The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data

Martín J Ramírez,Peter Michalik

doi:10.3390/d11100202

Abstract

Spiders are a diverse group with a high eco-morphological diversity, which complicates anatomical descriptions especially with regard to its terminology. New terms are constantly proposed, and definitions and limits of anatomical concepts are regularly updated. Therefore, it is often challenging to find the correct terms, even for trained scientists, especially when the terminology has obstacles such as synonyms, disputed definitions, ambiguities, or homonyms. Here, we present the Spider Anatomy Ontology (SPD), which we developed combining the functionality of a glossary (a controlled defined vocabulary) with a network of formalized relations between terms that can be used to compute inferences. The SPD follows the guidelines of the Open Biomedical Ontologies and is available through the NCBO BioPortal (ver. 1.1). It constitutes of 757 valid terms and definitions, is rooted with the Common Anatomy Reference Ontology (CARO), and has cross references to other ontologies, especially of arthropods. The SPD offers a wealth of anatomical knowledge that can be used as a resource for any scientific study as, for example, to link images to phylogenetic datasets, compute structural complexity over phylogenies, and produce ancestral ontologies. By using a common reference in a standardized way, the SPD will help bridge diverse disciplines, such as genomics, taxonomy, systematics, evolution, ecology, and behavior.

Highlights

Spiders are an impressively diverse group that have specialized to very diverse habitats, life styles, and preys [1]
The names of these structures may be widely used in animals, in other arthropods, or only arachnids, while some are specific to spiders or even to definite spider groups
Similar to many other taxa [2], morphological terminology is plagued with complications such as synonyms, subtle differences, disputed definitions, ambiguities, same name used for different structures, functional names for structurally different structures, and misleading

Summary

Introduction

Spiders are an impressively diverse group that have specialized to very diverse habitats, life styles, and preys [1]. The Spider Anatomy Ontology (SPD) provides an open repository for anatomical terms and a forum where researchers and users with different background can discuss and refine definitions, argue about preferred names, correct mistakes, or contribute new terms. Anatomical ontologies were originally designed for cross-disciplinary work over large communities, especially to link phenotypic and genetic data (where the genes are expressed, what organ affects a gene inactivation or mutant), with the objective to accumulate knowledge and mining the data for potential genotype–phenotype associations [21] For this reason, only some parts of the ontology are friendly to the human eye (i.e., the definitions, many of the relations between entities), while other components are more technical or abstract, intended for automated computation and compatibility (e.g., the alphanumeric identifiers, some higher-level abstract entities). Synonyms: We used exact synonyms for interchangeable names with the same definition (e.g., abdomen and opisthosoma), and related synonyms for terms that are often used with similar meaning but do not correspond exactly (maxillary gland and sieve plate)

How to Contribute

Limitations and Future