BFO: Basic Formal Ontology1

Otte, J. Neil; Beverley, John; Ruttenberg, Alan

doi:10.3233/ao-220262

Cited by 38 publications

(17 citation statements)

References 22 publications

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“…objects, attributes and spatial regions, and occurrent, e.g. processes and temporal regions (Otte et al, 2022). In SFWO, an organism is either (1) a taxon, e.g.…”

Section: Individual (Instance)mentioning

confidence: 99%

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

Guillarme

Hedde

Potapov

et al. 2023

Preprint

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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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“…objects, attributes and spatial regions, and occurrent, e.g. processes and temporal regions (Otte et al, 2022). In SFWO, an organism is either (1) a taxon, e.g.…”

Section: Individual (Instance)mentioning

confidence: 99%

“…Research 11 (BIOfid), which aims at extracting structured data from legacy Central European literature through semantic role labelling. With its large and ever-increasing terminology related to soil trophic ecology, SFWO is a valuable lexical resource for trophic information extraction.…”

Section: Trophic Information Extractionmentioning

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

Preprint

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“…In the domain of life science, BFO ( 81 , 82 ), the Basic Formal Ontology has found the widest acceptance. Figure 3 demonstrates its upper level.…”

Section: Ontological Perspectivementioning

confidence: 99%

Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems

et al. 2023

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This paper provides an overview of current linguistic and ontological challenges which have to be met in order to provide full support to the transformation of health ecosystems in order to meet precision medicine (5 PM) standards. It highlights both standardization and interoperability aspects regarding formal, controlled representations of clinical and research data, requirements for smart support to produce and encode content in a way that humans and machines can understand and process it. Starting from the current text-centered communication practices in healthcare and biomedical research, it addresses the state of the art in information extraction using natural language processing (NLP). An important aspect of the language-centered perspective of managing health data is the integration of heterogeneous data sources, employing different natural languages and different terminologies. This is where biomedical ontologies, in the sense of formal, interchangeable representations of types of domain entities come into play. The paper discusses the state of the art of biomedical ontologies, addresses their importance for standardization and interoperability and sheds light to current misconceptions and shortcomings. Finally, the paper points out next steps and possible synergies of both the field of NLP and the area of Applied Ontology and Semantic Web to foster data interoperability for 5 PM.

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“…This paper leverages categories and relations that are relatively widely accepted in upper ontologies. In particular, it avails of the general structure of upper ontologies that have the category of disposition (which is vital for theorizing on core affordances) such as Basic Formal Ontology (Arp et al, 2015;Otte et al, 2022) and the Unified Foundational Ontology (Guizzardi, 2005;Guizzardi et al, 2015Guizzardi et al, , 2022. In the first place, a distinction is drawn between instances (synonym: "particular", "individual") and classes (synonym: "universal", "kind").…”

Section: Basic Ontological Frameworkmentioning

confidence: 99%

Affordances and their ontological core

Toyoshima

Barton

Éthier

2022

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The notion of affordance remains elusive, notwithstanding its importance for the representation of agency, cognition, and behaviors. This paper lays down a foundation for an ontology of affordances by elaborating the idea of “core affordance” which would serve as a common ground for explaining existing diverse conceptions of affordances and their interrelationships. For this purpose, it analyzes M. T. Turvey’s dispositional theory of affordances in light of a formal ontology of dispositions. Consequently, two kinds of so-called “core affordances” are proposed: specific and general ones. Inspired directly by Turvey’s original account, a specific core affordance is intimately connected to a specific agent, as it is reciprocal with a counterpart effectivity (which is a disposition) of this agent within the agent-environment system. On the opposite, a general core affordance does not depend on individual agents; rather, its realization involves an action by an instance of a determinate class of agents. The utility of such core affordances is illustrated by examining how they can be leveraged to formalize other major accounts of affordances. Additionally, it is briefly outlined how core affordances can be employed to analyze three notions that are closely allied with affordances: the environment, image schemas, and intentions.

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BFO: Basic Formal Ontology1

Cited by 38 publications

References 22 publications

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

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

Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems

Affordances and their ontological core

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