The EMO-BON data model is designed with a strong emphasis on interoperability and reuse. To support this, it incorporates terms from established, widely adopted ontologies wherever possible. This approach ensures consistency and enhances the integration of EMO-BON data within broader semantic frameworks.
The following is a preliminary list of ontologies reused within the EMO-BON model:
SOSA (Sensor, Observation, Sample, and Actuator)
Modeling observations, samples, and sampling events.
e.g.Observation,Sample,Sampling,hasResult,isResultOf, ...Dublin Core
General metadata properties.
e.g.title,description,creator,date,isPartOf, ...Schema.org
General-purpose metadata for describing entities.
e.g.name,description,url,identifier, ...PROV-O (Provenance Ontology)
Representing provenance metadata.
e.g.Activity,Entity, ......
Not all concepts relevant to EMO-BON could be adequately represented using existing ontologies. To address these gaps and ensure a complete and coherent data model, EMO-BON defines its own suite of ontologies, available at:
https://
These ontologies are organized into thematic namespaces, each covering a specific aspect of the data lifecycle - from observatory metadata and sampling events to analytical outputs and organizational processes. Together, they provide a structured and interoperable foundation for describing marine biodiversity observations, supporting rich, consistent, and machine-readable data integration across the EMO-BON ecosystem:
core ontology
Defines core metadata related to observatories, sampling events, and samples. e.g.Observatory,SampleType,hasBiome,waterColumnDepth, ...core vocabulary
Describes basic environmental concepts used in sampling.
e.g.Hard,Soil,Waterproduct ontology
Terms for describing outputs from taxonomic and functional analyses of samples.
e.g.Product,TaxonomicAnnotation,FunctionalAnnotation,ofSample, ...product vocabulary
Defines terms used within functional and taxonomic annotations.
e.g.GO,InterPro, ...sampling ontology
Metadata for describing sampling activities and sample characteristics.
e.g.tidalStage,minSamplingDepth,longStorage,hasSampleSize, ...sequence ontology
Describes sequencing-related data and analyses.
e.g.SequencingRun,associatedBatch, ....
⚠️ Relevance and usage of this namespace should be confirmed.
governance ontology
Terms related to governance processes and organizational structures in EMO-BON. e.g.SOP, ....
⚠️ Relevance and usage of this namespace should be confirmed.
Vocabularies¶
EMO-BON uses a range of controlled vocabularies and ontologies to support consistent, semantically rich data annotation and integration:
MIxS (Minimum Information about any (x) Sequence) – for environmental and contextual metadata standards from the Genomic Standards Consortium
BODC Vocabularies – maintained by the British Oceanographic Data Centre for oceanographic and marine terms
ENVO (Environment Ontology) – an ontology for environmental features and habitats, part of the OBO Foundry
EFO (Experimental Factor Ontology) – for describing experimental variables and sample characteristics
EDAM (EMBRACE Data and Methods Ontology) – for describing bioinformatics operations, data types, formats, and topics