This step creates mappings, translations and alternative representations that allow the research object to meet integration and interoperability requirements of the primary use cases.
Different communities, repositories, services, tools and workflows may use other identifier schemes, vocabularies, models or representations. This step connects the canonical representation, developed through the previous steps, to those external requirements through documented mappings and transformations.
An alternative representation may be stored, generated on demand or exposed through a service. Its relationship to the canonical representation and its status as an authoritative, derived, provisional or application-specific representation should be explicit.
This step does not require every transformation to be bidirectional or lossless. A one-way or simplified representation may be appropriate where it meets the intended use, provided that its direction, limitations and information loss are documented.
Use this step during project examination to identify integration requirements, assess available mapping and transformation capabilities and define the required outputs. During an implementation cycle, use it to create, apply and validate the mappings, translations and alternative representations within scope.
Standards discovery and reuse
Developing standards
Applying standards
Validating against standards
Identifier mapping
Vocabulary alignment
Model mapping
Identifier mapping
Establish and maintain documented relationships between identifiers used by different schemes, authorities, repositories or systems.
This capability allows integrations to recognise when identifiers refer to the same subject or to subjects connected through version, component, derivation, replacement or other defined relationships. Since mapping are not always assertions of an exact identity match, the relations should be stated explicitly:
- Exactly the same subject.
- Different records describing the same subject.
- Different versions or releases.
- A collection and one of its components.
- An original and a derived research object.
- A deprecated and replacement identifier.
- Closely related but distinct subjects.
The capability may be provided through authoritative registries, repository cross-references, identifier-resolution services, community mapping resources, lookup services or project-maintained mappings (that themselves can be shared).
Resources
5 ELIXIR Stories items
- Intrinsically Disordered Protein Community Interoperability Showcase: Exploiting Bioschemas Markup Cascade mapping from FT 6: transform data for increased interoperability via creation of knowledge graph
- Plant Sciences Community Showcase Cascade mapping from FT 2–6: integration of multiple resources, data harmonisation
- Rare Disease Community Interoperability Showcase: examples from EJP RD Cascade mapping from FT 6: transform data for increased interoperability by connecting resources via KGs/SPARQL endpoints
-
Mapping the DCAT-based EJP RD Metadata Model to Bioschemas for improved interoperability Cascade mapping from FT 6: transform data for interoperability: mapping of identifiers and vocabularies to Bioschemas for further analysis and dissemination
- FAIRtracks: FAIRtracks and Omnipy - FAIRtracks interoperability story Cascade mapping from FT 6: Transform data for inter- operability: Convert metadata from avirous schema to Track Hub format and FAIRtracks metadata exchange format using Omnipy ETL flows
2 FAIR Metroline items
- Use ontologies in the model Semantic relations can help connect equivalent identifiers across systems and contexts.
- Apply (meta)data model Representing mapped identifiers consistently in the applied model makes identifier mapping usable in practice.
3 FAIR Cookbook items
Vocabulary alignment
Establish and maintain documented semantic relationships between concepts from different controlled vocabularies, terminologies, taxonomies or ontologies.
This capability allows the concepts used in the canonical representation to be interpreted or translated for communities and systems that use other semantic resources. Possible alignment relationships include:
- Exact match.
- Close match.
- Broader match.
- Narrower match.
- Related match.
- Context-dependent correspondence.
- Composite or one-to-many correspondence.
- No suitable match.
The capability may be provided through mappings published by vocabulary authorities, community alignment projects, ontology services, mapping registries, specialist tools or project-generated mapping sets.
Resources
5 ELIXIR Stories items
- Intrinsically Disordered Protein Community Interoperability Showcase: Exploiting Bioschemas Markup Cascade mapping from FT 6: transform data for increased interoperability via creation of knowledge graph
- Plant Sciences Community Showcase Cascade mapping from FT 2–6: integration of multiple resources, data harmonisation
- Rare Disease Community Interoperability Showcase: examples from EJP RD Cascade mapping from FT 6: transform data for increased interoperability by connecting resources via KGs/SPARQL endpoints
-
Mapping the DCAT-based EJP RD Metadata Model to Bioschemas for improved interoperability Cascade mapping from FT 6: transform data for interoperability: mapping of identifiers and vocabularies to Bioschemas for further analysis and dissemination
- FAIRtracks: FAIRtracks and Omnipy - FAIRtracks interoperability story Cascade mapping from FT 6: Transform data for inter- operability: Convert metadata from avirous schema to Track Hub format and FAIRtracks metadata exchange format using Omnipy ETL flows
2 FAIR Metroline items
- Use ontologies in the model Alignment depends on relating equivalent or closely related terms through semantic links.
- Creating a FAIR Implementation Profile (FIP) Shared documentation of semantic choices can support alignment across communities.
1 FAIR Cookbook items
Model mapping
Relate entities, properties, relationships, structures and constraints across domain, data, metadata or structural models.
This capability connects the canonical model and representation to the models expected by target communities, repositories, services, tools and workflows. Model mapping may describe conceptual correspondences, structural crosswalks or executable transformation rules.
Mappings are not limited to one-to-one equivalence. A source element may correspond to several target elements, several source elements may be combined, or a target value may need to be derived.
The capability may be provided through standards crosswalks, repository mappings, schemas, transformation specifications, ETL workflows, query languages or project-developed mapping artefacts.
Resources
5 ELIXIR Stories items
- Intrinsically Disordered Protein Community Interoperability Showcase: Exploiting Bioschemas Markup Cascade mapping from FT 6: transform data for increased interoperability via creation of knowledge graph
- Plant Sciences Community Showcase Cascade mapping from FT 2–6: integration of multiple resources, data harmonisation
- Rare Disease Community Interoperability Showcase: examples from EJP RD Cascade mapping from FT 6: transform data for increased interoperability by connecting resources via KGs/SPARQL endpoints
-
Mapping the DCAT-based EJP RD Metadata Model to Bioschemas for improved interoperability Cascade mapping from FT 6: transform data for interoperability: mapping of identifiers and vocabularies to Bioschemas for further analysis and dissemination
- FAIRtracks: FAIRtracks and Omnipy - FAIRtracks interoperability story Cascade mapping from FT 6: Transform data for inter- operability: Convert metadata from avirous schema to Track Hub format and FAIRtracks metadata exchange format using Omnipy ETL flows
2 FAIR Metroline items
- Apply (meta)data model Mapping between data models depends on expressing those mappings in a model that can be implemented consistently.
- Create or reuse a semantic (meta)data model Clearly defined semantic models make equivalent concepts across sources easier to compare and map.