DOI: 10.5061/dryad.kv62d
title: Data from: The first organ-based ontology for arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its integration into a novel formalization scheme for morphological descriptions

description: 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 for morphological 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 end we present the first 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 formalized
 morphological description of the hemolymph vascular system in one specimen
 of the European garden spider Araneus diadematus. Our description targets
 five 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 (using ENVO, Environmental Ontology) factors.
description: Ad69_formal_description_2015-12-11Wordfile containing a formalized description of circulatory organ features of the specimen Ad69 of the Common Garden Spider (Araneus diadematus)Ad69_formal_description_2016-10-07OWL file containing a formalized description of circulatory organ features of the specimen Ad69 of the Common Garden Spider (Araneus diadematus).Ad69_semantic_statements_12112015.owlOArCS_2016-10-21OWL file containing the Ontology of Arthropod Circulatory Systems (OArCS)oarcs.owlAd69_semantic_statements_12112015OWL file containing semantic statements in Manchester syntax describing circulatory features in the specimen Ad69 of the Common Garden Spider (Araneus diadematus)