is because preservation and accessibility are not the same thing. How many people today can open a file from 1997 WordPerfect or 1999 PowerPoint, particularly if it has been saved on a floppy disk? How confident are we that PDFs of protocols will be accessible and readable in seventy years by the scientists of the future?
 
With the above concerns in mind, we have been exploring over the last year more reliable solutions that take advantage of modern technology. And so, we are excited to announce a partnership with

and

for low-cost physical preservation of protocols, using laser cutters. The PLOS editorial team will be in charge of selecting protocols that warrant physical preservation and Addgene, with their expertise in physical storage, will be handling the long-term archiving in their freezers….”

 

Centuries-Old Plant Collection Now Online — A Treasure Trove For Researchers : NPR

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“Funded by the National Science Foundation, the Mid-Atlantic Megalopolis Project will put about 800,000 records from about a dozen herbaria online via high-resolution photos of plant specimens that span the urbanized corridor from New York City to Washington, D.C….”

Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences | The National Academies Press

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“Biologists communicate to the research community and document their scientific accomplishments by publishing in scholarly journals. This report explores the responsibilities of authors to share data, software, and materials related to their publications. In addition to describing the principles that support community standards for sharing different kinds of data and materials, the report makes recommendations for ways to facilitate sharing in the future.”

Green digitization: Botanical collections data answer real-world questions | EurekAlert! Science News

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“Special issue of Applications in Plant Sciences explores new developments and applications of digital plant data

Even as botany has moved firmly into the era of “big data,” some of the most valuable botanical information remains inaccessible for computational analysis, locked in physical form in the orderly stacks of herbaria and museums. Herbarium specimens are plant samples collected from the field that are dried and stored with labels describing species, date and location of collection, along with various other information including habitat descriptions. The detailed historical record these specimens keep of species occurrence, morphology, and even DNA provides an unparalleled data source to address a variety of morphological, ecological, phenological, and taxonomic questions. Now efforts are underway to digitize these data, and make them easily accessible for analysis. Two symposia were convened to discuss the possibilities and promise of digitizing these data–at the Botanical Society of America’s 2017 annual meeting in Fort Worth, Texas, and again at the XIX International Botanical Congress in Shenzhen, China. The proceedings of those symposia have been published as a special issue of Applications in Plant Sciences; the articles discuss a range of methods and remaining challenges for extracting data from botanical collections, as well as applications for collections data once digitized. Many of the authors contributing to the issue are involved in iDigBio (Integrated Digitized Biocollections), a new “national coordinating center for the facilitation and mobilization of biodiversity specimen data,” as described by Dr. Gil Nelson, a botanist at Florida State University and coeditor of this issue….”