Impacts on Genome Science
From HAO Wiki
Hymenoptera play increasingly important roles in genome-level research, with one whole genome completed (the honey bee, Apis mellifera), one in assembly (a parasitoid wasp, Nasonia vitripennis), and one in progress (Nasonia longicornis). The members of this knowledge domain require ontology-enabled tools to annotate genes and gene expression data. The current gene annotation workflow employs software that searches for open reading frames (ORFs; sequences that potentially encode proteins) and attempts to predict their function based on existing knowledge of the Drosophila melanogaster genome. A gene that is identified as being involved in “haltere” development (e.g. Weatherbee et al. 1998), however, is meaningless with respect to Apis and Nasonia; the haltere is a modified, stub-like hind wing found only in flies (Diptera). In this case, a Hymenoptera anatomical ontology mapped to the Mosquito and Drosophila Gross Anatomy Ontology would greatly facilitate the transfer of this knowledge by identifying the haltere as structurally homologous to "hind wing."
Further evidence for a new anatomical ontology
Aside from the terminological omissions and inconsistencies between the model organisms and the megadiverse lineage Hymenoptera, other conditions clearly point to the need for development of a broad, Hymenoptera-specific ontology that maps to existing model organism ontologies. The Drosophila Gross Anatomy Ontology (DGAO), for example, was specifically developed for the annotation of mutant phenotypes in FlyBase and their associated genetic causes, as well as for the description of transcript and protein expression patterns in Drosophilidae (Grumbling et al. 2006). Unlike in our effort to develop the HO, however, DGAO developers did not intend to be exhaustive in their coverage of terminology, nor did they seek to reference each concept with a publication or to typify these concepts with instances – which are critical to understanding the contexts of these terms. Flybase is partially illustrated (872 images, mostly interpretive line drawings, for 6,125 terms), but some illustrations include multiple structures, with no indication as to which one an image typifies (i.e., no annotations). As the Apis (BeeSpace) and Nasonia genomes mature, researchers will require anatomical ontologies that refer to structures in these organisms. The HAO will satisfy this role with exceptional transparency and with substantial input from these users.
Benefiting from the HO in genome science
Many of the genes originally described in Drosophila, of course, are also found in hymenopterans and indeed most of Life (Crozier & Crozier 1993). Intuitively, one would expect that the historical continuity of morphological characters is underpinned by the continuity of the genes that govern the development of these characters. As interest in the mechanisms that underpin phenotypic expression proliferates, anatomical ontologies will be increasingly employed to mine genomes for genes/gene families to target for further exploration (e.g., see Mabee et al. 2007a, b for examples of how existing tools, mainly Phenote and the teleost anatomy ontology, are being employed to explore the zebrafish mutant phenotype library for candidate genes involved in wildtype phenotypes of non-model fishes). A potential example in Hymenoptera: several major lineages of Hymenoptera (Proctotrupoidea, Cynipoidea, Ichneumonoidea, Evanioidea) are defined, in part, by the absence of the tergal depressor of trochanter (a muscle involved in the movement of legs). In Drosophila we know that a point mutation in one gene, troponin I, resulted in the absence of the tergal depressor of trochanter. Are there mutations in this gene or family of genes in those lineages of Hymenoptera? These kinds of data explorations will be enabled by a Hymenoptera anatomy ontology mapped to the insect model organism anatomy ontologies. Numerous such discoveries undoubtedly remain hidden by disparities in language.