The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

Christian S. Wirkner, Torben Göpel, Jens Runge, Jonas Keiler, Bastian Jesper Klussmann-Fricke, Katarina Huckstorf, Stephan Scholz, István Mikó, Matthew Jon Yoder, Stefan Richter

Research output: Contribution to journalArticle

Abstract

Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology.We therefore argue, that formorphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology)may be exerted for a broad use in evolutionary phenomics.To this endwe present thefirst organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions.We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the ontology. That is, descriptions in ontologies are only descriptions of individuals if they are necessary/and or sufficient representations of attributes (independently) observed and recorded for an individual. In addition, we here present for the first time an entirely new approach to formalizing phenotypic research, a semantic model for the description of a complex organ system in a highly disparate taxon, the arthropods.We demonstrate this with a formalizedmorphological description of the hemolymph vascular systemin one specimen of the European garden spider Araneus diadematus.Ourdescription targetsfive categories of descriptive statement: "position", "spatial relationships", "shape", "constituents", and "connections", as the corresponding formalizations constitute exemplary patterns useful not only when talking about the circulatory system, but also in descriptions in general. The downstream applications of computer-parsable morphological descriptions are widespread, with their core utility being the fact that they make it possible to compare collective description sets in computational time, that is, very quickly. Among other things, this facilitates the identification of phenotypic plasticity and variation when single individuals are compared, the identification of those traits which correlate between and within taxa, and the identification of links between morphological traits and genetic (using GO, Gene Ontology) or environmental (usingENVO, Environmental Ontology) factors.

Original languageEnglish (US)
Pages (from-to)754-768
Number of pages15
JournalSystematic biology
Volume66
Issue number5
DOIs
StatePublished - Sep 1 2017

Fingerprint

Systems Integration
cardiovascular system
circulatory system
Arthropods
Cardiovascular System
homology
arthropod
arthropods
Araneus diadematus
Arthropoda
organizational framework
terminology
phenotypic plasticity
Gene Ontology
phenotypic variation
blood vessels
Spiders
Hemolymph
arteries
hemolymph

Keywords

  • Arthropoda
  • concept
  • function
  • hemolymph vascular system
  • homology
  • terminology

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions. / Wirkner, Christian S.; Göpel, Torben; Runge, Jens; Keiler, Jonas; Klussmann-Fricke, Bastian Jesper; Huckstorf, Katarina; Scholz, Stephan; Mikó, István; Yoder, Matthew Jon; Richter, Stefan.

In: Systematic biology, Vol. 66, No. 5, 01.09.2017, p. 754-768.

Research output: Contribution to journalArticle

Wirkner, Christian S. ; Göpel, Torben ; Runge, Jens ; Keiler, Jonas ; Klussmann-Fricke, Bastian Jesper ; Huckstorf, Katarina ; Scholz, Stephan ; Mikó, István ; Yoder, Matthew Jon ; Richter, Stefan. / The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions. In: Systematic biology. 2017 ; Vol. 66, No. 5. pp. 754-768.
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T1 - The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

AU - Wirkner, Christian S.

AU - Göpel, Torben

AU - Runge, Jens

AU - Keiler, Jonas

AU - Klussmann-Fricke, Bastian Jesper

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