List of Standards for Matter

Helmholtz Metadata Collaboration List of Standards for Matter July 2025 Helmholtz Metadata Collaboration | List of Standards for Matter 1 Contents List of Standards for Matter .................................................................................................................. 3 Preamble ........................................................................................................................................ 3 Matter-specific standards ................................................................................................................ 3 ANZLIC Metadata Profile ............................................................................................................. 3 Astronomy Visualization Metadata (AVM) .................................................................................... 3 Core Scientific Metadata Model (CSMD) ....................................................................................... 4 Crystallographic Information Framework (CIF) .............................................................................. 4 Electron Microscopy (EM) Glossary .............................................................................................. 4 FITS (Flexible Image Transport System) ......................................................................................... 4 FITS World Coordinate System (WCS) ........................................................................................... 4 ICAT Schema............................................................................................................................... 5 IMPEx Data Model ...................................................................................................................... 5 IUPAC Gold Book ........................................................................................................................ 5 International Virtual Observatory Alliance Technical Specifications ................................................. 5 Metadata Schemas for Materials Science (KIT DM) ........................................................................ 5 NeXus and the NeXus Definition Language (NXDL) ......................................................................... 6 OME-xml (newer version OME-tiff) .............................................................................................. 6 Open Databases Integration for Materials Design (OPTIMADE) ....................................................... 6 Open Particle-Mesh Data (OpenPMD) .......................................................................................... 6 Open Reflectometry Standards Organisation (ORSO) ..................................................................... 6 Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework (PDBx/mmCIF) .......................................................................................................... 7 Quantities, Units, Dimensions and Types (QUDT)........................................................................... 7 Resource Metadata for the Virtual Observatory ............................................................................ 7 Sample Environment Communication Protocol (SECoP) ................................................................. 7 Standard for Documentation of Astronomical Catalogues (SDAC) ................................................... 7 SPASE Data Model ...................................................................................................................... 8 XAS Data Interchange Format (XDI) .............................................................................................. 8 Generic Standards ........................................................................................................................... 8 Common European Research Information Format (CERIF): ............................................................. 8 CSV on the Web (CSVW): ............................................................................................................. 8 Datacite Metadata Schema .......................................................................................................... 9 DCAT.......................................................................................................................................... 9 Dublin Core 1.1 ........................................................................................................................... 9 ISO-Standards ............................................................................................................................. 9 PROV-O ...................................................................................................................................... 9 Schema.org .............................................................................................................................. 10 Generic (Meta)data Formats or Models .......................................................................................... 10 Helmholtz Metadata Collaboration | List of Standards for Matter 2 Citation File Format................................................................................................................... 10 JSON ........................................................................................................................................ 10 JSON-LD ................................................................................................................................... 10 HDF5 ........................................................................................................................................ 11 odML ....................................................................................................................................... 11 RDF .......................................................................................................................................... 11 RO-Crate .................................................................................................................................. 11 ROOT ....................................................................................................................................... 12 SKOS ........................................................................................................................................ 12 XML ......................................................................................................................................... 12 References ................................................................................................................................... 12 Helmholtz Metadata Collaboration | List of Standards for Matter 3 List of Standards for Matter Özlem Özkan, Oonagh Brendike-Mannix, Gerrit Günther, Markus Kubin & Heike Görzig Helmholtz-Zentrum Berlin für Materialien und Energie & Helmholtz Metadata Collaboration Hub Matter Preamble This list provides an overview of data standards relevant to the Helmholtz research field Matter. It was compiled by integrating several sources: results from the HMC 2021 Community Survey (Helmholtz Metadata Collaboration, 2022) (in which participants identified data formats and standards used or generated in recent research projects), standards associated with specific use cases, manual mapping of standards found in repositories relevant to the field (Kubin et al., 2024), and additional manual searches. To support easier navigation and application, the list is organized into three sections: • Standards in Matter – standards that are specifically used within the research field Matter; • Generic Standards – broadly applicable standards that are not domain-specific but relevant; • Generic (Meta)Data Formats or Models – data formats or models which often lack semantic enrichment but support interoperability and data management. Please note that this list is not exhaustive. It is intended as a starting point to help community members identify and explore relevant data standards. Matter-specific standards ANZLIC Metadata Profile Link: https://www.anzlic.gov.au/ The ANZLIC Metadata Profile is a geospatial metadata standard based on ISO 19115 and the AGLS extension of Dublin Core. It is used for describing and discovering spatial and geographic datasets and services, particularly in Australia and New Zealand. Although primarily relevant to Earth science and environmental research, it has potential relevance in geospatially aware astronomy datasets (Karlsruhe Institute of Technology, n.d.). Astronomy Visualization Metadata (AVM) Link: https://www.virtualastronomy.org/avm_metadata.php Helmholtz Metadata Collaboration | List of Standards for Matter 4 AVM is a metadata schema developed to support cross-searching of astronomy images, especially those generated for public and educational use. It is compatible with the Adobe XMP specification and can be embedded in formats such as JPEG, PNG, and TIFF (Karlsruhe Institute of Technology, n.d.). Core Scientific Metadata Model (CSMD) Link: http://icatproject-contrib.github.io/CSMD/ The Core Scientific Metadata Model (CSMD) is a data-oriented framework developed at STFC, designed to capture comprehensive information about scientific studies and the data they generate. It serves as the foundation for the ICAT schema, although ICAT incorporates additional implementation-specific features. CSMD supports the organization and management of metadata related to scientific research activities. Please note that CSMD was last updated in 2013. Inclusion here is for completeness and potential users should instead consider the ICAT schema (Karlsruhe Institute of Technology, n.d.). Crystallographic Information Framework (CIF) Link: https://www.iucr.org/resources/cif CIF, which stands for Crystallographic Information File, serves as a standard format for data exchange in crystallography. It also refers to the Crystallographic Information Framework, which encompasses a set of exchange protocols based on data dictionaries and relational rules that can be represented in various machine-readable formats, including XML (International Union of Crystallography, n.d.). Electron Microscopy (EM) Glossary Link: https://emglossary.helmholtz-metadaten.de/ The EM Glossary is an initiative to standardize terminology in electron microscopy by bringing together experts in the field with metadata and information engineering professionals. It aims to create a harmonized vocabulary to enhance communication and interoperability within the electron microscopy community (HMC, n.d.). FITS (Flexible Image Transport System) Link: https://fits.gsfc.nasa.gov/ FITS is the standard data format used in astronomy for storing, transmitting, and processing scientific and image data. It supports metadata in ASCII headers and enables complex data structures like images, tables, and multidimensional arrays (Karlsruhe Institute of Technology, n.d.). FITS World Coordinate System (WCS) Helmholtz Metadata Collaboration | List of Standards for Matter 5 Link: https://fits.gsfc.nasa.gov/fits_wcs.html WCS is an extension to the FITS format that provides a standard for mapping image pixels to physical (sky) coordinates. It was proposed in 2002 and integrated into the 3.0 release of the FITS standard to enable celestial referencing in image data (Karlsruhe Institute of Technology, n.d.). ICAT Schema Link: https://repo.icatproject.org/site/icat/server/5.0.0/schema.html The ICAT Schema extends the Core Scientific Metadata Model (CSMD) with practical elements for managing experimental data at large-scale facilities. It is typically used for internal organization of the ICAT metadata catalogue, and should be understood as such (ICAT Project, n.d.). IMPEx Data Model Link: https://impex-fp7.oeaw.ac.at/ The IMPEx (Integrated Medium for Planetary Exploration) Data Model extends the SPASE model to support planetary and heliospheric simulations, providing interoperability across simulation tools and data archives (Karlsruhe Institute of Technology, n.d.). IUPAC Gold Book Link: https://goldbook.iupac.org/ The IUPAC Compendium of Chemical Terminology, known as the Gold Book, provides authoritative definitions of terms in chemistry. It serves as a reference for standardized chemical nomenclature and terminology (IUPAC, n.d.). International Virtual Observatory Alliance Technical Specifications Link: https://www.ivoa.net/documents/ The International Virtual Observatory Alliance (IVOA) develops and maintains a suite of metadata standards and models to enable interoperability of astronomical archives worldwide. These include models for photometry, spectra, time coordinates, and simulation data (Karlsruhe Institute of Technology, n.d.). Metadata Schemas for Materials Science (KIT DM) Link: https://github.com/kit-data-manager/Metadata-Schemas-for-Materials-Science The Metadata Schemas for Materials Science initiative, developed by the Karlsruhe Institute of Technology (KIT), provides a modular and extensible framework for describing experimental and simulation data in materials science (KIT DM, n.d.). Helmholtz Metadata Collaboration | List of Standards for Matter 6 NeXus and the NeXus Definition Language (NXDL) Link: https://www.nexusformat.org/ NeXus is an international standard created by scientists and programmers to enhance collaboration in the analysis and visualization of data from neutron, x-ray, and muon experiments. It aims to provide a standardized data format based on HDF5 (see below) and the NeXus Definition Language (NXDL) terminology to facilitate data sharing and interoperability among scientific communities (NeXus Data Format, n.d.). OME-xml (newer version OME-tiff) Link: http://www.openmicroscopy.org/Schemas/ OME-XML is a standardized metadata schema for biological light microscopy data, developed by the Open Microscopy Environment Consortium. It is vendor-neutral and supports metadata for light microscopy experiments. OME-TIFF is an extension of OME-XML, allowing metadata to be embedded within TIFF or BigTIFF files, ensuring consistent data and metadata integration for biological imaging (Open Microscopy Environment, n.d.). Open Databases Integration for Materials Design (OPTIMADE) Link: https://www.optimade.org/ OPTIMADE is a consortium-driven initiative aimed at enhancing interoperability between materials science databases. It establishes a common REST API specification, enabling consistent and standardized data access across different materials databases. The goal is to promote data sharing and integration within the materials design community (OPTIMADE Consortium, n.d.). Open Particle-Mesh Data (OpenPMD) Link: https://github.com/openPMD/openPMD-standard OpenPMD, or Open Particle-Mesh Data, is a standard for metadata and naming conventions used to exchange particle and mesh-based data from scientific simulations and experiments. It is not a file format but provides standardized naming and attribute guidelines to promote interoperability in scientific data sharing (OpenPMD Collaboration, n.d.). Open Reflectometry Standards Organisation (ORSO) Link: https://www.reflectometry.org/ The Open Reflectometry Standards Organisation (ORSO) is a global community of scientists dedicated to advancing neutron and X-ray reflectometry through international collaboration and standardization. ORSO focuses on improving reproducibility, interoperability, and data sharing within the reflectometry community (Open Reflectometry Standards Organisation ORSO, n.d.). Helmholtz Metadata Collaboration | List of Standards for Matter 7 Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework (PDBx/mmCIF) Link: https://mmcif.wwpdb.org/ The Protein Data Bank (PDB) is the central global archive for 3D structures of proteins, nucleic acids, and complex biological assemblies, managed by the Worldwide PDB (wwPDB). The PDB Exchange Dictionary (PDBx) is utilized to define the metadata for the deposition, annotation, and storage of PDB entries. It incorporates the Macromolecular Crystallographic Information Framework (mmCIF), which was developed under the guidance of the International Union of Crystallography (IUCr). The PDBx framework has been extended to include metadata for other structural determination methods, such as Nuclear Magnetic Resonance Spectroscopy and 3D Electron Microscopy (Worldwide Protein Data Bank, n.d.). Quantities, Units, Dimensions and Types (QUDT) Link: http://qudt.org/ QUDT (Quantities, Units, Dimensions, and Types) provides ontologies that define the fundamental classes, properties, and limitations necessary for representing physical quantities, measurement units, and dimensions across various systems. It establishes a cohesive framework for measurable quantities, units, numerical values in different units, and the data structures used to store and manipulate them within software systems (QUDT.org, n.d.). Resource Metadata for the Virtual Observatory Link: https://www.ivoa.net/documents/ResourceMetadata/ This standard defines the metadata necessary for discovering and using astronomical data services. It extends the Dublin Core model with astronomy-specific elements and is used in the Virtual Observatory registry systems (Karlsruhe Institute of Technology, n.d.). Sample Environment Communication Protocol (SECoP) Link: https://content.iospress.com/articles/journal-of-neutron-research/jnr190143 SECoP is a global communication standard that facilitates interaction between sample environment equipment and experimental control software, particularly in neutron and photon research facilities. It ensures seamless integration and communication within scientific research infrastructures (Schulz, M., et al., 2019). Standard for Documentation of Astronomical Catalogues (SDAC) Link: https://cds.unistra.fr/doc/catstd.htx Helmholtz Metadata Collaboration | List of Standards for Matter 8 Developed by the Centre de Données astronomiques de Strasbourg (CDS), SDAC defines conventions for archiving astronomical data in human-readable formats. It specifies naming, structure, and metadata requirements for tabular data and associated documentation (Karlsruhe Institute of Technology, n.d.). SPASE Data Model Link: https://spase-group.org/data/model/ The Space Physics Archive Search and Extract (SPASE) Data Model is designed for describing heliophysics data and its scientific context, including data sources, content, provenance, and access. It supports a federated data system, and the preferred serialization format is XML. It is maintained by the SPASE Consortium (Karlsruhe Institute of Technology, n.d.). XAS Data Interchange Format (XDI) Link: https://github.com/XraySpectroscopy/XAS-DataInterchange/blob/master/specification/spec.md XDI is a standard file format for storing X-ray Absorption Spectroscopy (XAS) data. It provides a consistent and well-defined structure for tabular data and metadata associated with XAS experiments. Designed for interoperability and archival purposes, XDI ensures reproducibility and easier sharing of XAS datasets across the scientific community (XraySpectroscopy GitHub, n.d.). Generic Standards Common European Research Information Format (CERIF): Link: https://eurocris.org/Uploads/Web%20pages/CERIF-1.6/documentation/MInfo.html CERIF is a metadata standard recommended by the European Union for documenting research activities. It supports the structured recording of metadata related to research projects, publications, datasets, and other research outputs. CERIF is maintained by EuroCRIS and promotes interoperability within the European research ecosystem (EuroCRIS, n.d.). CSV on the Web (CSVW): Link: https://csvw.org/standards.html CSVW extends the basic CSV format by including machine-readable metadata in JSON format. It defines table structures, column data types, and relationships, making tabular data more interoperable and easier to integrate across systems. It improves interoperability of CSV files by providing machine-readable descriptions of the data structure, such as column names, data types, and relationships (W3C, n.d.-a).