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This paper examines the concept of open-source data interoperability in the United States' K-12 education domain, specifically addressing the implications of interoperability for data justice. The term 'data justice' is a relatively recent coinage; the framing and meaning of this term are still evolving, and it has not yet been applied in the educational domain. Building on the nascent research and theorizing in the fields of both data justice and interoperability in educational contexts, this paper provides an overview of the current state of this intersection. Additionally, the authors draw on their direct experiences implementing interoperability initiatives in several U.S. states in order to build a foundational understanding of the risks and opportunities for data justice in the realm of interoperability and data standards in education. The paper concludes with a call for more research to be completed on this complex sociotechnical topic. [ABSTRACT FROM AUTHOR]

[Display omitted] • Data standard for macromolecular structures from integrative and hybrid modeling (IHM). • Infrastructure for deposition, archiving, and public dissemination of integrative structures. • Representation and tools to enable interoperation of structural biology resources. • Community-driven effort that is extensible to handle novel methods. • Supports FAIR data delivery and accelerates scientific discovery. IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB. [ABSTRACT FROM AUTHOR]

Keywords: Analytical chemistry; cheminformatics: data and standards; data standard; file format; mass spectrometry; NMR EN Analytical chemistry cheminformatics: data and standards data standard file format mass spectrometry NMR 725 736 12 08/09/22 20220601 NES 220601 Introduction The amount of research data is growing in all disciplines, and chemistry is no exception. The NMR record in NMReDATA format includes the instrument (raw) data, a SDFile and, since version 2, also spectral data in JCAMP format in a folder, which can be compressed in the zip format for data exchange. Data standards for NMR spectroscopy NMR is an indispensable analytical technique providing rich information on bonding and structure as well as molecule interaction and abundance of molecules in samples. Data formats for analytical data When developing infrastructures for chemistry, one of the major tasks is to adopt or define data models and formats for exchange, storage and archival of analytical data. [Extracted from the article]

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints. [Display omitted] • The wwPDB validation report has been expanded to include restraint analysis • NMR-STAR and NEF serve as the standardized format for NMR data at wwPDB • Standardized restraint format facilitates model versus data assessment • More comprehensive and better assessment of biomolecular NMR structures Baskaran et al. outlined the rationale for model-versus-data assessment of NMR structures by wwPDB, along with a summary of validation tools for NMR distance and dihedral-angle restraints implemented in the wwPDB validation pipeline. These tools enhance the assessment of biomolecular NMR structure quality, benefiting users of the wwPDB archive. [ABSTRACT FROM AUTHOR]

• Allotrope Data Model ensures data integrity through validation. • Allotrope Framework's foundation is built upon the versatile HDF5. • Multiple tools enable easy access to Allotrope Data Format datasets. • Advances in AF technologies made it easy for users to adopt the standard. Recent Allotrope Foundation (AF) Connect Workshops (2021–2023) showcased some of the latest advancements in data standardization for analytical data in the pharmaceutical industry. These workshops demonstrated the adaption of two key technologies, the Allotrope Data Format (ADF) and the Allotrope Simple Model (ASM), which streamline instrument data representation and terminology to enhance interoperability across systems. Notably, ASM has facilitated broader adoption of the standard. The increasing significance of data-driven decision-making in the life sciences is underscored by the evolving landscape of open-source solutions and commercial implementations, as demonstrated by industry leaders adopting these standards. Here, we highlight selected examples that illustrate the collective efforts of the community in advancing data standards and data management in the life sciences. [ABSTRACT FROM AUTHOR]

The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to store, exchange, and disseminate nuclear magnetic resonance (NMR) data and physical and chemical metadata of chemical compounds. In this paper, we report on analytical workflows that take advantage of the uniform and standardized NMReDATA format. We also give access to a repository of sample data, which can serve for validating software packages that encode or decode files in NMReDATA format. [ABSTRACT FROM AUTHOR]

[Display omitted] • Community-driven data representation for computed structure models (CSMs) of biological macromolecules. • Provides common data representation and tools that enable interoperation of structural biology data resources. • Provides data and software infrastructure for deposition, archiving, and public dissemination of CSMs. • Provides data infrastructure that supports FAIR (Findable, Accessible, Interoperable, Reusable) data delivery and accelerates scientific discovery. ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable , Accessible , Interoperable , and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described. [ABSTRACT FROM AUTHOR]

The complexities of the intricate geospatial resources and formats make preservation and distribution of GIS data difficult even among experts. The proliferation of, for instance, KML, Internet map services, etc, reflects the need for sharing geodata but a comprehensive solution when having to deal with data and metadata of a certain complexity is not currently provided. Original geospatial data is usually divided into several parts to record its different aspects (spatial and thematic features, etc), plus additional files containing, metadata, symbolization specifications and tables, etc; these parts are encoded in different formats, both standard and proprietary. To simplify data access, software providers encourage the use of an additional element that we call generically “map project”, and this contains links to other parts (local or remote). Consequently, in order to distribute the data and metadata refereed by the map in a complete way, or to apply the Open Archival Information System (OAIS) standard to preserve it for the future, we need to face the multipart problem. This paper proposes a package allowing the distribution of real (comprehensive although diverse and complex) GIS data over the Internet and for data preservation. This proposal, complemented with the right tools, hides but keeps the multipart structure, so providing a simpler but professional user experience. Several packaging strategies are reviewed in the paper, and a solution based on ISO 29500-2 standard is chosen. The solution also considers the adoption of the recent Open Geospatial Consortium Web Services common standard (OGC OWS) context document as map part, and as a way for also combining data files with geospatial services. Finally, and by using adequate strategies, different GIS implementations can use several parts of the package and ignore the rest: a philosophy that has proven useful (e.g. in TIFF). [ABSTRACT FROM AUTHOR]

Background: To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD). MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice. Methods: We developed MVLD through a consensus approach by i) reviewing clinical actionability interpretations from institutions participating in the WG, ii) conducting extensive literature search of clinical somatic interpretation schemas, and iii) survey of cancer variant web portals. A forthcoming guideline on cancer variant interpretation, from the Association of Molecular Pathology (AMP), can be incorporated into MVLD. Results: Along with harmonizing standardized terminology for allele interpretive and descriptive fields that are collected by many databases, the MVLD includes unique fields for cancer variants such as Biomarker Class, Therapeutic Context and Effect. In addition, MVLD includes recommendations for controlled semantics and ontologies. The Somatic WG is collaborating with ClinVar to evaluate MVLD use for somatic variant submissions. ClinVar is an open and centralized repository where sequencing laboratories can report summary-level variant data with clinical significance, and ClinVar accepts cancer variant data. Conclusions: We expect the use of the MVLD to streamline clinical interpretation of cancer variants, enhance interoperability among multiple redundant curation efforts, and increase submission of somatic variants to ClinVar, all of which will enhance translation to clinical oncology practice. [ABSTRACT FROM AUTHOR]

The archiving of scientific data is a sophisticated mission in nearly all research projects. In this paper, we introduce a new online archive of atmospheric measurement data from the "High definition clouds and precipitation for advancing climate prediction" (HD(CP)2) research initiative. The project data archive is quality managed, easy to use, and is now open for other atmospheric research data. The archive's creation was already taken into account during the HD(CP)2 project planning phase and the necessary resources were granted. The funding enabled the HD(CP)2 project to build a sound archive structure, which guarantees that the collected data are accessible for all researchers in the project and beyond. [ABSTRACT FROM AUTHOR]

[Display omitted] • Community Driven Data Representation for structural biology data. • Provides common data representation and tools that accelerates scientific discovery. • Provides data and software infrastructure for the Protein Data Bank (PDB) Core Archive. • Provides essential data infrastructure supporting FAIR data delivery. PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide. [ABSTRACT FROM AUTHOR]

The paper compares hydrographic and terrain categories in the geospatial data standards of the United States, Taiwan, and Russian Federation where the dominant languages used are from different language families. It aims to identify structural and semantic differences between similar categories across three geospatial data standards. By formalizing the data standard structures and identifying the properties that differentiate sibling categories in each geospatial data standard using well-known formal relations and quality universals, we develop a common basis on which hydrographic and terrain categories in the three data standards can be compared. The result suggests that all the three data standards structure categories with a mixture of relations even though most of them are well-known relations in top-level ontologies. Similar categories can be found across all the three standards. Cases of categories from different standards carrying identical meaning are rare. Partial overlaps in the meaning of the similar categories can be a direct result of different quality universals at work in defining and distinguishing these categories, or in the case of these categories being ordered by size, the threshold values for distinguishing the categories are ambiguous and language-dependent. Understanding these differences avoids incorrect mappings of categories in multilingual applications. More importantly, it provides a starting point for more effective mapping between hydrographic and terrain categories between English, Mandarin, and Russian. [ABSTRACT FROM AUTHOR]

We propose the use of existing data standards and web technologies to modeling and development of digital twin ships. Our research provides an open framework that can be linked to services such as visualizations, simulations and remote control. The case study applies the standards-based framework to an experiment that involved a scale model ship equipped with a dynamic positioning system under artificial waves. The digital twin prototype illustrated the capability of mirroring and controlling the model's position in real-time, and predicting motion responses across wave conditions via a web application. Thus, it closes the loop between test and design in the life cycle by allowing validation of results in comparison to empirical data during operation. The results from these experiments are used to discuss an expanded version of the digital twin for validation and optimization of motion response, as well as its implications to the system's (ship) taxonomy and data management. The conclusion summarizes lessons when using the adopted standards, as well as challenges when scaling the approach to real life operations. Future research is proposed toward extending the standardization to more complex cases. • Open and standards-based development of a digital twin for a dynamic positioning experiment in a wave basin. • The digital twin monitors wave motion response and controls dynamic positioning in real-time. • The data organization follows a function-oriented taxonomy based on the Vessel Information System, created by DNV. • Among the standards used are JSON for metadata, glTF for visualization and ISO 19848 for data logs. • Simulation interface is developed as a Web-app for wider compatibility across devices and remote access over the internet. [ABSTRACT FROM AUTHOR]

The Fish barcode of life (FISH-BOL) initiative seeks to establish a reference sequence library of short, standardized mitochondrial gene sequences derived from the 5′ end of the cytochrome c oxidase subunit I gene (DNA barcodes) to facilitate the rapid, accurate, and cost-effective DNA-based identification of all fishes, regardless of life-stage, sex, or specimen condition. This task requires the participation of scientists from around the world and its success is predicated on the development and acceptance of standard protocols for the collection of specimens associated provenance data. Here, we provide guidelines for specimen collection, imaging, preservation, and archival, as well as meta-data collection and submission protocols developed for the FISH-BOL campaign in order to promote efficient participation in FISH-BOL by a broadening array of international participants. [ABSTRACT FROM AUTHOR]

The SAS Clinical Standards Toolkit provides a framework for validating and documenting CDISC-compliant data. It is a free add-on package for SAS software available under Microsoft Windows and UNIX. At present, it contains the validation of datasets according to the SDTM model (inclusive of published WebSDM™ and Janus checks) plus the generation of a data definition document following CRT-DDS (define. xml) for the submission. As all metadata and rules reside in SAS tables, other standards or new versions of existing standards can be retrofitted. To begin with, this paper will outline the meaning of such a tool within the scope of CDISC-compliant data management. Following that, the concept of the SAS Clinical Standards Toolkit will be presented and some examples for usage and results will be given. Finally, the adaptability of the tool will be expanded upon and some practical hints will be given. [ABSTRACT FROM AUTHOR]

The main objective of this study is to develop a prototype model of Web-based Geographic Information System (GIS) application for efficient management of borehole and geological data. More than 10,000 boreholes and other geological data were archived into the database and Web-based GIS system was implemented for a local urban area of Seoul in Korea. A standard form of borehole data was suggested and the database was developed in the system. The system provides client users with geological information search function, on-line geological information function, statistical summaries, and administrative functions. As a result, the system makes the efficient management of geological data possible by adopting database and Web-based system. It is also expected that the system can be connected with other existing GIS applications for further applications. [Copyright &y& Elsevier]