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

Abstract

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.

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

“…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].…”

“…Continuing our efforts to develop more and more biodiversity ontologies [41, 24, 42, 7] would allow us to envision increasing semantification of the ecology domain in the near future. Combined with tools such as inteGraph, which facilitate the conversion of biodiversity datasets into graph knowledge bases, these semantic resources could support the creation by different communities of numerous domain-specific KGs, which could eventually be interconnected to form a single biodiversity KG covering the entire tree of life and the full diversity of global ecosystems.…”

“…To reconcile schematic and semantic heterogeneities between our trophic data sources, we will use a global schema consisting of two ontologies: the NCBITaxon ontology and the Soil Food Web Ontology (SFWO) [7]. NCBITaxon is a formal translation of the NCBI Taxonomy database into an ontology, in which each taxon is treated as a class whose instances would be individual organisms, e.g.…”

“…Data integration is of growing interest in the ecological domain, with much efforts directed towards the creation of standard terminologies for describing, sharing and facilitating the aggregation of biodiversity data, e.g. organismal trait data [4, 5, 6, 7], into large open databases. Recent initiatives in trait-based ecology have targeted specific taxonomic groups, e.g.…”

A practical approach to constructing a knowledge graph for soil ecological research

“…Data integration is of growing interest in the ecological domain, with much effort directed towards the creation of standard terminologies for describing, sharing and facilitating the aggregation of biodiversity data, e.g. organismal trait data [4,5,6,7], into large open databases. Recent initiatives in trait-based ecology have targeted specific taxonomic groups, e.g.…”