Title: Opening Doors to Physical Sample Data Discovery, Integration, and Credit
Physical samples and their associated (meta)data underpin scientific discoveries across disciplines, and can enable new science when appropriately archived. However, there are significant gaps in community practices and infrastructure that currently prevent accurate provenance tracking, reproducibility, and attribution. For the vast majority of samples, descriptive metadata is often sparse, inaccessible, or absent. Samples and associated (meta)data may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkages or provenance tracking as new information is generated over time. The Physical Samples Curation Cluster has therefore developed ‘A Scientific Author Guide for Publishing Open Research Using Physical Samples.’ This involved synthesizing existing practices, community feedback, and assessing real-world examples to identify community and infrastructure needs. We identified areas of work needed to enable authors to efficiently reference samples and related data, link related samples and data, and track their use. Our goal is to help improve the discoverability, interoperability, use of physical samples and associated (meta)data into the future. more »« less
Scientific data, along with its analysis, accuracy, completeness, and reproducibility, plays a vital role in advancing science and engineering. Open Science Chain (OSC) provides a Cyberinfrastructure platform, built using distributed ledger technologies, where verification information about scientific dataset is stored and managed in a consortium blockchain. Researchers have the ability to independently verify the authenticity of scientific results using the information stored with OSC. Researchers can also build research workflows by linking data entries in the ledger and external repositories such as GitHub that will allow for detailed provenance tracking. OSC enables answers to questions such as: how can we ensure research integrity when different research groups share and work on the same datasets across the world? Is it possible to enable quick verification of the exact data sets that were used for particular published research? Can we check the provenance of the data used in the research? In this poster, we highlight our work in building a secure, scalable architecture for OSC including developing a security module for storing identities that can be used by the researchers of science gateways communities to increase the confidence of their scientific results.
Davies, Neil; Deck, John; Kansa, Eric C; Kansa, Sarah Whitcher; Kunze, John; Meyer, Christopher; Orrell, Thomas; Ramdeen, Sarah; Snyder, Rebecca; Vieglais, Dave; et al
(, GigaScience)
null
(Ed.)
Abstract Sampling the natural world and built environment underpins much of science, yet systems for managing material samples and associated (meta)data are fragmented across institutional catalogs, practices for identification, and discipline-specific (meta)data standards. The Internet of Samples (iSamples) is a standards-based collaboration to uniquely, consistently, and conveniently identify material samples, record core metadata about them, and link them to other samples, data, and research products. iSamples extends existing resources and best practices in data stewardship to render a cross-domain cyberinfrastructure that enables transdisciplinary research, discovery, and reuse of material samples in 21st century natural science.
Valdez, J.
(, On the Move to Meaningful Internet Systems. OTM 2017 Conferences. OTM 2017.)
Provenance metadata describing the source or origin of data is critical to verify and validate results of scientific experiments. Indeed, reproducibility of scientific studies is rapidly gaining significant attention in the research community, for example biomedical and healthcare research. To address this challenge in the biomedical research domain, we have developed the Provenance for Clinical and Healthcare Research (ProvCaRe) using World Wide Web Consortium (W3C) PROV specifications, including the PROV Ontology (PROV-O). In the ProvCaRe project, we are extending PROV-O to create a formal model of provenance information that is necessary for scientific reproducibility and replication in biomedical research. However, there are several challenges associated with the development of the ProvCaRe ontology, including: (1) Ontology engineering: modeling all biomedical provenance-related terms in an ontology has undefined scope and is not feasible before the release of the ontology; (2) Redundancy: there are a large number of existing biomedical ontologies that already model relevant biomedical terms; and (3) Ontology maintenance: adding or deleting terms from a large ontology is error prone and it will be difficult to maintain the ontology over time. Therefore, in contrast to modeling all classes and properties in an ontology before deployment (also called precoordination), we propose the “ProvCaRe Compositional Grammar Syntax” to model ontology classes on-demand (also called postcoordination). The compositional grammar syntax allows us to re-use existing biomedical ontology classes and compose provenance-specific terms that extend PROV-O classes and properties. We demonstrate the application of this approach in the ProvCaRe ontology and the use of the ontology in the development of the ProvCaRe knowledgebase that consists of more than 38 million provenance triples automatically extracted from 384,802 published research articles using a text processing workflow.
Lehnert, Kerstin; Klump, Jens; Wyborn, Lesley; Ramdeen, Sarah
(, Biodiversity Information Science and Standards)
There is growing recognition that unambiguous citation and tracking of physical samples allows previously impossible linking of samples to data and publications, linking and integration of sample-based observations across data systems, and paves the road towards advanced data mining of sample-based data. And in recent years, there has been an uptake in the use of Persistent Identifiers (PIDs) for physical samples to support such citation and tracking. The IGSN (International Geo Sample Number) is a PID for physical samples. It was originally developed for the solid earth sciences, and has evolved into an international PID system with members in five continents and a network of active allocating agents. It has been adopted by a growing number and range of stakeholders worldwide, including national geological surveys, research infrastructure providers, collection curators, researchers, and data managers, and by other disciplines that need to refer to physical samples. Nearly 6.9 million samples have been registered with IGSNs so far. The IGSN system uses the Handle System (Kahn and Wilensky 1995; see also Handle.Net ® ) and has an international organization, IGSN e.V., to manage its governance structure and the technical architecture. The recent expansion of the IGSN beyond the geosciences into other domains such as biodiversity, archeology, and material sciences confirms the power of its concept and implementation, but imposes substantial pressures on the existing capacity and capabilities of the IGSN architecture and its governing organization. Modifications to the IGSN organizational and technical architecture are necessary at this point to keep pace with the growing demand and expectations. These changes are also necessary to ensure trustworthy and sustainable services for PID registration and resolution in a maturing research data ecosystem. The essential criteria for a trustworthy system include an organizational foundation that ensures longevity, sustainability, proper governance, and regular quality assessment of registration services. It also includes a reliable and secure technical platform, based on open standards, which is sufficiently scalable and flexible to accommodate the growing diversity of specimen types, use cases, and stakeholder requirements. In 2018, a major planning project for the IGSN was funded by the Alfred P. Sloan Foundation. An international group of experts participates in re-designing and improving the existing organization and technical architecture of the IGSN system, revising the current business model of the IGSN e.V. and professionalizing its operations. The goal is for the IGSN system to be able to respond to, and support in a sustainable manner, the rapidly growing demands of a global and increasingly multi-disciplinary user community, and to ensure that the IGSN will be a trustworthy, stable, and adaptable persistent identifier system for material samples, both technically and organizationally. The end result should also satisfy and facilitate participation across research domains, and will be a reliable component of the evolving research data ecosystem. Finally, it will ensure that the IGSN is recognized as a trusted partner by data infrastructure providers and the science community alike.
Zheng, Nan; Ives, Zachary G.
(, Proceedings of the VLDB Endowment)
null
(Ed.)
Data provenance tools aim to facilitate reproducible data science and auditable data analyses, by tracking the processes and inputs responsible for each result of an analysis. Fine-grained provenance further enables sophisticated reasoning about why individual output results appear or fail to appear. However, for reproducibility and auditing, we need a provenance archival system that is tamper-resistant , and efficiently stores provenance for computations computed over time (i.e., it compresses repeated results). We study this problem, developing solutions for storing fine-grained provenance in relational storage systems while both compressing and protecting it via cryptographic hashes. We experimentally validate our proposed solutions using both scientific and OLAP workloads.
@article{osti_10528006,
place = {Country unknown/Code not available},
title = {Opening Doors to Physical Sample Data Discovery, Integration, and Credit},
url = {https://par.nsf.gov/biblio/10528006},
DOI = {10.31223/X5ST2K},
abstractNote = {Physical samples and their associated (meta)data underpin scientific discoveries across disciplines, and can enable new science when appropriately archived. However, there are significant gaps in community practices and infrastructure that currently prevent accurate provenance tracking, reproducibility, and attribution. For the vast majority of samples, descriptive metadata is often sparse, inaccessible, or absent. Samples and associated (meta)data may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkages or provenance tracking as new information is generated over time. The Physical Samples Curation Cluster has therefore developed ‘A Scientific Author Guide for Publishing Open Research Using Physical Samples.’ This involved synthesizing existing practices, community feedback, and assessing real-world examples to identify community and infrastructure needs. We identified areas of work needed to enable authors to efficiently reference samples and related data, link related samples and data, and track their use. Our goal is to help improve the discoverability, interoperability, use of physical samples and associated (meta)data into the future.},
journal = {},
publisher = {Nature Scientific Data},
author = {Damerow, Joan and Raia, Natalie and Stanley, Val and Choe, Saebyul and Borton, Mikayla and Byers, Neil and Cassidy, Ellen and Cholia, Shreyas and Edmunds, Rorie and Forbes, Brieanne and Forrest, Kathleen and Goldman, Amy and Kunze, John and Lafia, Sara and Lehnert, Kerstin and McIntyre-Redden, Marcella and Naples, Richard and O'Ryan, Dylan and Parker, Charles and Plomp, Esther and Powers-McCormack, Beck and Ramdeen, Sarah and Richard, Stephen and Thessen, Anne and Thompson, Cody and Vieglais, Dave and Vrouwenvelder, Kristina and Wood-Charlson, Elisha and Wyborn, Lesley and Reddy, TBK and Thomer, Andrea},
}
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