@article{bertone_miko_yoder_seltmann_balhoff_deans_2013, title={Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment}, ISSN={["1758-0463"]}, DOI={10.1093/database/bas057}, abstractNote={Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each ontology or gaps in representing each group’s anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process. Database URL: http://purl.obolibrary.org/obo/hao/2012-07-18/arthropod-mappings.obo}, journal={DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION}, author={Bertone, Matthew A. and Miko, Istvan and Yoder, Matthew J. and Seltmann, Katja C. and Balhoff, James P. and Deans, Andrew R.}, year={2013}, month={Jan} }
 @article{miko_friedrich_yoder_hines_deitz_bertone_seltmann_wallace_deans_2012, title={On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0030137}, abstractNote={A spectacular hypothesis was published recently, which suggested that the “helmet” (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the “helmet” was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the “helmet” could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the “helmet”-wing homology, the relationship of the “helmet” to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the “helmet”-wing homology hypothesis as originally conceived: 1) the “helmet” actually represents T1 (excluding the fore legs); 2) the “T1 tergum” is actually the anterior dorsal area of T2; 3) the putative articulation between the “helmet” and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies.}, number={1}, journal={PLOS ONE}, author={Miko, Istvan and Friedrich, Frank and Yoder, Matthew J. and Hines, Heather M. and Deitz, Lewis L. and Bertone, Matthew A. and Seltmann, Katja C. and Wallace, Matthew S. and Deans, Andrew R.}, year={2012}, month={Jan} }
 @article{yoder_miko_seltmann_bertone_deans_2010, title={A Gross Anatomy Ontology for Hymenoptera}, volume={5}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0015991}, abstractNote={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.}, number={12}, journal={PLOS ONE}, author={Yoder, Matthew J. and Miko, Istvan and Seltmann, Katja C. and Bertone, Matthew A. and Deans, Andrew R.}, year={2010}, month={Dec} }