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Investigating One Million XRefs in Thirthy Ontologies from the OBO World

Amir Laadhar 1 Elcio Abrahão 1 Clement Jonquet 1, 2
1 FADO - Fuzziness, Alignments, Data & Ontologies
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 WIMMICS - Web-Instrumented Man-Machine Interactions, Communities and Semantics
CRISAM - Inria Sophia Antipolis - Méditerranée , Laboratoire I3S - SPARKS - Scalable and Pervasive softwARe and Knowledge Systems
Abstract : The more ontologies are produced, the more need to identify mappings between them becomes important. Several practices and tools have been developed to support ontology alignment, but still, it remains a challenge. In the OBO world, ontology developers use cross reference annotations (formally using the oboInOwl:hasDbXRef property) to link a term to an external entity, including another term in another ontology (i.e., a mapping). These XRefs contains information of high value, because they were manually declared/verified by domain experts when the ontology was built. However, extracting and exploiting them remains a challenge for users due to their heterogeneous and chaotic descriptions. In this paper , we report on analysis of approximately 1 million XRefs in 30 ontologies from the OBO world. Our results show that 10.7% of these XRefs are ontology map-pings, but confirm that semantically-ambiguous usage of the cross-reference property which make it impractical or even impossible to reuse. We describe and quantify several issues identified (e.g., different kind of XRefs, miscellaneous formatting , ambiguous targets), and discuss some way to mitigate them especially by using more relevant specific properties taken from standard semantic Web metadata vocabularies.
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Contributor : Amir Laadhar <>
Submitted on : Tuesday, September 22, 2020 - 10:00:25 AM
Last modification on : Friday, October 23, 2020 - 3:59:28 PM


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  • HAL Id : lirmm-02945170, version 1


Amir Laadhar, Elcio Abrahão, Clement Jonquet. Investigating One Million XRefs in Thirthy Ontologies from the OBO World. 11th International Conference on Biomedical Ontologies (ICBO), Sep 2020, Bozen-Bolzano, Italy. ⟨lirmm-02945170⟩



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