ORCID Profile
0000-0001-5212-7052
Current Organisation
University of California, San Diego
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Publisher: Springer Science and Business Media LLC
Date: 27-01-2021
DOI: 10.1007/S12021-020-09509-0
Abstract: There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating erse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2021
Publisher: F1000 Research Ltd
Date: 19-11-2015
DOI: 10.12688/F1000RESEARCH.6555.2
Abstract: A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( esources ). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources.
Publisher: Springer Science and Business Media LLC
Date: 20-11-2015
Publisher: F1000 Research Ltd
Date: 04-03-2019
DOI: 10.12688/F1000RESEARCH.18357.1
Abstract: The increasing richness and ersity of biomedical data types creates major organizational and analytical impediments to rapid translational impact in the context of training and education. As biomedical data-sets increase in size, variety and complexity, they challenge conventional methods for sharing, managing and analyzing those data. In May 2017, we convened a two-day meeting between the BD2K Training Coordinating Center (TCC), ELIXIR Training/TeSS, GOBLET, H3ABioNet, EMBL-ABR, bioCADDIE and the CSIRO, in Huntington Beach, California, to compare and contrast our respective activities, and how these might be leveraged for wider impact on an international scale. Discussions focused on the role of i) training for biomedical data science ii) the need to promote core competencies, and the ii) development of career paths. These led to specific conversations about i) the values of standardizing and sharing data science training resources ii) challenges in encouraging adoption of training material standards iii) strategies and best practices for the personalization and customization of learning experiences iv) processes of identifying stakeholders and determining how they should be accommodated and v) discussions of joint partnerships to lead the world on data science training in ways that benefit all stakeholders. Generally, international cooperation was viewed as essential for accommodating the widest possible participation in the modern bioscience enterprise, providing skills in a truly “FAIR” manner, addressing the importance of data science understanding worldwide. Several recommendations for the exchange of educational frameworks are made, along with potential sources for support, and plans for further cooperative efforts are presented.
Location: United States of America
No related grants have been discovered for Jeffrey Grethe.