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International Journal of Digital... 2020This paper reports on the ongoing activities and curation practices of the National Center for Biomolecular NMR Data Processing and Analysis. Over the past several...
This paper reports on the ongoing activities and curation practices of the National Center for Biomolecular NMR Data Processing and Analysis. Over the past several years, the Center has been developing and extending computational workflow management software for use by a community of biomolecular NMR spectroscopists. Previous work had been to refactor the workflow system to utilize the PREMIS framework for reporting retrospective provenance as well as for sharing workflows between scientists and to support data reuse. In this paper, we report on our recent efforts to embed analytics within the workflow execution and within provenance tracking. Important metrics for each of the intermediate datasets are included within the corresponding PREMIS intellectual object, which allows for both inspection of the operation of individual actors as well as visualization of the changes throughout a full processing workflow. These metrics can be viewed within the workflow management system or through standalone metadata widgets. Our approach is to support a hybrid approach of both automated, workflow execution as well as manual intervention and metadata management. In this combination, the workflow system and metadata widgets encourage the domain experts to be avid curators of the data which they create, fostering both computational reproducibility and scientific data reuse.
PubMed: 33767737
DOI: 10.2218/ijdc.v15i1.709 -
Studies in Health Technology and... Aug 2019To characterize the scientific reproducibility of biomedical research studies by query and analysis of semantic provenance graphs generated from provenance metadata...
OBJECTIVE
To characterize the scientific reproducibility of biomedical research studies by query and analysis of semantic provenance graphs generated from provenance metadata terms extracted from PubMed articles.
METHODS
We develop a new semantic provenance graph generation algorithm that uses a provenance ontology developed as part of the Provenance for Clinical and Health Research (ProvCaRe) project. The ProvCaRe project has processed and extracted provenance metadata from more than 1.6 million full text articles from the PubMed database.
RESULTS
The semantic provenance graph generation algorithm is evaluated using provenance terms extracted from 75 selected articles describing sleep medicine research studies. In addition, we use eight provenance queries to evaluate the quality of semantic provenance graphs generated by the new algorithm.
CONCLUSION
The ProvCaRe project has created a unique resource to characterize the reproducibility of biomedical research studies and the semantic provenance graph generation algorithm enables users to effectively query and analyze the provenance metadata in the ProvCaRe knowledge repository.
Topics: Biological Ontologies; Biomedical Research; Metadata; Reproducibility of Results; Semantics
PubMed: 31437939
DOI: 10.3233/SHTI190237 -
Botanical Studies Dec 2016As a highly valued and multiple function tree species, Cyclocarya paliurus is planted and managed for timber production and medical use. However, limited information is...
BACKGROUND
As a highly valued and multiple function tree species, Cyclocarya paliurus is planted and managed for timber production and medical use. However, limited information is available on its genotype selection and cultivation for growth and phytochemicals. Responses of growth and secondary metabolites to light regimes and genotypes are useful information to determine suitable habitat conditions for the cultivation of medicinal plants.
RESULTS
Both light regime and provenance significantly affected the leaf characteristics, leaf flavonoid contents, biomass production and flavonoid accumulation per plant. Leaf thickness, length of palisade cells and chlorophyll a/b decreased significantly under shading conditions, while leaf areas and total chlorophyll content increased obviously. In the full light condition, leaf flavonoid contents showed a bimodal temporal variation pattern with the maximum observed in August and the second peak in October, while shading treatment not only reduced the leaf content of flavonoids but also delayed the peak appearing of the flavonoid contents in the leaves of C. paliurus. Strong correlations were found between leaf thickness, palisade length, monthly light intensity and measured flavonoid contents in the leaves of C. paliurus. Muchuan provenance with full light achieved the highest leaf biomass and flavonoid accumulation per plant.
CONCLUSIONS
Cyclocarya paliurus genotypes show diverse responses to different light regimes in leaf characteristics, biomass production and flavonoid accumulation, highlighting the opportunity for extensive selection in the leaf flavonoid production.
PubMed: 28597438
DOI: 10.1186/s40529-016-0145-7 -
PLoS Biology Aug 2018Whereas biological materials were once transferred freely, there has been a marked shift in the formalisation of exchanges involving these materials, primarily through...
Whereas biological materials were once transferred freely, there has been a marked shift in the formalisation of exchanges involving these materials, primarily through the use of Material Transfer Agreements (MTAs). This paper considers how risk aversion dominates MTA negotiations and the impact it may have on scientific progress. Risk aversion is often based on unwarranted fears of incurring liability through the use of a material or loss of control or missing out on commercialisation opportunities. Evidence to date has suggested that complexity tends to permeate even straightforward transactions despite extensive efforts to implement simple, standard MTAs. We argue that in most cases, MTAs need do little more than establish provenance, and any attempt to extend MTAs beyond this simple function constitutes stifling behaviour. Drawing on available examples of favourable practice, we point to a number of strategies that may usefully be employed to reduce risk-averse tendencies, including the promotion of simplicity, education of those engaged in the MTA process, and achieving a cultural shift in the way in which technology transfer office (TTO) success is measured in institutions employing MTAs.
Topics: Humans; Laboratory Chemicals; Liability, Legal; Ownership; Research; Risk
PubMed: 30102688
DOI: 10.1371/journal.pbio.2006031 -
PloS One 2023Since predynastic times, baboons (Papio hamadryas and Papio anubis) were important in ancient Egypt for ritual and religious purposes. These species did not occur...
Since predynastic times, baboons (Papio hamadryas and Papio anubis) were important in ancient Egypt for ritual and religious purposes. These species did not occur naturally in Egypt and therefore had to be imported, but little is known about their exact provenance and the conditions in which they were kept through time. Here, we analyse the skeletal remains of a collection of baboon mummies coming from Thebes (Egypt), representing a minimum of 36 individuals, from a palaeopathological and demographic point of view. The pathological cases are described, figured where relevant, and the discussion attempts to understand their aetiology. The prevalence of the different types of deformations and pathologies is compared with that of other captive baboon populations from more or less contemporary (Tuna el-Gebel and Saqqara) or older (predynastic Hierakonpolis) sites. This is combined with observations on the age and sex distribution and the proportion of hamadryas and anubis baboons to draw conclusions about the conditions of keeping, possible breeding on-site, provenance of the animals and the trade routes used for import. As in Tuna el-Gebel and Saqqara, the baboons from Gabbanat el-Qurud suffered from numerous metabolic diseases due to chronic lack of sunlight and an unbalanced diet. This and the demographic data suggest that there was a local breeding population derived from animals captured downstream from the Sudanese Nile Valley (for anubis) and from the Horn of Africa or the southern part of the Arabian Peninsula (for hamadryas). A new series of radiocarbon dates is provided, placing the baboons from Gabbanat el-Qurud between the end of the Third Intermediate Period and the beginning of the Late Period.
Topics: Humans; Animals; Papio; Papio hamadryas; Egypt; Plant Breeding; Papio anubis; Demography
PubMed: 38055690
DOI: 10.1371/journal.pone.0294934 -
IEEE Access : Practical Innovations,... 2020Recent advancements in the Internet of Health Things (IoHT) have ushered in the wide adoption of IoT devices in our daily health management. For IoHT data to be...
Recent advancements in the Internet of Health Things (IoHT) have ushered in the wide adoption of IoT devices in our daily health management. For IoHT data to be acceptable by stakeholders, applications that incorporate the IoHT must have a provision for data provenance, in addition to the accuracy, security, integrity, and quality of data. To protect the privacy and security of IoHT data, federated learning (FL) and differential privacy (DP) have been proposed, where private IoHT data can be trained at the owner's premises. Recent advancements in hardware GPUs even allow the FL process within smartphone or edge devices having the IoHT attached to their edge nodes. Although some of the privacy concerns of IoHT data are addressed by FL, fully decentralized FL is still a challenge due to the lack of training capability at all federated nodes, the scarcity of high-quality training datasets, the provenance of training data, and the authentication required for each FL node. In this paper, we present a lightweight hybrid FL framework in which blockchain smart contracts manage the edge training plan, trust management, and authentication of participating federated nodes, the distribution of global or locally trained models, the reputation of edge nodes and their uploaded datasets or models. The framework also supports the full encryption of a dataset, the model training, and the inferencing process. Each federated edge node performs additive encryption, while the blockchain uses multiplicative encryption to aggregate the updated model parameters. To support the full privacy and anonymization of the IoHT data, the framework supports lightweight DP. This framework was tested with several deep learning applications designed for clinical trials with COVID-19 patients. We present here the detailed design, implementation, and test results, which demonstrate strong potential for wider adoption of IoHT-based health management in a secure way.
PubMed: 34192116
DOI: 10.1109/ACCESS.2020.3037474 -
Journal of Biomedical Informatics Mar 2022Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through...
Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through standard and rich metadata, as encouraged by open data initiatives such as the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. This helps data re-users to understand and reuse the shared data with confidence. Therefore, dedicated frameworks are required. The provenance reporting throughout a biomedical study lifecycle has been proposed as a way to increase confidence in data while reusing it. The Biomedical Study - Lifecycle Management (BMS-LM) data model has implemented provenance and lifecycle traceability for several multimodal-imaging techniques but this is not enough for data understanding while reusing it. Actually, in the large scope of biomedical research, a multitude of metadata sources, also called Knowledge Organization Systems (KOSs), are available for data annotation. In addition, data producers uses local terminologies or KOSs, containing vernacular terms for data reporting. The result is a set of heterogeneous KOSs (local and published) with different formats and levels of granularity. To manage the inherent heterogeneity, semantic interoperability is encouraged by the Research Data Management (RDM) community. Ontologies, and more specifically top ontologies such as BFO and DOLCE, make explicit the metadata semantics and enhance semantic interoperability. Based on the BMS-LM data model and the BFO top ontology, the BioMedical Study - Lifecycle Management (BMS-LM) core ontology is proposed together with an associated framework for semantic interoperability between heterogeneous KOSs. It is made of four ontological levels: top/core/domain/local and aims to build bridges between local and published KOSs. In this paper, the conversion of the BMS-LM data model to a core ontology is detailed. The implementation of its semantic interoperability in a specific domain context is explained and illustrated with examples from small animal preclinical research.
Topics: Animals; Biological Ontologies; Biomedical Research; Data Curation; Metadata; Research Design; Semantics
PubMed: 35124236
DOI: 10.1016/j.jbi.2022.104007 -
Advances in Database Technology :... Mar 2016Many modern applications involve collecting large amounts of data from multiple sources, and then aggregating and manipulating it in intricate ways. The complexity of...
Many modern applications involve collecting large amounts of data from multiple sources, and then aggregating and manipulating it in intricate ways. The complexity of such applications, combined with the size of the collected data, makes it difficult to understand the application logic and how information was derived. has been proven helpful in this respect in different contexts; however, maintaining and presenting the full and exact provenance may be infeasible, due to its size and complex structure. For that reason, we introduce the notion of approximated summarized provenance, where we seek a compact representation of the provenance at the possible cost of information loss. Based on this notion, we have developed PROX, a system for the management, presentation and use of data provenance for complex applications. We propose to demonstrate PROX in the context of a movies rating crowd-sourcing system, letting participants view provenance summarization and use it to gain insights on the application and its underlying data.
PubMed: 27570843
DOI: No ID Found -
Heliyon Dec 2021The upper Cretaceous Lokoja Formation is the earliest deposited stratigraphic unit in the intracratonic Bida Basin, Nigeria. It consists predominantly of sandstone and...
The upper Cretaceous Lokoja Formation is the earliest deposited stratigraphic unit in the intracratonic Bida Basin, Nigeria. It consists predominantly of sandstone and offers a potential hydrocarbon reservoir in the basin. In this study, we investigated the bulk elemental (major, trace and rare earth elements) and mineralogical compositions of the sandstones for the determination of their compositional maturity, tectonic setting, source and weathering history. The sandstone geochemical data indicates that the samples contain moderate amount of SiO and AlO with average values of 78.3 % and 9.75 % respectively. Relatively high average values of KO (1.59 %) and NaO (1.52 %) and low FeO (2.56 %), MnO (0.05 %), TiO (0.31 %) and PO (0.018 %) were obtained. Plots of relevant geochemical elements reveal that the sandstones are predominantly arkose and litharenite types with minor sub-litharenites. Application of some trace element geochemical proxies; La/Co (11.78), Th/Co (1.32), La/Th (7.04) and Eu/Eu∗ (0.82) to constrain the source history suggest protolith dominated by felsic rock. Relatively low average values of ΣREEs (12.81) and ΣHREEs (1.52) support the felsic provenance of the sandstones and the tectonic setting discriminant function plots indicate passive margin depositional basin. Paleo-weathering plot reveals a moderate humid climatic condition and the mean values of CIA (79.21), CIW (90.51), PIA (66.55) and A-CN-K diagram indicates low to moderate chemical weathering in the source area and compositional immaturity for the sediments. This study concludes that the sandstones of the Lokoja Formation are immature and were derived from the faulted blocks of granitic basement rocks at the margin of the basin and deposited proximally.
PubMed: 34917824
DOI: 10.1016/j.heliyon.2021.e08564 -
The Science of the Total Environment Oct 2016Restoration efforts in the Mediterranean Basin have been changing from a silvicultural to an ecological restoration approach. Yet, to what extent the projects are guided...
Restoration efforts in the Mediterranean Basin have been changing from a silvicultural to an ecological restoration approach. Yet, to what extent the projects are guided by ecological restoration principles remains largely unknown. To analyse this issue, we built an on-line survey addressed to restoration practitioners. We analysed 36 restoration projects, mostly from drylands (86%). The projects used mainly soil from local sources. The need to comply with legislation was more important as a restoration motive for European Union (EU) than for non-EU countries, while public opinion and health had a greater importance in the latter. Non-EU countries relied more on non-native plant species than EU countries, thus deviating from ecological restoration guidelines. Nursery-grown plants used were mostly of local or regional provenance, whilst seeds were mostly of national provenance. Unexpected restoration results (e.g. inadequate biodiversity) were reported for 50% of the projects and restoration success was never evaluated in 22%. Long term evaluation (>6years) was only performed in 31% of cases, and based primarily on plant diversity and cover. The use of non-native species and species of exogenous provenances may: i) entail the loss of local genetic and functional trait diversity, critical to cope with drought, particularly under the predicted climate change scenarios, and ii) lead to unexpected competition with native species and/or negatively impact local biotic interactions. Absent or inappropriate monitoring may prevent the understanding of restoration trajectories, precluding adaptive management strategies, often crucial to create functional ecosystems able to provide ecosystem services. The overview of ecological restoration projects in the Mediterranean Basin revealed high variability among practices and highlighted the need for improved scientific assistance and information exchange, greater use of native species of local provenance, and more long-term monitoring and evaluation, including functional and ecosystem services' indicators, to improve and spread the practice of ecological restoration.
Topics: Africa, Northern; Biota; Environmental Restoration and Remediation; Mediterranean Region; Middle East; Plants; Soil
PubMed: 27239715
DOI: 10.1016/j.scitotenv.2016.05.136