A gross anatomy ontology for hymenoptera

Abstract

Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology, phylogenetic, taxonomic, and morphological research can be actualized. Inherent mechanisms for feedback and content delivery demonstrate the effectiveness of remote, collaborative ontology development and facilitate future refinement of the HAO.

Figure 1. Usage of the term “paramere” as defined in different publications.

The term “paramere” (highlighted in blue) is a homonym in this example, since it is used to describe different classes ( = concepts) in various publications. Within the HAO the A, B, C, D, E overlays respectively refer to the concepts HAO:0000707, HAO:0000395, HAO:0000389, (HAO:0000389+HAO: 0001084), and (HAO:0000707+ HAO:0000389+HAO: 0001084). See Introduction for citations.

Figure 2. Screenshot of the curatorial interface for ontology classes.

The class with labels “propodeum” and “abdominal tergum 1” is illustrated.

Figure 3. Simplified model of the data types in the HAO.

Above- 6 of the 7 major data types, the 7th, a “sensu”, is described in Fig. 4. Below- an example with data from the HAO. A tag is a text annotation that references a keyword (from a configurable controlled vocabulary) and which may have additional notes, in this case the alternative definition. References can be associated in various places to provide additional context, as here in the relationship to a tag.

Figure 4. The sensu model.

A sensu is the combination of a reference, concept and term. Given this model, independent observations (e.g. A–D) can be inferred across to compute synonyms (terms sharing classes), homonyms (a term with many classes), and acts of synonymy and homonymy. For example, given A–D, we can infer that: 1) T1, T2, and T3 are synonyms (all referenced C1); 2) T3 is homonymous (it refers to C1 and C2); and that 3) the author of R1 synonymized T2 and T3. An example from the HAO is provided in E. Here two sensus are defined both referencing the same class, the result being that the labels “phallobase” and “gonocoxite IX” are synonyms.

Figure 5. Illustration of the hierarchy annotation and visualization functionality of the ontology management features of mx.

Top left: is_a hierarchy for all of HAO. Detail: sclerite hierarchy. Colors indicate the number of unique labels for the given class (edge). Tree exported from mx and drawn with Figtree (http://tree.bio.ed.ac.uk/software/figtree/).