Initial Implementation of a Comparative Data Analysis Ontology

Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie; Stoltzfus, Arlin

doi:10.4137/ebo.s2320

Cited by 33 publications

(30 citation statements)

References 63 publications

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“…Some of the data relationships shown, such as PHENOSCAPE:exhibits and those from CDAO (Comparative Data Analysis Ontology, [30]), are not explicit in Phenex. Instead, these are generated by the interpretation of NeXML documents within the Phenoscape Knowledgebase data loading software.…”

Section: Resultsmentioning

confidence: 99%

Phenex: Ontological Annotation of Phenotypic Diversity

et al. 2010

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BackgroundPhenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Methodology/Principal FindingsHere we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Conclusions/SignificanceAnnotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

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Section: Resultsmentioning

confidence: 99%

Phenex: Ontological Annotation of Phenotypic Diversity

et al. 2010

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“…1). The OWL-formatted descriptive data were represented using terms from the Comparative Data Analysis Ontology (CDAO) (Prosdocimi et al 2009) and Darwin-SW, an ontology of Darwin Core terms (http://code.google.com/p/darwin-sw/ last accessed May 13, 2013). These data, along with ontologies listed in Table 1, were loaded into Protégé 4.1 (http://protege.stanford.edu/ last accessed May 13, 2013).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2013

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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.]

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“…We searched repositories such as BioPortal [11], Ontobee [12] and AberOWL [13], and identified ontologies containing classes and properties for the entities identified in our analysis. This list of ontologies is described next: Comparative Data Analysis Ontology (CDAO) 1 [14]: Classes and properties relevant for evolutionary studies.Relations Ontology (RO) 2 [15]: Collection of biomedical properties to support standardization across biomedical ontologies.Homology Ontology (HOM) 3 [16]: Classes related to homology.Sequence Ontology (SO) 4 [17]: A set of classes and properties to define sequence features used in biological sequence annotation.Ontology of Genes and Genomes (OGG) 5 [18]: Classes and properties to represent relations among genes, genomes and organisms.Protein Ontology (PR) 6 [19]: Protein-related entities, including evolutionary relations between proteins.Semanticscience Integrated Ontology (SIO) 7 [20]: Classes and properties for rich description of biomedical objects and processes.NCBI Taxonomy (NCBIT) 8 [21]: Curated classification and nomenclature for all the organisms.Clusters of Orthologous Groups Analysis Ontology (CAO) 9 [22]: Classes to support the Clusters of Orthologous Groups enrichment method using Fisher’s exact test.…”

Section: Construction and Contentmentioning

confidence: 99%

“…Comparative Data Analysis Ontology (CDAO) 1 [14]: Classes and properties relevant for evolutionary studies.…”

Section: Construction and Contentmentioning

confidence: 99%

The Orthology Ontology: development and applications

et al. 2016

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BackgroundComputational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide variations in current orthology databases necessitate the research toward the shareability of the content that is generated by different tools and stored in different structures. Exchanging the content with other research communities requires making the meaning of the content explicit.DescriptionThe need for a common ontology has led to the creation of the Orthology Ontology (ORTH) following the best practices in ontology construction. Here, we describe our model and major entities of the ontology that is implemented in the Web Ontology Language (OWL), followed by the assessment of the quality of the ontology and the application of the ORTH to existing orthology datasets. This shareable ontology enables the possibility to develop Linked Orthology Datasets and a meta-predictor of orthology through standardization for the representation of orthology databases. The ORTH is freely available in OWL format to all users at http://purl.org/net/orth.ConclusionsThe Orthology Ontology can serve as a framework for the semantic standardization of orthology content and it will contribute to a better exploitation of orthology resources in biomedical research. The results demonstrate the feasibility of developing shareable datasets using this ontology. Further applications will maximize the usefulness of this ontology.

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Initial Implementation of a Comparative Data Analysis Ontology

Cited by 33 publications

References 63 publications

Phenex: Ontological Annotation of Phenotypic Diversity

Phenex: Ontological Annotation of Phenotypic Diversity

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

The Orthology Ontology: development and applications

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