Biodiversity and Ecology track (biodiv)

General description

The main aim of this track is to motivate and attract ontology matching systems to work on matching ontologies and thesauri used in the biodiversity and ecology domains and available via the BiodivPortal ontology repository. In the current edition, we decided to keep the matching task to find alignments between the Environment Ontology (ENVO) and the Semantic Web for Earth and Environment Technology Ontology (SWEET) as these two ontologies have frequent updates.

We address since 2021, the alignment of two new biological taxonomies with rather different but complementary scopes: the well-known, world-wide NCBI taxonomy, and TAXREF-LD [3], a more fined-grained, manually curated taxonomy that spans French metropolitan and overseas territories. A challenging aspect is the discrepancies between (1) the size and scope of both taxonomies, and (2) the RDF model to account for taxonomy and nomenclatural information.

In 2023, we partnered with the EcoPortal project to include two new matching tasks involving important thesauri in environmental sciences (originally developed in SKOS): finding alignments between the Macroalgae Traits Thesaurus (MACROALGAE) and the Macrozoobenthos Traits Thesaurus (MACROZOOBENTHOS) and between the Fish Traits Thesaurus (FISH) and the Zooplankton Traits Thesaurus (ZOOPLANKTON).

Results

The preliminary results have been generated and are available now: link to results page.

Dataset

The biodiv dataset (4 ontologies, 4 thesauri and 4 reference alignments together with modules for the bigger matching task) can be downloaded here.

Schedule

The schedule is available at the OAEI main page.

Former editions

OAEI 2022: [description] [results]
OAEI 2021: [description] [results]
OAEI 2020: [description] [results]
OAEI 2019: [description] [results]
OAEI 2018: [description] [results]

Organizers

Naouel Karam (Fraunhofer FOKUS & InfAI e.V., Berlin, Germany), main contact for the track: naouel [.] karam [at] fokus [.] fraunhofer [.] de
Alsayed Algergawy (Friedrich Schiller University Jena, Germany)

Acknowledgements

The track is supported by the AquaDiva, the NFDI4Biodiversity and the EcoPortal projects.

We would like to thank Jessica Titocci, Martina Pulieri and Ilaria Rosati for their support and for providing the datasets for the MACROALGAE-MACROZOOBENTHOS and FISH-ZOOPLANKTON tasks.

References

[1] Naouel Karam, Abderrahmane Khiat, Alsayed Algergawy, Melanie Sattler, Claus Weiland, Marco Schmidt: Matching biodiversity and ecology ontologies: challenges and evaluation results. Knowledge Eng. Review 35: e9 (2020).

[2] F. Michel, O. Gargominy, S. Tercerie and C. Faron-Zucker: A Model to Represent Nomenclatural and Taxonomic Information as Linked Data. Application to the French Taxonomic Register, TAXREF. 2nd workshop on Semantics for Biodiversity (S4BioDiv), 2017.