A UML profile for the OBO relation ontology

Background: Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results: We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions: The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

A Fuzzy Ontology-Driven Approach to Semantic Interoperability in e-Government Big Data

With the increasing production of information from e-government initiatives, there is also the need to transform a large volume of unstructured data into useful information for society. All this information should be easily accessible and made available in a meaningful and effective way in order to achieve semantic interoperability in electronic government services, which is a challenge to be pursued by governments round the world. Our aim is to discuss the context of e-Government Big Data and to present a framework to promote semantic interoperability through automatic generation of ontologies from unstructured information found in the Internet. We propose the use of fuzzy mechanisms to deal with natural language terms and present some related works found in this area. The results achieved in this study are based on the architectural definition and major components and requirements in order to compose the proposed framework. With this, it is possible to take advantage of the large volume of information generated from e-Government initiatives and use it to benefit society.

Ontology for Data Representation in the Production of Cotton Fiber in Brazil

An important feature in computer systems developed for the agricultural sector is to satisfy the heterogeneity of data generated in different processes. Most problems related with this heterogeneity arise from the lack of standard for different computing solutions proposed. An efficient solution for that is to create a single standard for data exchange. The study on the actual process involved in cotton production was based on a research developed by the Brazilian Agricultural Research Corporation (EMBRAPA) that reports all phases as a result of the compilation of several theoretical and practical researches related to cotton crop. The proposition of a standard starts with the identification of the most important classes of data involved in the process, and includes an ontology that is the systematization of concepts related to the production of cotton fiber and results in a set of classes, relations, functions and instances. The results are used as a reference for the development of computational tools, transforming implicit knowledge into applications that support the knowledge described. This research is based on data from the Midwest of Brazil. The choice of the cotton process as a study case comes from the fact that Brazil is one of the major players and there are several improvements required for system integration in this segment.

An ontology-based approach to define and manage B2B interoperability

Electronic business surely represents the new development perspective for world-wide trade. Together with the idea of ebusiness, and the exigency to exchange business messages between trading partners, the concept of business-to-business (B2B) integration arouse. B2B integration is becoming necessary to allow partners to communicate and exchange business documents, like catalogues, purchase orders, reports and invoices, overcoming architectural, applicative, and semantic differences, according to the business processes implemented by each enterprise. Business relationships can be very heterogeneous, and consequently there are variousways to integrate enterprises with each other. Moreover nowadays not only large enterprises, but also the small- and medium- enterprises are moving towards ebusiness: more than two-thirds of Small and Medium Enterprises (SMEs) use the Internet as a business tool. One of the business areas which is actively facing the interoperability problem is that related with the supply chain management. In order to really allow the SMEs to improve their business and to fully exploit ICT technologies in their business transactions, there are three main players that must be considered and joined: the new emerging ICT technologies, the scenario and the requirements of the enterprises and the world of standards and standardisation bodies. This thesis presents the definition and the development of an interoperability framework (and the bounded standardisation intiatives) to provide the Textile/Clothing sectorwith a shared set of business documents and protocols for electronic transactions. Considering also some limitations, the thesis proposes a ontology-based approach to improve the functionalities of the developed framework and, exploiting the technologies of the semantic web, to improve the standardisation life-cycle, intended as the development, dissemination and adoption of B2B protocols for specific business domain. The use of ontologies allows the semantic modellisation of knowledge domains, upon which it is possible to develop a set of components for a better management of B2B protocols, and to ease their comprehension and adoption for the target users.

An architecture for scaling ontology networks

Constructing ontology networks typically occurs at design time at the hands of knowledge engineers who assemble their components statically. There are, however, use cases where ontology networks need to be assembled upon request and processed at runtime, without altering the stored ontologies and without tampering with one another. These are what we call "virtual [ontology] networks", and keeping track of how an ontology changes in each virtual network is called "multiplexing". Issues may arise from the connectivity of ontology networks. In many cases, simple flat import schemes will not work, because many ontology managers can cause property assertions to be erroneously interpreted as annotations and ignored by reasoners. Also, multiple virtual networks should optimize their cumulative memory footprint, and where they cannot, this should occur for very limited periods of time. We claim that these problems should be handled by the software that serves these ontology networks, rather than by ontology engineering methodologies. We propose a method that spreads multiple virtual networks across a 3-tier structure, and can reduce the amount of erroneously interpreted axioms, under certain raw statement distributions across the ontologies. We assumed OWL as the core language handled by semantic applications in the framework at hand, due to the greater availability of reasoners and rule engines. We also verified that, in common OWL ontology management software, OWL axiom interpretation occurs in the worst case scenario of pre-order visit. To measure the effectiveness and space-efficiency of our solution, a Java and RESTful implementation was produced within an Apache project. We verified that a 3-tier structure can accommodate reasonably complex ontology networks better, in terms of the expressivity OWL axiom interpretation, than flat-tree import schemes can. We measured both the memory overhead of the additional components we put on top of traditional ontology networks, and the framework's caching capabilities.

The Art of Aidagara: Ethics, Aesthetics, and the Quest for an Ontology of Social Existence in Watsuji Tetsurō’s Rinrigaku

This paper provides an analysis of the key term aidagara (“betweenness”) in the philosophical ethics of Watsuji Tetsurō (1889-1960), in response to and in light of the recent movement in Japanese Buddhist studies known as “Critical Buddhism.” The Critical Buddhist call for a turn away from “topical” or intuitionist thinking and towards (properly Buddhist) “critical” thinking, while problematic in its bipolarity, raises the important issue of the place of “reason” versus “intuition” in Japanese Buddhist ethics. In this paper, a comparison of Watsuji’s “ontological quest” with that of Martin Heidegger (1889-1976), Watsuji’s primary Western source and foil, is followed by an evaluation of a corresponding search for an “ontology of social existence” undertaken by Tanabe Hajime (1885-1962). Ultimately, the philosophico-religious writings of Watsuji Tetsurō allow for the “return” of aesthesis as a modality of social being that is truly dimensionalized, and thus falls prey neither to the verticality of topicalism nor the limiting objectivity of criticalism.