@article{balhoff_miko_yoder_mullins_deans_2013, title={A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia}, volume={62}, ISSN={["1076-836X"]}, DOI={10.1093/sysbio/syt028}, abstractNote={Taxonomic descriptions are unparalleled sources of knowledge of life's phenotypic diversity. As natural language prose, these data sets are largely refractory to computation and integration with other sources of phenotypic data. By formalizing taxonomic descriptions using ontology-based semantic representation, we aim to increase the reusability and computability of taxonomists' primary data. Here, we present a revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New Caledonia using this new model for species description. Descriptive matrices, specimen data, and taxonomic nomenclature are gathered in a unified Web-based application, mx, then exported as both traditional taxonomic treatments and semantic statements using the OWL Web Ontology Language. Character:character-state combinations are then annotated following the entity–quality phenotype model, originally developed to represent mutant model organism phenotype data; concepts of anatomy are drawn from the Hymenoptera Anatomy Ontology and linked to phenotype descriptors from the Phenotypic Quality Ontology. The resulting set of semantic statements is provided in Resource Description Framework format. Applying the model to real data, that is, specimens, taxonomic names, diagnoses, descriptions, and redescriptions, provides us with a foundation to discuss limitations and potential benefits such as automated data integration and reasoner-driven queries. Four species of ensign wasp are now known to occur in New Caledonia: Szepligetella levipetiolata, Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster. A fifth species, Szepligetella sericea, including Szepligetella impressa, syn. nov., has not yet been collected in New Caledonia but can be found on islands throughout the Pacific and so is included in the diagnostic key. [Biodiversity informatics; Evaniidae; New Caledonia; new species; ontology; semantic phenotypes; semantic species description; taxonomy.]}, number={5}, journal={SYSTEMATIC BIOLOGY}, author={Balhoff, James P. and Miko, Istvan and Yoder, Matthew J. and Mullins, Patricia L. and Deans, Andrew R.}, year={2013}, month={Sep}, pages={639–659} }
 @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{ernst_miko_deans_2013, title={Morphology and function of the ovipositor mechanism in Ceraphronoidea (Hymenoptera, Apocrita)}, volume={33}, ISSN={["1314-2607"]}, DOI={10.3897/jhr.33.5204}, abstractNote={The ovipositor of apocritan Hymenoptera is an invaluable source of phylogenetically relevant characters, and our understanding of its functional morphology stands to enlighten us about parasitoid life history strategies. Although Ceraphronoidea is one of the most commonly collected Hymenoptera taxa with considerable economic importance, our knowledge about their natural history and phylogenetic relationships, both to other apocritan lineages and within the superfamily itself, is limited. As a first step towards revealing ceraphronoid natural diversity we describe the skeletomuscular system of the ceraphronoid ovipositor for the first time. Dissections and Confocal Laser Scanning Microscopy 3D media files were used to visualize the ovipositor complex and to develop character concepts. Morphological structures were described in natural language and then translated into a character-character state format, whose terminology was linked to phenotype-relevant ontologies. Four unique anatomical phenotypes were revealed: 1. The first valvifer (gonangulum) of the genus Trassedia is composed of two articulating sclerites, a condition present only in a few basal insect taxa. The bipartition of the first valvifer in Trassedia is most likely secondary and might allow more rapid oviposition. 2. Ceraphronoids, unlike other Hymenoptera, lack the retractor muscle of the terebra; instead the egg laying device is retracted by the seventh sternite. 3. Also unlike other Hymenoptera, the cordate apodeme and the anterior flange of the second valvifer are fused and compose one ridge that serves as the site of attachment for the dorsal and ventral T9-second valvifer muscles. Overall, the ceraphronoid ovipositor system is highly variable and can be described by discrete, distinguishable character states. However, these differences, despite their discrete nature, do not reflect the present classification of the superfamily and might represent parallelisms driven by host biology. JHR 33: 25–61 (2013) doi: 10.3897/JHR.33.5204 www.pensoft.net/journals/jhr Copyright Andrew F. Ernst et al. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ReseARCH ARtiCle Andrew F. Ernst et al. / Journal of Hymenoptera Research 33: 25–61 (2013) 26}, journal={JOURNAL OF HYMENOPTERA RESEARCH}, author={Ernst, Andrew F. and Miko, Istvan and Deans, Andrew R.}, year={2013}, pages={25–61} }
 @article{seltmann_yoder_miko_forshages_bertone_agosti_austin_balhoff_borowiec_brady_et al._2012, title={A hymenopterists' guide to the Hymenoptera anatomy ontology: Utility, clarification, and future directions}, volume={27}, journal={Journal of Hymenoptera Research}, author={Seltmann, K. C. and Yoder, M. J. and Miko, I. and Forshages, M. and Bertone, M. A. and Agosti, D. and Austin, A. D. and Balhoff, J. P. and Borowiec, M. L. and Brady, S. G. and et al.}, year={2012}, pages={67–88} }
 @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} }
 @article{vilhelmsen_miko_krogmann_2010, title={Beyond the wasp-waist: structural diversity and phylogenetic significance of the mesosoma in apocritan wasps (Insecta: Hymenoptera)}, volume={159}, number={1}, journal={Zoological Journal of the Linnean Society}, author={Vilhelmsen, L. and Miko, I. and Krogmann, L.}, year={2010}, pages={22–194} }
 @article{miko_deans_2009, title={Masner, a new genus of Ceraphronidae (Hymenoptera, Ceraphronoidea) described using controlled vocabularies}, number={20}, journal={ZooKeys}, author={Miko, I. and Deans, A. R.}, year={2009}, pages={127–153} }