Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics

Version 1 : Received: 13 January 2022 / Approved: 18 January 2022 / Online: 18 January 2022 (11:49:54 CET)

How to cite: Girón, J.C.; Tarasov, S.; González Montaña, L.A.; Matentzoglu, N.; Smith, A.D.; Koch, M.; Boudinot, B.E.; Bouchard, P.; Burks, R.; Vogt, L.; Yoder, M.; Osumi-Sutherland, D.; Friedrich, F.; Beutel, R.; Mikó, I. Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics. Preprints 2022, 2022010254 (doi: 10.20944/preprints202201.0254.v1). Girón, J.C.; Tarasov, S.; González Montaña, L.A.; Matentzoglu, N.; Smith, A.D.; Koch, M.; Boudinot, B.E.; Bouchard, P.; Burks, R.; Vogt, L.; Yoder, M.; Osumi-Sutherland, D.; Friedrich, F.; Beutel, R.; Mikó, I. Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics. Preprints 2022, 2022010254 (doi: 10.20944/preprints202201.0254.v1).

Abstract

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the last 250 years, research on insect systematics has generated hundreds of terms for naming and comparing those phenotypes. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Insect Anatomical Structures (MoDIAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of insect phenotypes. We applied the MoDIAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multi-species anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to (1) use controlled vocabularies and create semi-automated computer-parsable insect morphological descriptions; (2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and (3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This system will allow for clear and semantically interoperable integration of insect phenotypes in biodiversity studies.

Supplementary and Associated Material

https://github.com/insect-morphology/aism: Repository for AISM-related files, including owl file
https://github.com/insect-morphology/Manual: Repository for manual to edir AISM and related ontologies

Keywords

Morphology; insects; biodiversity research; ontology development

Subject

BIOLOGY, Anatomy & Morphology

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