Huge-scale video surveillance systems have become essential in crime prevention and situation recording. Traditional surveillance systems relied on human monitoring of video streams, which often led to errors and difficulties in understanding events. Furthermore, locating specific scenes within recorded videos required extensive human investigation. To overcome these challenges of inefficiency, inconvenience, and potential risks, we propose an intelligent analysis scheme that utilizes abnormal behavior recognition and metadata retrieval algorithms to replace human monitoring. The proposed method consists of three stages: i) metadata generation through object detection and tracking, ii) abnormal behavior recognition, and iii) SQL-based metadata retrieval. By incorporating specific information such as object color and aspect ratio, our technique enhances the usability of retrieval. Moreover, our abnormal behavior recognition module demonstrates robust classification capabilities for activities such as pushing, violence, falling, and crossing barriers. The proposed method can be seamlessly deployed on both edge cameras and analysis servers, making it adaptable to various surveillance setups. This approach revolutionizes the traditional surveillance paradigm, enabling more efficient, reliable, and secure video monitoring and analysis.

The historic view of metadata as “data about data” is expanding to include data about other items that must be created, used and understood throughout the data and project life cycles. In this context, metadata might better be defined as the structured and standard part of documentation and the metadata life cycle can be described as the metadata content that is required for documentation in each phase of the project and data life cycles. This incremental approach to metadata creation is similar to the spiral model used in software development. Each phase also has distinct users and specific questions they need answers to. In many cases, the metadata life cycle involves hierarchies where latter phases have increased numbers of items. The relationships between metadata in different phases can be captured through structure in the metadata standard or through conventions for identifiers. Metadata creation and management can be streamlined and simplified by re-using metadata across many records. Many of these ideas are being used in metadata for documenting the life cycle of research projects in the Arctic.

Peptides are promising drug development frameworks thanks to their high target selectivity, tolerability and relatively low production cost. However, despite the fact that several thousand potentially therapeutic peptides reported, only sixty have arrived at the market. This concerning low proportion is partially explained by undesired properties such as peptide-induced hemolytic activity. Hence, we aim to get a better insight into the chemical space of hemolytic peptides using a novel approach based on network science and interactive data mining as an alternative to design more effective peptide drugs with low hemolytic activity. Metadata networks (METNs) were used to characterize and find general patterns associated to hemolytic peptides, whereas Half-Space Proximal Networks (HSPNs), created using five different two-way dissimilarity measures, represented the hemolytic peptide space. Then, using the best candidate HSPNs, we extracted various scaffolds that capture information of almost all the chemical space but avoiding peptide overrepresentation. Such scaffolds can have many applications, such as training accurate ML-based prediction models, constructing one-class multi-query similarity searching models and characterizing the diversity of hemolytic peptides using a manageable set of peptides. Finally, by means of an alignment-free approach, we reported 47 putative hemolytic motifs, which might provide hints about the mechanisms of hemolysis and can also be used as toxic signatures when developing novel peptide-based drugs.

The multidisciplinary nature of the work required for research in the Covid-19 pandemic has created new challenges for health professionals in the battle against the virus. They need to be equipped with novel tools and resources ---that have emerged during the pandemic--- to gain access to breakthrough findings, know the latest developments, and to address their specific needs for rapid data acquisition, analysis, evaluation, and reporting. Because of the complex nature of the virus, the healthcare systems worldwide are severely impacted as the treatment and the vaccine for Covid-19 disease are not yet discovered. This leads to frequent changes in regulations and policies by governments and international organizations. Our analysis suggests that given the abundance of information sources, finding the most suitable tool for a given task is one of such challenges. But health professionals and policymakers need access to the most relevant, reliable, trusted, and latest information and tools that can be used in their day-to-day tasks of Covid-19 research and analysis. In this article, we present our analysis of various novel and important tools that have been specifically developed during the Covid-19 pandemic and that can be used by the health professionals community to help in advancing their analysis and research. These tools comprise of search engines, information repositories for literature and clinical trials, data sources, dashboards, and forecasting models. We present list of the minimally essential tools to serve a multitude of purposes, from hundreds of those developed since the beginning of the pandemic. A critical analysis is provided for the selected tools based on 17 parameters that can be useful for researchers and analysts for their evaluations. These parameters make up our evaluation framework and have not been used previously for analysis and evaluation. Hence, knowledge of the tools will not only increase the productivity but will also allow to explore new dimensions for using existing tools with more control, better management, and greater outcome of their research. In addition, the parameters used in our framework can be applied for future evaluations of similar tools and health professionals can adapt them for evaluation of other tools not covered in this analysis.

The reuse and integration of data give big opportunities, supported by the F.A.I.R. data principles. Seamless data integration from heterogenous sources has been interest of the geospatial community for long time. However, 3D city models, BIM and information supporting smart cities present higher semantic and geometrical complexity, which pose new challenges, never tackled in a comprehensive methodology. Building on previous theories and studies, this paper proposes an overarching workflow and framework for multisource (geo)spatial data integration. It starts from the definition of use case-based requirements for the integrated data, guides the analysis of integrability of the involved datasets, suggesting actions to harmonise them, until data merging and validation. It is finally tested and exemplified on a case study. This approach allows the development of consistent, well-documented and inclusive data integration workflows, for the sake of use cases automation in various geospatial domains and the production of Interoperable and Reusable data.

This paper describes a novel methodology of data management in materials characterisation, which has as starting point the creation and usage of Data Management Plan (DMP) for scientific data in the field of materials science and engineering, followed by the development and exploitation of ontologies for the harnessing of data created through experimental techniques. The case study that is discussed here is nanoindentation, a widely used method for the determination and/or modelling of mechanical properties on a small scale.The same methodology can be applicable to a large number of techniques that produce big amount of raw data, while at the same time it can be invaluable tool for big data analysis and for the creation of an open innovation environment, where data can be accessed freely and efficiently.Aspects covered include the taxonomy and curation of data, the creation of ontology and classification about characterization techniques, the harnessing of data in open innovation environments via database construction along with the retrieval of information via algorithms. The issues of harmonization and standardization of such novel approaches are also critically discussed.Finally, the possible implications for nanomaterial design and the potential industrial impact of the new approach are described and a critical outlook is given.

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. Identification and surveillance of viruses rely on understanding their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. Use of virus databases is integral to gain new insights into the biology, evolution, and transmission of viruses, and develop new strategies to manage virus outbreaks and preserve global health.

1) Background: We analyzed the corpus of three geoscientific journals to investigate if there are enough locational references in research articles to apply a geographical search method, on the example of New Zealand. 2) Methods: Based on all available abstracts and all freely available papers of the New Zealand Journal of Geology and Geophysics, the New Zealand Journal of Marine and Freshwater Research, and the Journal of Hydrology, New Zealand, we searched title, abstracts and full texts for place name occurrences that match records from the official Land Information New Zealand (LINZ) gazetteer. We generated ISO standard compliant metadata records for each article including the spatial references and make them available in a public catalogue service. This catalogue can be queried for articles based on authors, titles, keywords, topics as well as by spatial reference. We visualize the results in a map to show which area the research articles are about. 3) Results: We outline the methodology and technical framework for the geo-referencing of the journal articles and the platform design for this knowledge inventory. The results indicate that the use of well-crafted abstracts for journal articles with carefully chosen place names of relevance for the article provides a guideline for geographically referencing unstructured information like journal articles and reports in order to make such resources discoverable through geographical queries. 4) Conclusion: This approach can actively support integrated holistic assessment of water resources and support decision making.

The Genotype-Phenotype Working Group was established in November 2021 as part of the AgBioData Consortium (https://www.agbiodata.org) with the goal of identifying current challenges in annotating and integrating large-scale genotype and phenotype data. Over the course of the year, the members of this working group identified different types of data sets, explored experimental platforms and methods for data generation, and examined how these data are annotated including the metadata requirements. We conducted a thorough review of publicly funded repositories for raw and processed data for each data type. We also examined several secondary databases and knowledgebases that enable the integration of heterogeneous data types in the context of the Genome Browser, Pathway Networks and tissue-specific gene expression. The review revealed a need for additional infrastructural support, standards, and tools to connect Genotype to Phenotype data and enhance data interoperability for knowledge synthesis and to foster translational research.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations, as well as research. In order to make use of pathogen genomics data, it must be interpreted using contextual data (metadata). Contextual data includes sample metadata, laboratory methods, patient demographics, clinical outcomes, and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration, and its use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating, and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool’s web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission.In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.

As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower-quality datasets be made available for analysis and comparison alongside those of higher-quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays. Sharing of useful, but sub-optimal datasets requires careful annotation and documentation of known issues to enable appropriate interpretation, avoid being mistaken for better quality information, and for these data (and their derivatives) to be easily identifiable in repositories. Unfortunately, there are currently no standardized attributes or mechanisms for tagging poor-quality datasets, or datasets generated for a specific purpose, to maximize their utility, searchability, accessibility and reuse. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is an international community of scientists from public health, industry and academia focused on improving the reproducibility, interoperability, portability and openness of public health bioinformatic software, skills, tools and data. To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability. The contextual data tags were developed through consultations with the community including input from the International Nucleotide Sequence Data Collaboration (INSDC), and have been standardized using ontologies, community-based resources for defining the tag properties and the relationships between them. The standardized tags are agnostic to the organism and the sequencing technique used and thus can be applied to data generated from any pathogen using an array of sequencing techniques. The list of standardized tags is maintained by PHA4GE and can be found at https://github.com/pha4ge/contextual_data_QC_tags. Definitions, ontology IDs, examples of use, as well as a JSON representation, are provided. The PHA4GE QC tags were tested, and are now implemented, by the FDA’s GenomeTrakr laboratory network as part of its routine submission process for SARS-CoV-2 wastewater surveillance. We hope that these simple, standardized tags will help improve communication regarding quality control in public repositories, in addition to making datasets of variable quality more easily identifiable. Suggestions for additional tags can be submitted to PHA4GE via the New Term Request Form in the GitHub repository. By providing a mechanism for feedback and suggestions, we also expect that the tags will evolve with the needs of the community.

With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the affects of the pandemic. In this context, we review the data integration efforts required for accessing and searching genome sequences and metadata of SARS-CoV2, the virus responsible for the COVID-19 disease, which have been deposited into the most important repositories of viral sequences. Organizations that were already present in the virus domain are now dedicating special interest to the emergence of COVID-19 pandemics, by emphasizing specific SARS-CoV2 data and services. At the same time, novel organizations and resources were born in this critical period to serve specifically the purposes of COVID-19 mitigation, while setting the research ground for contrasting possible future pandemics. Accessibility and integration of viral sequence data, possibly in conjunction with the human host genotype and clinical data, are paramount to better understand the COVID-19 disease and mitigate its effects.

Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments, and can be used for connecting biological molecules into regulatory computational models that represent biological systems. However, including a molecular causal interaction into a model requires assessing its relevance to that model, based on detailed knowledge about the biomolecules, interaction type, and biological context. In order to standardize the representation of this knowledge in ‘causal statements’, we recently developed the MI2CAST guidelines. Here we introduce causalBuilder: an intuitive web-based curation interface for the annotation of molecular causal interactions that comply with the MI2CAST standard. The causalBuilder prototype essentially embeds the MI2CAST curation guidelines in its interface, and makes its rules easy to follow by a curator. In addition, causalBuilder serves as an original application of the VSM general-purpose curation technology, and provides both curators and tool developers with an interface that can be fully configured to allow focusing on selected MI2CAST concepts to annotate. After information is entered, the causalBuilder prototype produces genuine causal statements that can be exported in different formats.

Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer-review and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish high-quality data sets, we created a workflow for streamlined import of omics metadata directly into a data paper manuscript. An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. The workflow was based on REpresentational State Transfer services and Xpath to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases, which follow community-agreed standards. The workflow for automatic import of standard-compliant metadata into an omics data paper manuscript facilitates the authoring process. It demonstrates the importance and potential of creating machine-readable and standard-compliant metadata. The omics data paper structure and workflow to import omics metadata improves the data publishing landscape by providing a novel mechanism for creating high-quality, enhanced metadata records, peer reviewing and publishing of these. It constitutes a powerful addition for distribution, visibility, reproducibility and re-usability of scientific data. We hope that streamlined metadata re-use for scholarly publishing encourages authors to improve the quality of their metadata to achieve a truly FAIR data world.

The article is devoted to identifying promising research issues on the topic of Digital Industry based on the analysis of bibliometric data from Scopus platform for 2018–2022. The definition of promising issues derived from the titles, additionally abstracts, of highly cited works by authors with high publication activity. Authors' Scopus profiles were used to determine their affiliations, which are important for in-depth analysis of selected promising Digital Industry tasks. Metadata filtering to identify highly cited papers on particular issues was performed by keywords, Subject Areas, affiliations with countries and sponsoring organizations. Additionally, bibliometric metadata were clustered based on the co-occurrence of terms using VOSviewer. Within these clusters, articles of interest were identified for the formulation of promising research issues on the topic of Digital Industry, which will be subjected to in-depth analysis in separate papers.

Bayesian formulations of learning imply that whenever the evidence for a correlation between events in an animal’s habitat is sufficient, the correlation is learned. This implies that regularities can be learnt rapidly, from small numbers of learning examples. This speed of learning gives maximum possible fitness, and no faster learning is possible. There is evidence in many domains that animals and people can learn at nearly Bayesian optimal speeds. These domains include associative conditioning, and the more complex domains of navigation and language. There are computational models of learning which learn at near-Bayesian speeds in complex domains, and which can scale well – to learn thousands of pieces of knowledge (i.e., relations and associations). These are not neural net models. They can be defined in computational terms, as algorithms and data structures at David Marr’s [1] Level Two. Their key data structures are composite feature structures, which are graphs of multiple linked nodes. This leads to the hypothesis that animal learning results not from deep neural nets (which typically require thousands of training exam-ples), but from neural implementations of the Level Two models of fast learning; and that neu-rons provide the facilities needed to implement those models at Marr’s Level Three. The required facilities include feature structures, dynamic binding, one-shot memory for many feature struc-tures, pattern-based associative retrieval, unification and generalization of feature structures. These may be supported by multiplexing of data and metadata in the same neural fibres.

Environmental policy involving citizen science (CS) is of growing interest. In support of this open data stream, validation or quality assessment of the CS data and their appropriate usage for evidence-based policy making, needs a flexible and easily adaptable data curation process ensuring transparency. Addressing these needs, this paper describes an approach for automatic quality assurance as proposed by the Citizen OBservatory WEB (COBWEB) FP7 project. This approach is based upon a workflow composition that combines different quality controls, each belonging to seven categories or ‘pillars’. Each pillar focuses on a specific dimension in the types of reasoning algorithms for CS data qualification. These pillars attribute values to a range of quality elements belonging to three complementary quality models. Additional data from various sources, such as Earth Observation (EO) data, are often included as part of the inputs of quality controls within the pillars. However, qualified CS data can also contribute to the validation of EO data. Therefore, the question of validation can be considered as ‘two sides of the same coin’. Based on an invasive species CS study, concerning Fallopia japonica (Japanese knotweed), the paper discusses the flexibility and usefulness of qualifying CS data, either when using an EO data for the validation within the quality assurance process, or validating an EO data product that describes the risk of occurrence of the plant. Both validation paths are found to be improved by quality assurance of the CS data. Addressing the reliability of CS open data, issues and limitations of the role of quality assurance for validation, due to the quality of secondary data used within the automatic workflow, are described, e.g. error propagation, paving the route to improvements in the approach.

Focusing on the implementation of the 2003 UNESCO Convention for the Safeguarding of the Intangible Cultural Heritage (ICH), this article highlights the fact that the cataloging procedures, the way records are stored, and the metadata models used during recording, visualization, and storage of ICH expression elements, vary from country to country. Especially in these days of great uncertainty, war conflicts, and the systemic risks that may arise, it is vital to clarify what techniques will be used in the storage of ICH to ensure its unhindered preservation and dissemination over time across the globe. Using the systems thinking approach indicated for cases of great complexity, the process followed in Greece for depositing a new element in its local repository is described to demonstrate the need for a well-defined process by UNESCO, which must be followed worldwide and which has not been defined so far. What are the potential challenges not only in determining the type of data but also in choosing the best metadata model to use in each case when capturing this data? What technologies must be used for storing digital cultural heritage in such a way that will preserve it over time, defying physical and technological hazards? The article finally suggests how Blockchain Technologies (BT) can be effectively used to store the global ICH and ensure its continuity in future generations by creating a decentralized worldwide network between the heritage stakeholders.