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Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)-based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein's function. Many of these tools are available via PaperBLAST (http://papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein's function. Ideally, accurate annotations would allow us to predict a bacterium's capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest. Database URL: http://papers.genomics.lbl.gov.

We study a heterogeneous Rayleigh fading wireless sensor network (WSN) in which sensor nodes surveil a field of interest and communicate their sensory data with base stations with the aid of access points as relays. With the goal of improving the energy efficiency of the network, we consider both large-scale and small-scale signal propagation effects in our system model and aim to optimize the node deployment as an effective measure to reduce the wireless communication power consumption of the WSN. We propose a new framework, in which hard deterministic connectivity constraints on communication links are replaced with realistic limitations on outage due to severe stochastic fading. We also consider a radio energy model that reflects the exponential dependence of the transmission power on the rate. We derive the necessary conditions for the optimal deployment that not only minimize the power consumption, but also guarantee all wireless links to have an outage probability below the given threshold. Our theoretical findings are accompanied by simulations that indicate significant performance gains compared to existing node deployment algorithms in the literature.

The multivariate time series classification (MTSC) task aims to predict a class label for a given time series. Recently, modern deep learning-based approaches have achieved promising performance over traditional methods for MTSC tasks. The success of these approaches relies on access to the massive amount of labeled data (i.e., annotating or assigning tags to each sample that shows its corresponding category). However, obtaining a massive amount of labeled data is usually very time-consuming and expensive in many real-world applications such as medicine, because it requires domain experts’ knowledge to annotate data. Insufficient labeled data prevents these models from learning discriminative features, resulting in poor margins that reduce generalization performance. To address this challenge, we propose a novel approach: supervised contrastive learning for time series classification (SupCon-TSC). This approach improves the classification performance by learning the discriminative low-dimensional representations of multivariate time series, and its end-to-end structure allows for interpretable outcomes. It is based on supervised contrastive (SupCon) loss to learn the inherent structure of multivariate time series. First, two separate augmentation families, including strong and weak augmentation methods, are utilized to generate augmented data for the source and target networks, respectively. Second, we propose the instance-level, and cluster-level SupCon learning approaches to capture contextual information to learn the discriminative and universal representation for multivariate time series datasets. In the instance-level SupCon learning approach, for each given anchor instance that comes from the source network, the low-variance output encodings from the target network are sampled as positive and negative instances based on their labels. However, the cluster-level approach is performed between each instance and cluster centers among batches, as opposed to the instance-level approach. The cluster-level SupCon loss attempts to maximize the similarities between each instance and cluster centers among batches. We tested this novel approach on two small cardiopulmonary exercise testing (CPET) datasets and the real-world UEA Multivariate time series archive. The results of the SupCon-TSC model on CPET datasets indicate its capability to learn more discriminative features than existing approaches in situations where the size of the dataset is small. Moreover, the results on the UEA archive show that training a classifier on top of the universal representation features learned by our proposed method outperforms the state-of-the-art approaches.

Under DAPHNE4NFDI, the X‐ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user‐friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server‐side automatic authentication and (meta‐) data storage via MongoDB, PostgreSQL and (data‐) files via relevant APIs. [ABSTRACT FROM AUTHOR]

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL  https://www.agbiodata.org/databases.

Achieving a balance between accuracy and efficiency in target detection applications is an important research topic. To detect abnormal targets on power transmission lines at the power edge, this paper proposes an effective method for reducing the data bit width of the network for floating-point quantization. By performing exponent prealignment and mantissa shifting operations, this method avoids the frequent alignment operations of standard floating-point data, thereby further reducing the exponent and mantissa bit width input into the training process. This enables training low-data-bit width models with low hardware-resource consumption while maintaining accuracy. Experimental tests were conducted on a dataset of real-world images of abnormal targets on transmission lines. The results indicate that while maintaining accuracy at a basic level, the proposed method can significantly reduce the data bit width compared with single-precision data. This suggests that the proposed method has a marked ability to enhance the real-time detection of abnormal targets in transmission circuits. Furthermore, a qualitative analysis indicated that the proposed quantization method is particularly suitable for hardware architectures that integrate storage and computation and exhibit good transferability.

MicroRNAs (miRs) may contribute to disease etiology by influencing gene expression. Numerous databases are available for miR target prediction and validation, but their functionality is varied, and outputs are not standardized. The purpose of this review is to identify and describe databases for cataloging validated miR targets. Using Tools4miRs and PubMed, we identified databases with experimentally validated targets, human data, and a focus on miR-messenger RNA (mRNA) interactions. Data were extracted about the number of times each database was cited, the number of miRs, the target genes, the interactions per database, experimental methodology and key features of each database. The search yielded 10 databases, which in order of most cited to least were: miRTarBase, starBase/The Encyclopedia of RNA Interactomes, DIANA-TarBase, miRWalk, miRecords, miRGator, miRSystem, miRGate, miRSel and targetHub. Findings from this review suggest that the information presented within miR target validation databases can be enhanced by adding features such as flexibility in performing queries in multiple ways, downloadable data, ongoing updates and integrating tools for further miR-mRNA target interaction analysis. This review is designed to aid researchers, especially those new to miR bioinformatics tools, in database selection and to offer considerations for future development and upkeep of validation tools. Database URL http://mirtarbase.cuhk.edu.cn/.

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

In the originally published version of this manuscript em dashes were inadvertently added in place of short dashes and spaces, particularly in the canonical name of the database being described. In addition to this changes have also been made to the formatting of Table 1 to aid understanding. No changes have been made to the content. These errors, for which the publisher apologizes, have been corrected.

Having infrastructure survive over very long stretches of time is a nontrivial task. This is either because such infrastructure needs to be built extremely well from the outset or because it requires ongoing maintenance. The former may require prohibitively large initial investments. The latter requires ongoing investment from public agencies over the span of decades or centuries despite the pendulum swings of those governments from contrasting political aims. Without either the very high initial or ongoing investment, infrastructure can fail. Physical infrastructure failure is not inevitable-consider railways in Japan, the Panama Canal, and the U.S. Interstate Highway System.

IEEE Security & Privacy published Volume 1, Issue 1 20 years ago in January/February 2003. This year, beginning with this issue of IEEE Security & Privacy, we aim to celebrate those first 20 years with retrospectives on some of the challenges that we have overcome in that time as well as some of those on which we have not made as much progress as we had hoped to achieve. We also reflect on new challenges and even entire subdisciplines of computer security and privacy that didn't even exist 20 years ago.

AbstractHuang and Wong (Acta Inform 21(1):113–123, 1984) proposed a polynomial-time dynamic-programming algorithm for computing optimal generalized binary split trees. We show that their algorithm is incorrect. Thus, it remains open whether such trees can be computed in polynomial time. Spuler (Optimal search trees using two-way key comparisons, PhD thesis, 1994) proposed modifying Huang and Wong’s algorithm to obtain an algorithm for a different problem: computing optimal two-way comparison search trees. We show that the dynamic program underlying Spuler’s algorithm is not valid, in that it does not satisfy the necessary optimal-substructure property and its proposed recurrence relation is incorrect. It remains unknown whether the algorithm is guaranteed to compute a correct overall solution.

The future of the Internet of Things (IoT) demands the integration of synergetic applications to cater to societal needs. Examples of IoT-based confederated applications include Ambient Assisted Living with Active Healthy Ageing, CasAware with Smart Energy, Smart Gas Distribution Networks with GIS systems, and more. However, the data heterogeneity hinders integration, as these systems follow different standards, data formats, semantic models, and representations. Further, this leads to data interoperability issues in IoT. The major concern of academia and industry in the smooth integration of heterogeneous applications is interpreting different data formats and representing them in a common schema for further analysis. Existing solutions, such as message payload translation, middleware/cloud format, and Inter-IoT, are complex, time-consuming, and ineffective. Hence, this paper proposes the heterogeneous data format integration and conversion (HDFIC), a machine learning-based system to identify data formats using a Random Forest classifier and integrate them using the Data Format Description Language (DFDL). The content-based data format identification in the proposed HDFIC is trained with the standard features defined in RFC 7111, 8259, and 8996. Subsequently, the data is integrated into a single XML Schema Definition and converted into the required data format using the IBM App Connect Enterprise tool and DFDL. Finally, the performance of HDFIC is evaluated with the synergetic patient body vitals and room ambiance dataset for accuracy, data integration time, and conversion efficiency. [ABSTRACT FROM AUTHOR]

To preserve scientific data created by publicly and/or philanthropically funded research projects and to make it ready for exploitation using recent and ongoing advances in advanced and large-scale computational modeling methods, publicly available data must use in common, now-evolving standards for formatting, identifying and annotating should share data. The OpenNeuro.org archive, built first as a repository for magnetic resonance imaging data based on the Brain Imaging Data Structure formatting standards, aims to house and share all types of human neuroimaging data. Here, we present NEMAR.org, a web gateway to OpenNeuro data for human neuroelectromagnetic data. NEMAR allows users to search through, visually explore and assess the quality of shared electroencephalography (EEG), magnetoencephalography and intracranial EEG data and then to directly process selected data using high-performance computing resources of the San Diego Supercomputer Center via the Neuroscience Gateway (nsgportal.org, NSG), a freely available web portal to high-performance computing serving a variety of neuroscientific analysis environments and tools. Combined, OpenNeuro, NEMAR and NSG form an efficient, integrated data, tools and compute resource for human neuroimaging data analysis and meta-analysis. Database URL: https://nemar.org.

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community. Database URL: https://github.com/INCATools/ontology-development-kit.

Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.

Documenting the emergent social representations of COVID-19 in public communication is necessary for critically reflecting on pandemic responses and providing guidance for global pandemic recovery policies and practices. This study documents the dynamics of changing social representations of the COVID-19 pandemic on one of the largest Chinese social media, Weibo, from December 2019 to April 2020. We draw on the social representation theory (SRT) and conceptualize topics and topic networks as a form of social representation. We analyzed a dataset of 40 million COVID-19 related posts from 9.7 million users (including the general public, opinion leaders, and organizations) using machine learning methods. We identified 12 topics and found an expansion in social representations of COVID-19 from a clinical and epidemiological perspective to a broader perspective that integrated personal illness experiences with economic and sociopolitical discourses. Discussions about COVID-19 science did not take a prominent position in the representations, suggesting a lack of effective science and risk communication. Further, we found the strongest association of social representations existed between the public and opinion leaders and the organizations' representations did not align much with the other two groups, suggesting a lack of organizations' influence in public representations of COVID-19 on social media in China.

As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec.

In information science, writing, printing, telecommunication, and digital computing have been central concerns because of their ability to distribute information. Overlooked is the obvious fact that these technologies fashion copies, and the theorizing of copies has been neglected. We may think a copy is the same as what it copies, but no two objects can really be the same. “The same” means similar enough as an acceptable substitute for some purpose. The differences between usefully similar things are also often important, in forensic analysis, for example, or inferential processes. Status as a copy is only one form of relationship between objects, but copies are so integral to information science that they demand a theory. Indeed, theorizing copies provides a basis for a more complete and unified view of information science.

Hybrid fuzzing that combines fuzzing and concolic execution has become an advanced technique for software vulnerability detection. Based on the observation that fuzzing and concolic execution are complementary in nature, state-of-the-art hybrid fuzzing systems deploy 'optimal concolic testing' and 'demand launch' strategies. Although these ideas sound intriguing, we point out several fundamental limitations in them, due to unrealistic or oversimplified assumptions. Further, we propose a novel 'discriminative dispatch' strategy and design a probabilistic hybrid fuzzing system to better utilize the capability of concolic execution. Specifically, we design a Monte Carlo-based probabilistic path prioritization model to quantify each path's difficulty, and then prioritize them for concolic execution. Our model assigns the most difficult paths to concolic execution. We implement a prototype named DigFuzz and evaluate our system with two representative datasets and real-world programs. Results show that the concolic execution in DigFuzz outperforms than those in state-of-the-art hybrid fuzzing systems in every major aspect. In particular, the concolic execution in DigFuzz contributes to discovering more vulnerabilities (12 versus 5) and producing more code coverage (18.9 versus 3.8 percent) on the CQE dataset than the concolic execution in Driller.

Scientific communities are increasingly publishing data to evaluate, accredit, and build on published research. However, guidelines for curating data for publication are sparse for model-related research, limiting the usability of archived simulation data. In particular, there are no established guidelines for archiving data related to terrestrial models that simulate land processes and their coupled interactions with climate. Terrestrial modelers have a unique set of challenges when publishing data due to the diversity of scientific domains, research questions, and the types and scales of simulations. Researchers in the U.S. Department of Energy’s (DOE) projects use a variety of multiscale models to advance robust predictions of terrestrial and subsurface ecosystem processes. Here, we synthesize archiving needs for data associated with different DOE models, and provide guidelines for publishing terrestrial model data components following FAIR (Findable, Accessible, Interoperable, Reusable) principles. The guidelines recommend archiving model inputs and testing data used in final simulation runs along with associated codes, workflow scripts, and metadata in public repositories. Researchers should consider archiving model outputs if they are within the storage limits of the repository. We also provide considerations for how to bundle files into different data publications with citable digital object identifiers. Finally, we identify repository features and tools that would enable storage and reuse of model data. Given the diversity of DOE terrestrial models, these guidelines are transferable to other model types and will enable efficient reuse of simulation data for purposes such as model intercomparisons, initialization, benchmarking, synthesis, and comparisons with field observations.

Scientific workflows in High Performance Computing ( HPC ) environments are processing large amounts of data. The storage hierarchy on HPC systems is getting deeper, driven by new technologies (NVRAMs, SSDs, etc.) There is a need for new programming abstractions that allow users to seamlessly manage data at the workflow level on multi-tiered storage systems, and provide optimal workflow performance and use of storage resources. In previous work, we introduced a software architecture Managing Data on Tiered Storage for Scientific Workflows (MaDaTS ) that used a Virtual Data Space ( VDS ) abstraction to hide the complexities of the underlying storage system while allowing users to control data management strategies. In this article, we detail the data-centric programming abstractions that allow users to manage a workflow around its data on the storage layer. The programming abstractions simplify data management for scientific workflows on multi-tiered storage systems, without affecting workflow performance or storage capacity. We measure the overheads and effectiveness introduced by the programming abstractions of MaDaTS. Our results show that these abstractions can optimally use the storage capacity in lesser capacity storage tiers, and simplify data management without adding any performance overheads.

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology's compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR). Database URL http://obofoundry.org/.

Opportunistic sensors are increasingly used for rainfall measurement. However, their raw data are collected by a variety of systems that are often not primarily intended for rainfall monitoring, resulting in a plethora of different data formats and a lack of common standards. This hinders the sharing of opportunistic sensing (OS) data, their automated processing, and, at the end, their practical usage and integration into standard observation systems. This paper summarises the experiences of the more than 100 members of the OpenSense Cost Action involved in the OS of rainfall. We review the current practice of collecting and storing precipitation OS data and corresponding metadata, and propose new common guidelines describing the requirements on data and metadata collection, harmonising naming conventions, and defining human-readable and machine readable file formats for data and metadata storage. We focus on three sensors identified by the OpenSense community as prominent representatives of the OS of precipitation: Commercial microwave links (CML): fixed point-to-point radio links mainly used as backhauling connections in telecommunication networks Satellite microwave links (SML): radio links between geostationary Earth orbit (GEO) satellites and ground user terminals. Personal weather stations (PWS): non-professional meteorological sensors owned by citizens. The conventions presented in this paper are primarily designed for storing, handling, and sharing historical time series and do not consider specific requirements for using OS data in real time for operational purposes. The conventions are already now accepted by the ever growing OpenSense community and represent an important step towards automated processing of OS raw data and community development of joint OS software packages.

Monitoring and control systems integrated into agricultural machinery enable the development of agricultural analyses with advanced management tools, but the full use of all available data is often limited by the lack of uniformity among data transmitted from different agricultural machines. This paper presents an agricultural data aggregation and conversion model that allows for the collection and use of data captured from different agricultural machines in the course of work; these data differ in their original file formats and cannot be combined and used in a common analysis system. Programming work was carried out to create the model, and a specialised software interface enabled raster data processing using a Python library together with the open-source Hypertext Preprocessor and JavaScript programming language libraries. A PostGIS extension was utilised to engage field geometry and map-layering tools. Model validation showed that the data aggregation and conversion functions ensure the evaluation of semantic content and the transformation of the aggregated data into a unified format which is suitable for further use in intelligent farming management applications. The developed model will encourage precision agriculture, with the aim of improving work efficiency and the rational use of resources, the economy, and ecology in agriculture. [ABSTRACT FROM AUTHOR]

This paper presents an analysis and the research results of system couplers in CAx systems that ensure the correct transfer of product data from the "supplier" system to the "recipient" system. This study presents the results of the compatibility tests between the systems based on the verification of geometric models and their attributes after importing/exporting 2D and 3D objects using neutral data exchange formats. The purpose of the research was to identify neutral formats that do not introduce errors after data transversion in certain types of geometry. Tests and analyses were carried out on selected formats depending on the type of object, such as 2D objects (DXF), solid objects (IGES, STEP, SAT, and PARASOLID), and surface objects (IGES, STEP, SAT, and X_T). One of the results of our research and analysis is the need for continuous development of CAD/CAE systems because current neutral formats are not 100% effective. [ABSTRACT FROM AUTHOR]

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

Modern NoSQL database systems use log-structured merge (LSM) storage architectures to support high write throughput. LSM architectures aggregate writes in a mutable MemTable (stored in memory), which is regularly flushed to disk, creating a new immutable file called an SSTable. Some of the SSTables are chosen to be periodically merged—replaced with a single SSTable containing their union. A mergepolicy (a.k.a. compaction policy) specifies when to do merges and which SSTables to combine. A bounded depth merge policy is one that guarantees that the number of SSTables never exceeds a given parameter k, typically in the range 3–10. Bounded depth policies are useful in applications where low read latency is crucial, but they and their underlying combinatorics are not yet well understood. This paper compares several bounded depth policies, including representative policies from industrial NoSQL databases and two new ones based on recent theoretical modeling, as well as the standard Tiered policy and Leveled policy. The results validate the proposed theoretical model and show that, compared to the existing policies, the newly proposed policies can have substantially lower write amplification with comparable read amplification.

High-quality metadata annotations for data hosted in large public repositories are essential for research reproducibility and for conducting fast, powerful and scalable meta-analyses. Currently, a majority of sequencing samples in the National Center for Biotechnology Information's Sequence Read Archive (SRA) are missing metadata across several categories. In an effort to improve the metadata coverage of these samples, we leveraged almost 44 million attribute-value pairs from SRA BioSample to train a scalable, recurrent neural network that predicts missing metadata via named entity recognition (NER). The network was first trained to classify short text phrases according to 11 metadata categories and achieved an overall accuracy and area under the receiver operating characteristic curve of 85.2% and 0.977, respectively. We then applied our classifier to predict 11 metadata categories from the longer TITLE attribute of samples, evaluating performance on a set of samples withheld from model training. Prediction accuracies were high when extracting sample Genus/Species (94.85%), Condition/Disease (95.65%) and Strain (82.03%) from TITLEs, with lower accuracies and lack of predictions for other categories highlighting multiple issues with the current metadata annotations in BioSample. These results indicate the utility of recurrent neural networks for NER-based metadata prediction and the potential for models such as the one presented here to increase metadata coverage in BioSample while minimizing the need for manual curation. Database URL: https://github.com/cartercompbio/PredictMEE.

A significant cybersecurity event has recently been discovered in which malicious actors gained access to the source code for the Orion monitoring and management software made by the company SolarWinds and inserted malware into that source code. This article describes brief perspectives from a few experts regarding that incident and probable solutions. The attackers inserted malware into that source code so that, when the software was distributed to and deployed by SolarWinds customers as part of an update, the malicious software could be used to surveil customers who unknowingly installed the malware and gain potentially arbitrary control over the systems managed by Orion. One of the solutions is to improve government software procurement. Software is critical to national security. Any system of procuring that software needs to evaluate the security of the software and the security practices of the company, in detail, to ensure that they are sufficient to meet the security needs of the network they are being installed in. If these evaluations are made public, along with the list of companies that meet them, all network buyers can benefit from them.

Respiratory rate measurement is important under different types of health issues. The need for technological developments for measuring respiratory rate has become imperative for healthcare professionals. The paper presents an approach to respiratory monitoring, with the aim to improve the accuracy and efficacy of the data monitored. We use multiple types of sensors on various locations on the body to continuously transmit real-time data, which is processed to calculate the respiration rate. Variations in the respiration rate will help us identify the current health condition of the patient also for diagnosis and further medical treatment. The software tools such as Keil μVision IDE, Mbed Studio IDE, Energia IDE are used to compile and build the system architecture and display information. EasyEDA is used to provide pin map details and complete architecture information.

We study closed-form interference-exploitation precoding for multi-level modulations in the downlink of multi-user multiple-input single-output (MU-MISO) systems. We consider two distinct cases: first, when the number of served users is not larger than the number of transmit antennas at the base station (BS), we mathematically derive the optimal precoding structure based on the Karush-Kuhn-Tucker (KKT) conditions. By formulating the dual problem, the precoding problem is transformed into a pre-scaling operation using quadratic programming (QP) optimization. We further consider the case where the number of served users is larger than the number of transmit antennas at the BS. By employing the pseudo inverse, we show that the optimal solution of the pre-scaling vector is equivalent to a linear combination of the right singular vectors corresponding to zero singular values, and derive the equivalent QP formulation. We also present the condition under which multiplexing more streams than the number of transmit antennas is achievable. For both considered scenarios, we propose a modified iterative algorithm to obtain the optimal precoding matrix, as well as a sub-optimal closed-form precoder. Numerical results validate our derivations on the optimal precoding structures for multi-level modulations, and demonstrate the superiority of interference-exploitation precoding for both scenarios.

Data outsourcing allows data owners to keep their data at \emph{untrusted}clouds that do not ensure the privacy of data and/or computations. One usefulframework for fault-tolerant data processing in a distributed fashion isMapReduce, which was developed for \emph{trusted} private clouds. This paperpresents algorithms for data outsourcing based on Shamir's secret-sharingscheme and for executing privacy-preserving SQL queries such as count,selection including range selection, projection, and join while using MapReduceas an underlying programming model. Our proposed algorithms prevent anadversary from knowing the database or the query while also preventingoutput-size and access-pattern attacks. Interestingly, our algorithms do notinvolve the database owner, which only creates and distributes secret-sharesonce, in answering any query, and hence, the database owner also cannot learnthe query. Logically and experimentally, we evaluate the efficiency of thealgorithms on the following parameters: (\textit{i}) the number ofcommunication rounds (between a user and a server), (\textit{ii}) the totalamount of bit flow (between a user and a server), and (\textit{iii}) thecomputational load at the user and the server.\B

Physical samples are foundational entities for research across biological, Earth, and environmental sciences. Data generated from sample-based analyses are not only the basis of individual studies, but can also be integrated with other data to answer new and broader-scale questions. Ecosystem studies increasingly rely on multidisciplinary team-science to study climate and environmental changes. While there are widely adopted conventions within certain domains to describe sample data, these have gaps when applied in a multidisciplinary context. In this study, we reviewed existing practices for identifying, characterizing, and linking related environmental samples. We then tested practicalities of assigning persistent identifiers to samples, with standardized metadata, in a pilot field test involving eight United States Department of Energy projects. Participants collected a variety of sample types, with analyses conducted across multiple facilities. We address terminology gaps for multidisciplinary research and make recommendations for assigning identifiers and metadata that supports sample tracking, integration, and reuse. Our goal is to provide a practical approach to sample management, geared towards ecosystem scientists who contribute and reuse sample data. (IGSN); physical samples; soil; water; plant; leaf; microbial communities; related identifiers; persistent identifiers.