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Metadata: beyond discovery, extending the Cross Domain Interoperability Framework

RDA Metadata IG

Stephen Richard, Simon Hodson, Flavio Rizzolo, Steven D McEachern, Milan Ojsteršek

Mon 13 October, 12:00-13:30 AEDT

25th RDA Plenary Meeting �Brisbane, 2025

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Acknowledgement of Country

We acknowledge and celebrate the First Australians on whose traditional lands we meet, and we pay our respect to their elders past and present.

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Welcome to new RDA members!

OPENNESS

COMMUNITY-�DRIVEN

CONSENSUS

NON-PROFIT AND TECHNOLOGY-�NEUTRAL

HARMONISATION

INCLUSIVITY

6 Guiding Principles are at the heart of the RDA community.

JOIN THE RDAwww.rd-alliance.org/register/

All RDA members are expected to adhere by the RDA Code of Conduct to foster a welcoming and inclusive environment.

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Metadata IG

  • Established May 2013 — First met Jan 2014 (P2, Munich) — New co-chairs 2024
  • Activities:
    • Provide forum for cross-domain discussions about metadata for research data
    • Identify and promote metadata solutions to data management challenges
    • Recommend how to improve quality and interoperability of metadata (better FAIRness)
  • Outputs:
  • Recommended Metadata Element Set
  • RDA Metadata Standards Catalog (via MSC WG)

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Goal

How to extend basic metadata to more fully support FAIR data

  • access policies and procedures,
  • provenance, quality,
  • data structure
  • domain-specific semantics.

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Agenda

  1. Overview of Cross Domain Interoperability Framework (CDIF)
  2. Documentation of datasets for data integration
  3. DISCUSSION: Examples of metadata documenting complex datasets; where are there gaps?
  4. Case study: Application of ODRL/DUO/DP to automate data access for sensitive data
  5. Case study: machine-actionable descriptions of data access protocols for distributed genomic data and biobank
  6. DISCUSSION: metadata conventions for extensions to enable automated data access and integration
  7. Wrap-up. 3 Take aways, call for input on notes, examples, challenges…

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Part 1: CROSS Domain Interoperability Framework

Simon Hodson

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  • Identifies a set of functional requirements for interoperability, particular for steps in data combination, and identifies good practices for each of these requirements.
  • Draws on work with the WorldFAIR case studies and with a number of international initiatives (ODIS, Science on Schema.org, UN Stats KG work, GBIF…)
  • Good web practices: Significant proportion of CDIF rests on good web practice, domain neutral standards and good practice: disciplines can adopt or map.
  • Use cases: domain or cross-domain projects or data services that need to combine data for analysis, modelling etc.
  • Directed at implementers: describes use cases, identifies standards, gives guidance and on how to implement them.
  • Categorically not a new standard. Rather it is a framework of existing and emerging standards.
  • A framework of standards/specifications to provide a lingua franca.

What is the CDIF (Cross-Domain Interoperability Framework)?

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What is CDIF?

  • The Cross Domain Interoperability Framework (CDIF) is a set of practical, implementation-level principles designed to improve data management practices within any community and lower the barriers to cross-domain data reuse. CDIF offers standards and methodologies for achieving different levels of interoperability necessary for reusing data across diverse domains. It is built around five core profiles that address the essential functions for implementing cross-domain FAIR principles.
  • CDIF was first released in May 2024 as an output of the WorldFAIR project: https://doi.org/10.5281/zenodo.11236871
  • The point of reference for CDIF and its component profiles is now the CDIF Book: https://cdif.codata.org
  • CDIF has attracted a lot of interest and has led directly to a set of additional projects and collaborations.

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Discovery Profile

  • Discovery profile: https://bit.ly/cdif-discovery
  • Variable description in the discovery metadata
    • Name of the variable as it appears in the dataset.
      • Uses schema.org variableMeasured.
    • Text description.
    • propertyID with URI for the represented concept.

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Description Profile: DDI CDI for Data Structure, Variable Cascade, Provenance…

  • Important to think about how we combine data for cross-domain research.
  • Data Documentation Initiative (DDI) Cross-Domain Integration (CDI) specification contains three modules to assist with this:
    • Structural Description: assists processing of data structure transformations across four data structures.
    • Data Description / Variable Cascade describes data at an atomic level, describes relationships between concepts, representations and instances (assists with combining data and documenting information loss).
    • Provenance and Processing: module uses PROV-O and SDTL to provide and relay provenance and processing information.
    • Now officially released: https://ddialliance.org/ddi-cdi

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CDIF, Next Steps

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CDIF-4-XAS: Overview and Next Steps

  • Overview of standards, vocabularies (and ontologies), data formats and practices within the XAS area (landscape analysis): https://doi.org/10.5281/zenodo.14920226
    • Survey of XAS database schemas and software dependent XAS schemas.
    • Survey of XAS community standardisation effort: observe an alignment around NXxas for multi-spectra raw and processed data and XDI for single spectra data (reinforced by an IUCr recommendation).

Next Steps

  • D2: ‘Semantic description of at least two XAS community standards using a CDIF profile (XAS-CDIF)’: i.e. mapping and description of NXxas and XDI data using CDIF.
    • description using the CDIF Discovery profile for metadata;
    • description using DDI-CDI data description for variables, struccture;
    • characterisation of the XDI (table) and Nxxas (HDF5) data structures using DDI-CDI;
    • mappings for key concepts;
    • will be published next week… !
  • Use cases: CDIF-4-XAS contends that increased standardisation of metadata and by following CDIF recommendations will increase the reuse potential of XAS data outside the original experiment. Concrete use cases need to be identified to demonstrate that this is indeed the case.

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  • Cluster of EC-funded projects, including Climate-Adapt4EOSC, looking at various case studies, including urban heat, coastal management and shrink-swell of soils.
    • CDIF for semantic and technical interoperability.
    • Incorporation and mapping of key semantics.
    • RO-Crates for packaging and orchestration.
  • Exploring how to maximise and automate solutions for Legal and Organisational Interoperability.
    • Identify commonly encountered LOI obstacles.
    • Identify corresponding LOI enablers (agreements/contracts, licences, conditions) and test them with case studies.
    • Express them in code (building on DPV, ODRL, DUO standards).
    • Report on landscape and proposed solutions, Dec 2025.
    • Legal and Organisational IFs, late 2027.

CDIF in Climate-Adapt4EOSC

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  • “FAIR Principles implementation for DDE”: Implementation of FAIR principles, alignment of IUGS CGI standards with CDIF, for cross-domain research topics and data reuse in geology. Three years. From August 2025. Global. Funding from IUGS.
    • Enabling the alignment of IUGS CGI and other geology standards with CDIF.
    • Envisage a similar methodology to the OSCARS project with XAS data.
    • Map and implement CDIF discovery profile.
    • Implement CDIF data description profile.
    • Highlight importance of authoritative and FAIR concept schemes.

CDIF in DDE

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  • Re-initiate the CDIF WG (break over summer, project proposals and deliverables…)
  • Continue exploring project and collaboration opportunities.
  • Upcoming Dagstuhl workshop will look at:
    • Provenance and context (and quality)…
    • Access (implementation of ODRL, DPV, DUO to manage responsibilities)
    • Metadata mapping and data integration
    • CDIF for XAS

CDIF: Next Steps

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Part 2: DDI-CDI documentation for Data Integration

Stephen Richard

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Data Integration

  • Use multiple datasets to produce a single unified data set that can be used in analysis
  • Issues:
    • what are the variables represented by the data
    • are the variables comparable
    • how to include domain-specific information
    • how is the information serialized

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What are the variables

CDIF Discovery profile

  • schema.org variableMeasured: name, alternateName, description, propertyID, unitText

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Are the variables comparable

This gets domain specific

  • measurement technique
  • context

iAdopt addresses the kinds of information require

This in general will require extension profile

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Domain-specific information

  • Profiles:
    • set of conventions for representing some information
    • vocabulary
    • serialization scheme (compatible with base scheme)
    • requirements
  • Has to be documented and identified
  • Open world-- anyone can define a new profile....
    • need registry for others to find existing profiles (Metadata IG?)
    • interoperability agreements in communities

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How to serialize

Need open-world serialization

RDF, JSON, YAML....

Metadata needs to self describe extensions included

"schema:about": {"@id": "xas:485749"},� "schema:description": "metadata about documentation for se_na2so4",� "dcterms:conformsTo": [� {"@id": "cdif:profile_basic_1.0"},� {"@id": "cdif:profile_xasCDIF"}�]

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Discussion

EXAMPLE complex datasets with metadata

Data Cubes, Time series, vector or tensor fields,

Add examples in notes,

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Part 3: automate data access for sensitive data

Steven D McEachern

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Use case: automation of data access for sensitive data

A standalone repository holding sensitive personal data wishes to provide ‘secondary access’ to other research groups.

A metadata aggregator wants to provide search clients with filters based on access policies

A central clearing house mediating access to data in federated repositories

Federated analytics over multiple sensitive data providers

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Proposed approach

Recommendation: Open Digital Rights Language (ODRL - W3C) to describe data asset access policies. https://www.w3.org/TR/odrl-model/

With

Data Use Ontology (DUO - GA4GH) to describe terms of use

Data Privacy Vocabulary (DPV - W3C) to describe and integrate legal and risk concepts

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Object Digital Rights Language (ODRL)

A policy expression language that provides a flexible and interoperable information model, vocabulary, and encoding mechanisms for representing statements about the usage of content and services. (https://www.w3.org/TR/odrl-model/ )

Core classes:

  • Parties - actors or agents who exercise ->
  • Rules - ODRL Permissions (can do), ODRL Duties (must do), ODRL Prohibitions (must not do) encompassing ->
  • Actions - operations performed on ->
  • Assets - digital objects in a CDIF context.

  • Policies are then structured artefacts that document the above information.

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Basic operation of ODRL

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DUO

The Data Use Ontology was developed by the Global Alliance for Genomic Health (GA4GH) to allow “data stewards to tag datasets with permitted use terms that facilitate data discovery and access”

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DUO and

automation

Restrictions and requirements specified in licenses and DUO codes

Access requests specified in DUO-aligned request systems

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Data Privacy Vocabulary (DPV)

“The motivation of DPV is to provide a 'data model' or an 'ontology' of concepts for interoperable representation and exchange of information about processing of (personal) data and the use of technologies.” Source: https://w3id.org/dpv/

  • Core conceptual model
  • With specific Risk and Impact Assessment (https://w3c.github.io/dpv/2.2/dpv/modules/risk.html )
    • “For risk and impact assessment, DPV's provides a 'lightweight risk ontology' based on commonly utilised concepts of Risk, RiskMitigationMeasure, Consequence, and Impact along with risk assessment concepts of RiskLevel, Severity, and Likelihood.”

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The core DPV model

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Combining

the three

Dataset policies as odrl:Offer

Data use requests as odrl:Request

Data use decisions as odrl:Agreement

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Proof of concept (Pandit and Esteves, 2024)

Work to be developed at Dagstuhl CDIF workshop, November 2025

Pilot implementation expected in 2026 at UKDS and ODISSEI

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Part 4. data access protocols for distributed genomic data

Milan Ojsteršek

University of Maribor, Slovenia

milan.ojstersek@um.si

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The main problems in biomedical data interoperability

The primary challenges in biomedical data interoperability stem from the absence of a uniform language and consistent context across the highly fragmented healthcare and research ecosystem. Solving these issues is crucial for enabling large-scale analysis, machine learning, and personalized medicine.

  • Semantic Interoperability (diverse terminologies and coding, contextual ambiguity).
  • Structural Interoperability (format heterogeneity, lack of standardisation in APIs, closed data models in vendors‘ applications).
  • Organizational and Legal Interoperability (privacy and consent, trust and governance models).

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The Global Alliance for Genomics and Health (GA4GH) unites an international community dedicated to advancing human health through genomic data. They build technical standards, and policy frameworks, and tools that will expand responsible, voluntary, and secure use of genomic and other related health data.

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Rehm, Heidi L. et al.

Cell Genomics, Volume 1, Issue 2, 100029, 2021, DOI: 10.1016/j.xgen.2021.100029

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BBMRI-ERIC

BBMRI-ERIC is a European research infrastructure for biobanking. It brings together all the main players from the biobanking field – researchers, biobankers, industry, and patients – to boost biomedical research. To that end, they offer quality management services, support with ethical, legal and societal issues, and a number of online tools and software solutions for biobankers and researchers. BBMRI-ERIC currently includes 23 countries and one international organisation, making it one of the largest European research infrastructures.

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MIABIS (Minimum Information About BIobank data Sharing)

MIABIS is dedicated to standardising data elements used to describe biobanks, research on samples, and associated data. All BBMRI-ERIC‘s biobanks use MIABIS metadata standard for interoperability inside their federated platform.

BBMRI-ERIC utilises this metadata in the directory (the catalogue of sample collections), the locator (a real-time search on donor and sample levels), and the finder (a data analysis tool focused on clinical, phenotypic, and genomic data).

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European Health Data Space

The European Health Data Space is a health specific ecosystem comprised of rules, common standards and practices, infrastructures and a governance framework.

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1+MG Schema

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1+MG data models, standards and ontologies

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GDI Infrastructure

Centralised Discovery and Access Management

  • User Portal (DCAT - AP)
  • Passport and AAI
  • REMS

European level interconnectivity

  • Beacon Network (Beacon v2.2 data model and API)
  • Passport and AAI
  • REMS

National node level

  • Secure storage, secure computing and analysis, federated execution, federated learning. Common framework of standards and APIs.
  • Manage your own data and metadata.

Institutional level

  • Secure storage, execution of institutional processes, secure computing and analysis,

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Partial decentralised data access

GDI project receives funding from the European Union’s Digital Europe Programme under grant agreement number 101081813.

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Slovenian GDI architecture diagram

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DISCUSSION: conventions for modular metadata

Options:

  • dcTerms:conformsTo
  • http headers
  • Profiles Vocabulary https://www.w3.org/TR/dx-prof/
  • SHACL, JSON-schema, html....
  • Mapping classes and class values between different ontologies metadata schemas, data models and vocabularies in biomedical research
  • Is it possible to achieve complete machine actionability for genomic and biobank data? What would need to be done to enable these processes to be carried out without human intervention?

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Links

See Poster P45 'Implementation of metadata components for Cross Domain Interoperability (CDIF)'

CDIF GitHUB https://github.com/Cross-Domain-Interoperability-Framework

RDA Metadata Interest group:

session notes: https://docs.google.com/document/d/1v1yZM6Lj3spxpJIkRkhR9URUGbfcQ19b

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Thanks

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Addendum on Data Integration and DDI-CDI

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Towards practical interoperability for data integration

  • Data Integration: ability to combine, link, relate and different in various ways for data production, analysis, understanding complex phenomena, etc.
  • Large number of use cases in multiple domains (and across domains)
    • UN Statistical Division SDGs SDMX data -> Google Data Commons via DDI-CDI
    • NADA data catalogs (IHSN) with 1000’s of studies in DDI-Codebook -> SDMX via DDI-CDI
    • A growing number of WorldFAIR+ and CDIF projects

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Mapping approach

  • DDI-CDI comes in handy as a Rosetta stone for mappings and integration
    • Focuses on multidisciplinary (and interoperable) data sharing and integration
    • Provides multiple syntax representations for machine-actionability
    • Complements (and integrates with) other DDI products
  • Prerequisites for effective data integration
    • Include reference and structural metadata to describe data well enough to make it integration-ready (including structure, semantics and codesets)
      • Define mappings between concepts, variables and codesets as necessary (expressed in SKOS/SSSOM)
      • Harmonize concepts/variables/formats (whenever possible) or document the caveats (if not 100% possible)
    • Preserve process metadata for provenance (description of operations performed on the data)

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Interoperability between SDMX and DDI

  • Benefits
    • International standard suites with large adoption base
    • Include DDI Codebook, DDI Lifecycle, DDI CDI, SDMX 2.1 and 3.x, XKOS, VTL and others.
    • Open and collaborative development
    • Growing ecosystem of tools and libraries readily available (key for efficient development)
    • Support for structural and semantic harmonization and alignment
  • Issues
    • Developed independently by difference communities with little intentional alignment
    • Impedance mismatch: varying emphasis on semantics, structures and granularity
    • Different strengths (and weaknesses)
  • Results
    • Developed guidelines on how to make both standards interoperate with each other and with VTL to enable data production pipelines for statistical production
    • Developed foundation for further work to include SDTL, XKOS, and other open implementation standards

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Mappings need to be “contextual”

Mappings are many-to-one and many-to-many

The usage of a class depends on the related classes (context)

The same class can be mapped differently in different contexts (and for different use cases)

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Expected outcomes

No prescriptive framework given the potential number of scenarios: we cannot know how exactly a user will work with the data for integration purposes

Data description elements (from DDI and SDMX) required to make the data integration-ready

Machine-actionable mappings based on standards (SKOS/SSSOM, others)

Clarification of potentially confusing terminology

DDI and SDMX tend to use similar terms for notions that are not exactly the same, e.g. Concepts, Categories, Codes, Components, etc. whereas some other notions are explicitly defined in one standards but not in the other, e.g. Variable.

Recommendations on how to define the integration process based on mappings and data structures

Identification of potential interoperability with other standards (DCAT, schema.org, etc.)