Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities
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1. The document discusses different approaches to modeling biodiversity data as linked data, including representing taxa as classes or class instances. Representing them the same way across datasets maximizes interlinking but may limit reasoning abilities. 2. It also outlines the differences between modeling from a thesaurus perspective versus a biological perspective. A thesaurus focuses on describing individuals while an ontology can define classes through necessary and sufficient conditions. 3. While pragmatism in modeling linked data can increase interoperability now, it may reduce opportunities for reasoning and inference in the future as perspectives are not fully aligned. Choosing a clear modeling approach is important.
Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities
- 1. 1Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France F. Michel1, C. Faron-Zucker1, S. Tercerie2, O. Gargominy2 1Universit辿 C担te dAzur, CNRS, Inria, I3S, France. 2Service du Patrimoine Naturel, MNHN, CNRS, France. Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities SPNHC+TDWG 2018 Dunedin, New Zealand
- 2. 2Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France Source: Sangya Pundir. https://fr.wikipedia.org/wiki/Fichier:FAIR_data_principles.jpg
- 3. 3Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France LOD Cloud: 1184 datasets, 150B Statements Linking Open Data cloud diagram, 2018. J.P. McCrae, A. Abele, P. Buitelaar, A. Jentzsch, V. Andryushechkin and R. Cyganiak. http://lod-cloud.net/ On the Web, under open licenses Machine-readable (RDF) URIs to name things Common vocabularies Linked with each other Queryable
- 4. 4Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France TAXREF-LD NCBI Taxon TaxonConcept GeoSpecies Plant Ontology ENVO
- 5. 5Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France The Semantic Web is more than the Web of Data The Semantic Web provides an environment where applications can publish and link data, define vocabularies, query data at web scale, and draw inferences. (adapted from W3C website) Linked Data Querying Vocabularies Inference
- 6. 6Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France One class for all taxa AGROVOC thesaurus (skos:Concept) OpenBiodiv-O, EOL trait bank (dwc:Taxon) Wikidata (wd:Q16521) parent/broader Delphinus Delphinus delphis Taxon Model a thing as a class or a class instance? One class per taxonomic rank GeoSpecies, TaxonConcept, DBpedia, BBC WO, BioFid.de hasGenus/broader Delphinus Delphinus delphis Species Genus Delphinus delphis Delphinus subClassOf One class per taxon NCBI Org. Classification, VTO, TAXREF-LD Flipper Thesaurus perspective Biological perspective Taxonomic Rank perspective Flipper
- 7. 7Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France Biological Formal conceptualization of domain knowledge in a machine-processable format Define and organize terms Hierarchy of concepts using subclass of (subsumption), is part of (composition), or other relations Concepts are classes = sets of individuals Classes can be described and/or defined Thesaurus Representation of a domain knowledge in a machine-processable format Define and organize terms Hierarchy of concepts using relations between concepts (broader, narrower, match) Concepts are individuals = class instances Individuals are described Thesaurus vs. Biological perspectives
- 8. 8Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France An individual is described by stating its properties A class can be defined by a set of necessary and/or sufficient membership conditions Description vs. Definition Flipper is a Mammals restriction (habitat, marine) restriction (parental care, none) habitat marine none parental care Delphinus delphis habitat marine Avg. body length 2,44m species none parental care rank Delphinus delphis Avg. body length 2,44m species rank subClassOf
- 9. 9Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France The Semantic Web is more than the Web of Data Linked Data Querying Vocabularies Inference Infer subsumption relationships between classes Classify individuals: compute instance relationships between individuals and classes Improve query answering: query expansion, infer new triples to improve performance Align similar classifications
- 10. 10Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France The Semantic Web is more than the Web of Data Linked Data Querying Vocabularies Inference Infer subsumption relationships between classes Classify individuals: compute instance relationships between individuals and classes Improve query answering: query expansion, infer new triples to improve performance Align similar classifications
- 11. 11Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France Modelling LD requires tackling several questions What is my modelling perspective? For what use? Thesaurus? Ontology? Other? Will I need some type of automatic reasoning eventually? How to maximize interlinking with related datasets? Theoretical issue: DL best practices discourage aligning classes and class instances Linking thesauruses and ontologies not always possible, e.g.: A taxon in NCBI (class) A taxon in Agrovoc (instance of the SKOS concept class) Pragmatism adopt the majority trend to maximize interlinking Taxa = class instances in Agrovoc, EoL, Wikidata, OpenBiodiv-O, DBpedia, GeoSpecies, TaxonConcept Taxa = classes in VTO, NCBI, TAXREF-LD Trade-off between interlinking and reasoning?
- 12. 12Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France Take-home messages The Semantic Web is not just Linked Data. Think of what inference may solve in my context. Choose a modelling perspective for my LD: controlled vocabulary, thesaurus, ontology, Pragmatism can be beneficial in the short term, but may come with a price.
- 13. 13Franck MICHEL - Universit辿 C担te dAzur, CNRS, Inria, I3S, France Citation: Michel F., Faron-Zucker C., Tercerie S. and Gargomony O. (2018). Modelling Biodiversity Linked Data: Pragmatism May Narrow Future Opportunities. Biodiversity Information Science and Standards 2: e26235. https://doi.org/10.3897/biss.2.26235 Thank you