FishEUTrust Fish Sample Analytical Data Knowledge Base

## Description This repository contains a semantic RDF/OWL knowledge base representing analytical measurements (IRMS isotope ratios and ICP-MS elemental concentrations) from gilthead seabream (*Sparus aurata*) samples. The knowledge base integrates chemical measurement data with standardized ontology annotations, enabling FAIR-compliant data sharing, food traceability, and authenticity verification research. ### Key Features - **115 fish samples** from aquaculture and wild-caught sources- **2,745 chemical measurements** with full semantic annotation- **16,750 RDF triples** linking to standard ontologies- **Multi-ontology integration**: ChEBI, Unit Ontology (UO), FoodOn, NCBITaxon- **24 analytes mapped**: 4 stable isotopes (δ13C, δ15N, δ34S, δ18O) + 20 elements ### Dataset Summary | Metric | Value ||--------|-------|| Host species | *Sparus aurata* (Gilthead Seabream) || Total samples | 115 || Total measurements | 2,745 || IRMS isotope ratios | 4 (δ13C, δ15N, δ34S, δ18O) || ICP-MS elements | 20 (Na, Mg, P, S, K, Ca, V, Cr, Mn, Fe, Co, Cu, Zn, As, Se, Rb, Sr, Mo, Ba, Hg) || Production methods | Aquaculture, Wild || RDF triples | 16,750 | ## Files | File | Description ||------|-------------|| `README_zenodo_fisheutrust_samples.md` | This documentation file || `FishEUTrust_samples_JSI.xlsx` | Original Excel file with IRMS and ICP-MS analytical data || `fisheutrust_knowledge_base.ttl` | RDF knowledge base in Turtle format (~650 KB) || `fisheutrust_knowledge_base.rdf` | RDF knowledge base in RDF/XML format (~1.7 MB) || `FishEUTrust_Complete_Ontology_Mapping.xlsx` | Complete ontology mapping tables || `FishEUTrust_Semantic_Annotation_Deliverable.docx` | Project deliverable document with methodology || `create_fisheutrust_knowledge_base.py` | Python script to generate the knowledge base || `README.md` | Technical documentation for the Python script || `requirements.txt` | Python package dependencies | ## Usage ### Loading the Knowledge Base **Python (rdflib):**```pythonfrom rdflib import Graph g = Graph()g.parse("fisheutrust_knowledge_base.ttl", format="turtle")print(f"Loaded {len(g)} triples")``` **Apache Jena:**```bashriot --validate fisheutrust_knowledge_base.ttl``` ### SPARQL Query Examples **Find all aquaculture samples:**```sparqlPREFIX fish: <http://example.org/fisheutrust/> SELECT ?sample ?sampleIDWHERE { ?sample a fish:FishSample ; fish:hasSampleID ?sampleID ; fish:hasProductionMethod fish:Aquaculture .}``` **Get iron (Fe) measurements for all samples:**```sparqlPREFIX fish: <http://example.org/fisheutrust/>PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> SELECT ?sampleID ?valueWHERE { ?sample fish:hasSampleID ?sampleID ; fish:hasMeasurement ?meas . ?meas fish:measuresAnalyte chebi:18248 ; fish:hasValue ?value .}ORDER BY ?sampleID``` **Find samples with mercury (Hg) above threshold:**```sparqlPREFIX fish: <http://example.org/fisheutrust/>PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> SELECT ?sampleID ?hg_valueWHERE { ?sample fish:hasSampleID ?sampleID ; fish:hasMeasurement ?meas . ?meas fish:measuresAnalyte chebi:25195 ; fish:hasValue ?hg_value . FILTER(?hg_value > 0.5)}``` **Compare δ13C between aquaculture and wild samples:**```sparqlPREFIX fish: <http://example.org/fisheutrust/>PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> SELECT ?method (AVG(?value) as ?avg_d13c)WHERE { ?sample fish:hasProductionMethod ?method ; fish:hasMeasurement ?meas . ?meas fish:measuresAnalyte chebi:36928 ; fish:hasValue ?value .}GROUP BY ?method``` ### Regenerating the Knowledge Base ```bashpip install -r requirements.txtpython create_fisheutrust_knowledge_base.py FishEUTrust_samples_JSI.xlsx output.ttl output.rdf``` ## Technical Specifications ### RDF Statistics | Component | Count ||-----------|-------|| Total triples | 16,750 || OWL classes | 6 || Object properties | 7 || Datatype properties | 4 || Sample instances | 115 || Measurement instances | 2,745 | ### Namespaces ```turtle@prefix fish: <http://example.org/fisheutrust/> .@prefix chebi: <http://purl.obolibrary.org/obo/CHEBI_> .@prefix uo: <http://purl.obolibrary.org/obo/UO_> .@prefix foodon: <http://purl.obolibrary.org/obo/FOODON_> .@prefix ncbitaxon: <http://purl.obolibrary.org/obo/NCBITaxon_> .@prefix pubchem: <http://pubchem.ncbi.nlm.nih.gov/compound/> .``` ### OWL Classes | Class | Description ||-------|-------------|| `fish:FishSample` | A biological sample from a fish specimen || `fish:FishSpecies` | A species of fish || `fish:Measurement` | Abstract measurement class || `fish:IRMSMeasurement` | Isotope ratio measurement (subclass) || `fish:ICPMSMeasurement` | Elemental concentration measurement (subclass) || `fish:ProductionMethod` | Aquaculture or Wild production | ## Requirements ### For using the knowledge base:- Any RDF-compatible triple store (Apache Jena, GraphDB, Blazegraph, Virtuoso, etc.)- Or: Python 3.8+ with rdflib ### For regenerating the knowledge base:- Python 3.8+- rdflib >= 7.0.0- pandas >= 2.0.0- openpyxl >= 3.1.0 ## License This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). You are free to:- **Share** — copy and redistribute the material in any medium or format- **Adapt** — remix, transform, and build upon the material for any purpose, even commercially Under the following terms:- **Attribution** — You must give appropriate credit, provide a link to the license, and indicate if changes were made. ## Citation If you use this knowledge base in your research, please cite: ```bibtex@dataset{fisheutrust_sample_kb_2026, author = {{FishEUTrust Consortium}}, title = {{FishEUTrust Fish Sample Analytical Data Knowledge Base: Semantic Annotation of IRMS and ICP-MS Measurements from Gilthead Seabream}}, year = {2026}, publisher = {Zenodo}, doi = {10.5281/zenodo.XXXXXXX}, url = {https://doi.org/10.5281/zenodo.XXXXXXX}}``` ## Related Resources - [FishEUTrust Project Website](https://fisheutrust.eu/)- [ChEBI - Chemical Entities of Biological Interest](https://www.ebi.ac.uk/chebi/)- [Unit Ontology](http://www.obofoundry.org/ontology/uo.html)- [FoodOn Food Ontology](http://www.obofoundry.org/ontology/foodon.html)- [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy)- [OBO Foundry](http://www.obofoundry.org/) ## Contact For questions or issues regarding this dataset, please contact: - **FishEUTrust Project Team**- Website: [https://fisheutrust.eu/](https://fisheutrust.eu/) ## Version History | Version | Date | Changes ||---------|------|---------|| 1.0.0 | 2026-02 | Initial release with ChEBI, UO, FoodOn, NCBITaxon mappings | ## Acknowledgments We thank:- The European Bioinformatics Institute (EBI) for maintaining ChEBI- The OBO Foundry community for maintaining the ontologies used in this work- Jožef Stefan Institute (JSI) for providing the analytical data