Suite Of Ontologies Research Articles

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals.

GWAS Atlas (https://bigd.big.ac.cn/gwas/) is a manually curated resource of genome-wide variant-trait associations for a wide range of species. Unlike existing related resources, it features comprehensive integration of a high-quality collection of 75 467 variant-trait associations for 614 traits across 7 cultivated plants (cotton, Japanese apricot, maize, rapeseed, rice, sorghum and soybean) and two domesticated animals (goat and pig), which were manually curated from 254 publications. We integrated these associations into GWAS Atlas and presented them in terms of variants, genes, traits, studies and publications. More importantly, all associations and traits were annotated and organized based on a suite of ontologies (Plant Trait Ontology, Animal Trait Ontology for Livestock, etc.). Taken together, GWAS Atlas integrates high-quality curated GWAS associations for animals and plants and provides user-friendly web interfaces for data browsing and downloading, accordingly serving as a valuable resource for genetic research of important traits and breeding application.

An Ontological Approach to Meaning Making through PATH and Gestalt Foregrounding in Climax

Climax is a compound rhetorical figure, consisting of the trope, Crementum, and the scheme, Gradatio (itself a series of Anadiploses), a combination that results in compelling semiotic effects. The component figures impact the conveyed meaning independently and collectively, which we chart by way of the PATH image schema and the Gestalt Figure-Ground relation. These layers of meaning function in a similar fashion to the dual figure visual phenomenon examined by Koffka and Rubin. Key elements of our project include knowledge representation of Climax and component figures, a suite of ontologies that map the cognitive features supporting these complex structures and a base model of surface entities augmented with the related cognitive functions. Our ontologies are developed in the Web Ontology Language (OWL), validated for consistency and published online.

Using a Suite of Ontologies for Preserving Workflow-Centric Research Objects

Using a Suite of Ontologies for Preserving Workflow-Centric Research Objects

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

BackgroundThe Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.DescriptionRecently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases.ConclusionsIn this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

Towards a satisfactory conversion of messages among agent-based information systems

Over the last years, there has been a change of perspective concerning the management of information systems, since they are no longer isolated and need to communicate with others. However, from a semantic point of view, real communication is difficult to achieve due to the heterogeneity of the systems. We present a proposal which, considering information systems are represented by software agents, provides a framework that favors a semantic communication among them, overcoming the heterogeneity of their agent communication languages. The main components of the framework are a suite of ontologies – conceptualizing communication acts – that will be used for generating the communication conversion, and an Event Calculus interpretation of the communications, which will be used for formalizing the notion of a satisfactory conversion. Moreover, we present a motivating example in order to complete the explanation of the whole picture.

Design and Development of Ontology Suite for Software Risk Planning, Software Risk Tracking and Software Risk Control

Problem statement: Ontology as a conceptual courseware structure may work as a mind tool for effective teaching and as a visual navigation interface to the learning objects. Knowledge visualization is defined as the use of visual representations to transfer knowledge between at least two persons. This study presents the design, development and visualization of ontologies for Software Risk Planning, Software Risk Tracking and Software Risk Controlling. Approach: The ontologies are developed using protege tool, an effective ontology editor and it is represented by the formal knowledge representational language OWL. In order to increase the richness of the knowledge available in the ontologies, its semantic representation is presented using ontology document generator. Finally the ontologies are effectively visualised using OntoViz. Results: The ontologies represent the domain knowledge Software Risk Planning, Software Risk Tracking and Software Risk Controlling respectively and is developed with the indention to use it as a knowledge base for effective knowledge representation, Knowledge Management and E-Learning applications. The constructed ontologies are evaluated using quantitative analysis and qualitative analysis. Conclusion: Since the average reuse ratio is 0.95, the developed ontologies are highly cohesive. Comparison of concepts and properties used in the ontologies proved that the developed ontologies are concept oriented ontology. The both quantitative and qualitative analysis says, the developed ontologies are ready to use for applications such as E-Learning, Knowledge Management.