A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia

Balhoff, James P.; Mikó, István; Yoder, Jeffrey A.; Mullins, Patricia L.; Deans, Andrew R.

doi:10.1093/sysbio/syt028

Cited by 58 publications

(74 citation statements)

References 34 publications

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“…Furthermore, the PhenomeNET ontology imports the ChEBI [32] and Mouse Pathology [33] ontologies using an OWL import statement. Additionally, PhenomeNET includes all classes from the UBERON, the GO, the BioSpatial Ontology [34], the Zebrafish Anatomy ontology [35], the PATO ontology [4], the Cell Ontology [36], and the Neuro-Behavior Ontology [37]. However, these ontologies are not directly imported but rather pre-processed so that all disjointness axioms from these ontologies are excluded while all other axioms contained within them are included in the PhenomeNET ontology.…”

Section: Resultsmentioning

confidence: 99%

Integrating phenotype ontologies with PhenomeNET

et al. 2017

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BackgroundIntegration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast.ResultsHere, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies.ConclusionsPhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s13326-017-0167-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Integrating phenotype ontologies with PhenomeNET

et al. 2017

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“…Statements were written in OWL Manchester Syntax (see examples from Balhoff et al 2014, Balhoff et al 2013, Mikó et al 2015, Mikó et al 2014). All definitions and descriptions of morphological structures were mapped to classes in phenotype-focused ontologies, including: Hymenoptera Anatomy Ontology (HAO), Phenotypic Quality Ontology (PATO), Biospatial Ontology (BSPO), OBO Relation Ontology (RO), Ontology for Biomedical Investigations (OBI) and Information Artifact Ontology (IAO); these ontologies are available at http://www.ontobee.org (Xiang et al 2011).…”

Section: Methodsmentioning

confidence: 99%

“…All definitions and descriptions of morphological structures were mapped to classes in phenotype-focused ontologies, including: Hymenoptera Anatomy Ontology (HAO), Phenotypic Quality Ontology (PATO), Biospatial Ontology (BSPO), OBO Relation Ontology (RO), Ontology for Biomedical Investigations (OBI) and Information Artifact Ontology (IAO); these ontologies are available at http://www.ontobee.org (Xiang et al 2011). By standardising taxonomic data through ontology-based semantic representation, we aim to facilitate future systematic work by facilitating the integration of taxonomic data sets from different sources, expediting computerised searches across these data (Balhoff et al 2013, Deans et al 2012, Mikó et al 2014). …”

Section: Methodsmentioning

confidence: 99%

Unique extrication structure in a new megaspilid, Dendrocerus scutellaris Trietsch & Mikó (Hymenoptera: Megaspilidae)

Trietsch

István

Notton

et al. 2018

BDJ

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531

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BackgroundA new species, Dendrocerus scutellaris Trietsch & Mikó (Hymenoptera: Megaspilidae), is described here from male and female specimens captured in Costa Rica. This species is the only known ceraphronoid wasp with a straight mandibular surface and raised dorsal projections on the scutellum, called the mesoscutellar comb. It is hypothesised that the function of the mesoscutellar comb is to aid the emergence of the adult from the host, especially since the mandibles lack a pointed surface to tear open the pupal case. The authors also provide phenotypic data in a semantic form to facilitate data integration and accessibility across taxa and provide an updated phenotype bank of morphological characters for megaspilid taxonomic treatments. In updating this phenotype bank, the authors continue to make taxonomic data accessible to future systematic efforts focusing on Ceraphronoidea.New informationA new species, Dendrocerus scutellaris (Hymenoptera: Megaspilidae) Trietsch & Mikó, is described from both male and female specimens captured in Costa Rica.

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“…material 2.) were composed in Protégé 5.0 (http://protege.stanford.edu/) using the OWL Manchester syntax (http://www.w3.org/TR/owl2-manchester-syntax/) following Balhoff et al (2013) and Mikó et al (2014). The full data set, represented in OWL (Web Ontology Language; http://www.w3.org/TR/owl2-overview/ last accessed February 4, 2014), was deposited as a Resource Description Framework (RDF)-XML file (http://www.w3.org/ TR/REC-rdf-syntax/ in Figshare (https://dx.doi.org/10.6084/m9.figshare.2008203).…”

Section: Methodsmentioning

confidence: 99%