A common framework for developing robust soil fauna classifications

Hedde, Mickaël; Blight, Olivier; Briones, Maria J.I.; Bonfanti, Jonathan; Brauman, Alain; Brondani, Margot; Sanou, Irene Calderón; Clause, Julia; Conti, Erminia; Cortet, Jérôme; Decaëns, Thibaud; Erktan, Amandine; Gérard, Sylvain; Goulpeau, Arnaud; Iannelli, Maeva; Joimel-Boulanger, Sophie; Jouquet, Pascal; Guillarme, Nicolas Le; Marsden, Claire; Almoyna, Camille Martinez; Mulder, Christian; Perrin, William F.; Pétillon, Julien; Pey, Benjamin; Potapov, Anton M.; Si-Moussi, Sara; Thuiller, Wilfried; Trap, Jean; Vergnes, Alan; Zaitsev, Andrey S.; Capowiez, Yvan

doi:10.1016/j.geoderma.2022.116073

Cited by 24 publications

(25 citation statements)

References 134 publications

(133 reference statements)

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“…Example of a SPARQL query returning the trophic groups to which Entomobrya ligata belongs. A trophic group is defined in the Soil Food Web Ontology as “a collection of organisms that feed on the same food sources and have the same consumers”[7, 30]. SFWO provides a logical formalization of the hierarchical classification of soil consumers proposed in [39].…”

Section: Resultsmentioning

confidence: 99%

“…Large trait databases have the potential to address this trade-off between feasibility and completeness. By supporting the assignment of species (or higher taxonomic ranks) to trophic and/or functional groups, they reduce the dimensionality of ecological communities without biasing studies toward a single trophic level or taxonomic group [30, 15]. Yet, challenges remain: although we have trait databases available for some of them, our trait knowledge is limited for most groups of soil organisms.…”

Section: Methodsmentioning

confidence: 99%

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A Practical Approach to Constructing a Knowledge Graph for Soil Ecological Research

Guillarme

Thuiller

2023

Preprint

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With the rapid accumulation of biodiversity data, data integration has emerged as a hot topic in soil ecology. Data integration has indeed the potential to advance our knowledge of global patterns in soil biodiversity by facilitating large-scale meta-analytical studies of soil ecosystems. However, ecologists are still poorly equipped when it comes to integrating disparate datasets into a unified knowledge graph with well-defined semantics. This paper presents a practical approach to constructing a knowledge graph from heterogeneous and distributed (semi-)structured data sources. To illustrate our approach, we integrate several datasets on the trophic ecology of soil organisms into a trophic knowledge graph and show how information can be retrieved from the graph to support multi-trophic studies.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A Practical Approach to Constructing a Knowledge Graph for Soil Ecological Research

Guillarme

Thuiller

2023

Preprint

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“…To deal with this huge diversity in forms and functions, soil biologists resort to classifying belowground biodiversity into guilds of organisms sharing similar niche requirements, or functional groups of organisms acting similarly on a specific ecological function [3]. In particular, when studying multitrophic assemblages, a common approach is to group organisms either into 'feeding guilds' of organisms that feed on the same resources, or into 'trophic groups' of organisms that both feed on the same resources and have the same consumers [3]. Classifying organisms into relevant trophic groups simplifies food web analysis by allowing the construction of tractable food web models across the whole spectrum of soil organisms [4].…”

Section: Introductionmentioning

confidence: 99%

The Soil Food Web Ontology: aligning trophic groups, processes, resources, and dietary traits to support food-web research

Guillarme

Hedde

Potapov

et al. 2023

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Although soil ecology has benefited from recent advances in describing soil organism trophic traits, large scale reconstruction of soil food webs is still impeded by (1) the dissemination of most data about trophic interactions and diets into distributed, heterogeneous repositories, (2) no well-established terminology for describing feeding preferences, processes, and resource types, and (3) much heterogeneity in the classification of different soil groups, or absence of such classifications. Soil trophic ecology could therefore benefit from standardisation efforts. Here, we propose the Soil Food Web Ontology as a new formal framework for representing knowledge on trophic ecology of soil organisms. This ontology captures the semantics of trophic concepts, including consumer-resource interactions, feeding preferences and processes, and provides a formalisation of trophic group definitions. The ontology can be used to add semantic annotations to trophic data, thus facilitating the integration of heterogeneous datasets. It also provides lexical resources that can support the development of information extraction tools to facilitate literature-based datasets creation. Finally, it enables automatic and consistent classification of soil organisms based on their trophic relationships. We argue that, by harmonising the terminology and underlying concepts of soil trophic ecology, our ontology allows for better use of available information on the feeding habits of soil organisms and sounder classifications, thus facilitating the reconstruction of soil food webs and making food web research more accessible, reusable and reproducible.

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“…The Special Issue contains six articles, divided into two parts. The first three articles proposed conceptual links between soil invertebrate traits and soil functioning, either globally (Hedde et al, 2022), in the context of ecological restoration (Auclerc et al, 2022) or to understand soil organic matter turnover (Coq et al, 2022). The three remaining articles experimentally explored these links for ecosystem engineers, such as earthworms (Le ) and termites (Jouquet et al, 2022) and for microbial-feeding nematodes (Brondani et al, 2022).…”

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confidence: 99%

“…The three remaining articles experimentally explored these links for ecosystem engineers, such as earthworms (Le ) and termites (Jouquet et al, 2022) and for microbial-feeding nematodes (Brondani et al, 2022). Hedde et al (2022) challenged the definition of various soil fauna classification. They provide a critical overview of the characteristics and limitations of the existing classifications in soil ecology, and propose clarifications and alternatives to current practices.…”

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confidence: 99%