The EVORAO Ontology provides a structured and harmonized vocabulary for describing shareable pathogens as characterized biological materials, along with their derived products and associated services, organized into collections. Developed within the EVORA project, it supports consistent metadata annotation across research infrastructures, promoting findability, accessibility, interoperability, and reusability (FAIR). By aligning with relevant standards and ontologies, EVORAO facilitates cross-domain collaboration, integration, and sharing of pathogenic resources and services to enhance pandemic preparedness and response. While initially focused on virology, EVORAO is designed to be extensible and also supports metadata harmonization for other pathogens.
EVORAO is compatible with DCAT, making it well-suited for efficiently cataloguing pathogen collections and related resources.
EVORAO results from a collaborative effort within the EVORA project, involving three research infrastructures: EVA, ERINHA and ELIXIR.
The EVORAO ontology is available in OWL Turtle format in the /models/owl directory. The latest stable version can be accessed directly from the main branch of this repository, while the staging branch is used to simulate ontology generation before publication.
Ontology / vocabulary IRI: https://w3id.org/evorao/
Namespace IRI (for classes/properties): https://w3id.org/evorao/
OWL Turtle serialization: https://w3id.org/evorao/owl.ttl
GitHub source file: https://github.com/EVORA-project/evora-ontology/blob/main/models/owl/evora_ontology.owl.ttl
Release archive: https://github.com/EVORA-project/evora-ontology/releases
The ontology also declares publication metadata, including title, description, version, license, publisher, preferred namespace prefix/URI, documentation URL, prior release, download URL, and term status/provenance metadata.
For vocabulary registry submissions and metadata assessments, use the ontology / vocabulary IRI https://w3id.org/evorao/. The /owl.ttl URL is the concrete Turtle serialization.
The ontology can also be browsed using the OLS (Ontology Lookup Service).
The documentation files for EVORAO can be found in the /docs directory and are intended to be published with GitHub Pages:
HTML documentation: https://evora-project.github.io/evora-ontology/
It provides detailed information for consumers and developers working with EVORAO metadata.
Start exploring via the index file.
OLS remains a useful ontology browser, but the GitHub Pages documentation is the canonical human-readable documentation linked from the ontology metadata for vocabulary publication.
EVORAO is generated from a Google Sheet using schemasheets and processed with LinkML, which compiles the schema into multiple formats.
The generation workflow is tested on the staging branch. It regenerates the LinkML schema, OWL Turtle file, root /docs documentation, and subsidiary models. After OWL generation, the workflow adds publication metadata that is not emitted by the standard LinkML OWL generator.
Publication from main is handled separately: documentation is deployed to GitHub Pages, and a GitHub release is created from the schema version with the generated OWL Turtle and LinkML schema attached as release assets.
The staging generation workflow runs a deterministic QA gate before committing or pushing generated artefacts. The same gate can be started locally with Docker using:
./qa/run_qa.shThe gate validates the generated ontology structure, runs OWL reasoning with ROBOT/ELK, checks generated SHACL against positive and negative catalogue fixtures, executes SPARQL competency queries, and writes reports under qa/reports/. In CI these reports are uploaded as workflow artifacts and the generated commit is blocked when a deterministic check fails.
In addition to the core ontology, the repository includes subsidiary data models generated with LinkML from the EVORAO LinkML schema. These models can be found in the /models/subsidiary_models directory and provide starting points for using EVORAO metadata in different technical environments:
- Programming models: Python (Pydantic, Python classes, SQLAlchemy), Java, Go
- Database structure: SQL
- Serialization formats: JSON, JSON-LD, RDF, Protobuf
- Validation models: SHACL, ShEx
- Querying tools: SPARQL, GraphQL
- Spreadsheet template: Excel
These models facilitate integration of EVORAO metadata into diverse research workflows.
For a comprehensive overview, refer to the Google Sheet document, reviewed by scientists from the partner research infrastructures, and to its derived YAML-based LinkML schema (/models/evora_schema.yaml).
EVORAO is designed to be reused, extended, and adapted to evolving research needs. Reuse and extension can include:
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Contributing to EVORAO: Community-driven contributions are encouraged when the proposed change remains within the scope of pandemic preparedness and response. Contributions can be proposed through GitHub issues or pull requests, as described in the contribution guidelines.
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Creating custom ontologies: If a use case requires terms or structures beyond the current EVORAO scope, EVORAO can be imported and extended in a separate ontology.
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Mapping to EVORAO: EVORAO terms can be referenced alongside other ontologies or vocabularies by declaring the EVORAO prefix and using the relevant EVORAO IRIs in mappings.
When importing, extending, or mapping to EVORAO, declare the EVORAO prefix:
prefixes:
EVORAO: https://w3id.org/evorao/For guidance on extending EVORAO by contribution, please refer to the contribution guidelines.
Scientists and developers are welcome to contribute semantic improvements to EVORAO:
- By proposing new terms, relationships, and metadata refinements via GitHub issues.
- By suggesting revisions to parent classes or concepts for better domain coverage.
Developers are also invited to contribute technical improvements that affect how output files, data models, and documentation are generated:
- Improve the CI generation workflow in the .github/ directory.
- Improve the Google Sheet triggering process in the /GScript directory.
- Improve this README or the contribution guidelines.
- Improve the generation of the LinkML schema (/models/evora_schema.yaml) from the Google Sheet by contributing to the schemasheets GitHub repository.
- Improve generated outputs such as OWL, JSON-LD, SQL, Python, Java, or Go by contributing to the LinkML GitHub repository.
For guidance on extending EVORAO by contribution, please refer to the contribution guidelines.
EVORAO is released under the Creative Commons Universal (CC0 1.0) license, ensuring unrestricted reuse and alignment with FAIR principles. This allows:
- Free use, modification, and integration into other projects.
- Promotion of broad adoption and interoperability within the scientific community.
A recommended best practice for extending or reusing EVORAO is to contribute to the ontology as a community member. If the project scope differs, EVORAO can be imported partially for specific use cases; see Reusing and Extending EVORAO Metadata.
For more information about the EVORA project, visit https://evora-project.eu.