The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

The Aedes aegypti larval transcriptome: a comparative perspective with emphasis on trypsins and the domain structure of peritrophins

The genome sequence of Aedes aegypti was recently reported. A significant amount of Expressed Sequence Tags (ESTs) were sequenced to aid in the gene prediction process. In the present work we describe an integrated analysis of the genomic and EST data, focusing on genes with preferential expression in larvae (LG), adults (AG) and in both stages (SG). A total of 913 genes (5.4% of the transcript complement) are LG, including ion transporters and cuticle proteins that are important for ion homeostasis and defense. From a starting set of 245 genes encoding the trypsin domain, we identified 66 putative LG, AG, and SG trypsins by manual curation. Phylogenetic analyses showed that AG trypsins are divergent from their larval counterparts (LG), grouping with blood-induced trypsins from Anopheles gambiae and Simulium vittatum. These results support the hypothesis that blood-feeding arose only once, in the ancestral Culicomorpha. Peritrophins are proteins that interlock chitin fibrils to form the peritrophic membrane (PM) that compartmentalizes the food in the midgut. These proteins are recognized by having chitin-binding domains with 6 conserved Cys and may also present mucin-like domains (regions expected to be highly O-glycosylated). PM may be formed by a ring of cells (type 2, seen in Ae. aegypti larvae and Drosophila melanogaster) or by most midgut cells (type 1, found in Ae. aegypti adult and Tribolium castaneum). LG and D. melanogaster peritrophins have more complex domain structures than AG and T. castaneum peritrophins. Furthermore, mucin-like domains of peritrophins from T. castaneum (feeding on rough food) are lengthier than those of adult Ae. aegypti (blood-feeding). This suggests, for the first time, that type 1 and type 2 PM may have variable molecular architectures determined by different peritrophins and/or ancillary proteins, which may be partly modulated by diet.

Ontology learning from text: a soft computing paradigm

Text-based information accounts for more than 80% of today’s Web content. They consist of Web pages written in different natural languages. As the semantic Web aims at turning the current Web into a machine-understandable knowledge repository, availability of multilingual ontology thus becomes an issue at the core of a multilingual semantic Web. However, multilingual ontology is too complex and resource intensive to be constructed manually. In this paper, we propose a three-layer model built on top of a soft computing framework to automatically acquire a multilingual ontology from domain specific parallel texts. The objective is to enable semantic smart information access regardless of language over the Semantic Web.

An ontology-driven topic mapping approach to multi-level management of e-learning resources

An appropriate use of various pedagogical strategies is fundamental for the effective transfer of knowledge in a flourishing e-learning environment. The resultant information superfluity, however, needs to be tackled for developing sustainable e-learning. This necessitates an effective representation and intelligent access to learning resources. Topic maps address these problems of representation and retrieval of information in a distributed environment. The former aspect is particularly relevant where the subject domain is complex and the later aspect is important where the amount of resources is abundant but not easily accessible. Conversely, effective presentation of learning resources based on various pedagogical strategies along with global capturing and authentication of learning resources are an intrinsic part of effective management of learning resources. Towards fulfilling this objective, this paper proposes a multi-level ontology-driven topic mapping approach to facilitate an effective visualization, classification and global authoring of learning resources in e-learning.

An ontology-based learning resources management framework for exploratory e-learning

This paper presents an ontology-based conceptual framework for effectively managing exploratory e-learning resources. The proposed framework has five significant novel features including authentication of retrieved resources, automatic ontology-based query refinement, reuse-oriented management of retrieved resources, adaptive retrieval of learning resources based on the style and preference of individual learners, and synthesisation of retrieval and management activities for creating reusable learning repositories. The applicability of the framework is demonstrated using a sample fragment of an ontology developed in the database domain.

Capture, hold, release: an ontology of motion capture

In proposing an ontology of motion capture, this paper identifies three modalities — capture, hold, release — to conceptualise the peculiar affordances of motion capture technology in its relationship to a performer's movement. Motion capture is unique among contemporary moving image media in its capacity to re-perform a performer'srecorded movement a potentially limitless number of times, e.g. as applied to innumerable different CG characters. Unlike live-action film or even rotoscoping (motion capture's closest equivalent), the movement extracted from the captured performance lives on, but only by way of the inimagable (non-visible) domain of motion data.Motion data 'holds' movement itself in inimagable form, and 'releases' it in the domain of the digital moving image. This tri-fold conception relates an important dimension of (Heideggerian) Being to the idea of movement as fundamental to an ontology or 'being' of motion capture. At the same time, the proposed ontology challenges the 'illusion of life' metaphor as the accepted definition of (motion capture) animation.The Oscar's Special Rules for the Animated Feature Film Award asserts that 'by itself' motion capture does not qualify as an animation method. The notion that a technology could do or be anything 'by itself' affords a conceptual leap toward Heideggerian thinking on the nature of Being as embodied in temporality, in which past, present and future are unified.In its capacity to operate outside the domain of the digital moving image, the concept of 'movement itself' not only articulates an ontology of motion capture: motion capture itself can be understood to be brought into being by movement, thus also challenging the notion that capture technology has a parasitic relationship to a performer's originary performance.

Ontology-based automated support for goal–use case model analysis

Combining goal-oriented and use case modeling has been proven to be an effective method in requirements elicitation and elaboration. To ensure the quality of such modeled artifacts, a detailed model analysis needs to be performed. However, current requirements engineering approaches generally lack reliable support for automated analysis of consistency, correctness and completeness (3Cs problems) between and within goal models and use case models. In this paper, we present a goal–use case integration framework with tool support to automatically identify such 3Cs problems. Our new framework relies on the use of ontologies of domain knowledge and semantics and our goal–use case integration meta-model. Moreover, functional grammar is employed to enable the semiautomated transformation of natural language specifications into Manchester OWL Syntax for automated reasoning. The evaluation of our tool support shows that for representative example requirements, our approach achieves over 85 % soundness and completeness rates and detects more problems than the benchmark applications.

GUITAR: An ontology-based automated requirements analysis tool

Combining goal-oriented and use case modeling has been proven to be an effective method in requirements elicitation and elaboration. However, current requirements engineering approaches generally lack reliable support for automated analysis of such modeled artifacts. To address this problem, we have developed GUITAR, a tool which delivers automated detection of incorrectness, incompleteness and inconsistency between artifacts. GUITAR is based on our goal-use case integration meta-model and ontologies of domain knowledge and semantics. GUITAR also provides comprehensive explanations for detected problems and can suggest resolution alternatives.

The construction of a juridical ontology

The need for the representation of both semantics and common sense and its organization in a lexical database or knowledge base has motivated the development of large projects, such as Wordnets, CYC and Mikrokosmos. Besides the generic bases, another approach is the construction of ontologies for specific domains. Among the advantages of such approach there is the possibility of a greater and more detailed coverage of a specific domain and its terminology. Domain ontologies are important resources in several tasks related to the language processing, especially in those related to information retrieval and extraction in textual bases. Information retrieval or even question and answer systems can benefit from the domain knowledge represented in an ontology. Besides embracing the terminology of the field, the ontology makes the relationships among the terms explicit. Copyright 2007 ACM.

Computational linguistic systematization of a lexicon from the ibitinga embroidery industry conceptual domain

This work discusses a proposition for organizing the lexical items from the conceptual domain labeled THE EMBROIDERY INDUSTRY OF IBITINGA in terms of a natural ontology. It also aims to establish the alignment between this ontology and the bases WordNet.Pr and WordNet.Br. © 2009 IEEE.

Packaging controlled experiments using an evolutionary approach based on ontology

A body of knowledge in Software Engineering requires experiments replications. The knowledge generated by a study is registered in the so-called lab package, which, must be reviewed by an eventual research group with the intention to replicate it. However, researchers face difficulties reviewing the lab package, what leads to problems in share knowledge among research groups. Besides that, the lack of standardization is an obstacle to the integration of the knowledge from an isolated study in a common body of knowledge. In this sense, ontologies can be applied, since they can be seen as a standard that promotes the shared understanding of the experiment information structure. In this paper, we present a workflow to generate lab packages based on EXPEiiQntology, an ontology of controlled experiments domain. In addition, by means of lab packages instantiation, it is possible to evolve the ontology, in order to deal with new concepts that may appear in different lab packages. The iterative ontology evolution aims at achieve a standard that is able to accommodate different lab packages and, hence, facilitate to review and understand their content.

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.

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.

Engineering an Ontology for Autonomous Systems - The OASys Ontology

This paper describes the development of an ontology for autonomous systems, as the initial stage of a research programe on autonomous systems’ engineering within a model-based control approach. The ontology aims at providing a unified conceptual framework for the autonomous systems’ stakeholders, from developers to software engineers. The modular ontology contains both generic and domain-specific concepts for autonomous systems description and engineering. The ontology serves as the basis in a methodology to obtain the autonomous system’s conceptual models. The objective is to obtain and to use these models as main input for the autonomous system’s model-based control system.

Ontology driven description and engineering of autonomous systems: application to process system engineering

Autonomous systems refer to systems capable of operating in a real world environment without any form of external control for extended periods of time. Autonomy is a desired goal for every system as it improves its performance, safety and profit. Ontologies are a way to conceptualize the knowledge of a specific domain. In this paper an ontology for the description of autonomous systems as well as for its development (engineering) is presented and applied to a process. This ontology is intended to be applied and used to generate final applications following a model driven methodology.