Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks

Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or proteins. Using the intuition that the topological role of a gene in a network relates to its biological function, local or diffusion based "guilt-by-association" and graph-theoretic methods have had success in inferring gene functions. Here we seek to improve function prediction by integrating diffusion-based methods with a novel dimensionality reduction technique to overcome the incomplete and noisy nature of network data. In this paper, we introduce diffusion component analysis (DCA), a framework that plugs in a diffusion model and learns a low-dimensional vector representation of each node to encode the topological properties of a network. As a proof of concept, we demonstrate DCA's substantial improvement over state-of-the-art diffusion-based approaches in predicting protein function from molecular interaction networks. Moreover, our DCA framework can integrate multiple networks from heterogeneous sources, consisting of genomic information, biochemical experiments and other resources, to even further improve function prediction. Yet another layer of performance gain is achieved by integrating the DCA framework with support vector machines that take our node vector representations as features. Overall, our DCA framework provides a novel representation of nodes in a network that can be used as a plug-in architecture to other machine learning algorithms to decipher topological properties of and obtain novel insights into interactomes.Comment: RECOMB 201

Pattern-based design applied to cultural heritage knowledge graphs

Ontology Design Patterns (ODPs) have become an established and recognised practice for guaranteeing good quality ontology engineering. There are several ODP repositories where ODPs are shared as well as ontology design methodologies recommending their reuse. Performing rigorous testing is recommended as well for supporting ontology maintenance and validating the resulting resource against its motivating requirements. Nevertheless, it is less than straightforward to find guidelines on how to apply such methodologies for developing domain-specific knowledge graphs. ArCo is the knowledge graph of Italian Cultural Heritage and has been developed by using eXtreme Design (XD), an ODP- and test-driven methodology. During its development, XD has been adapted to the need of the CH domain e.g. gathering requirements from an open, diverse community of consumers, a new ODP has been defined and many have been specialised to address specific CH requirements. This paper presents ArCo and describes how to apply XD to the development and validation of a CH knowledge graph, also detailing the (intellectual) process implemented for matching the encountered modelling problems to ODPs. Relevant contributions also include a novel web tool for supporting unit-testing of knowledge graphs, a rigorous evaluation of ArCo, and a discussion of methodological lessons learned during ArCo development

Modeling views in the layered view model for XML using UML

In data engineering, view formalisms are used to provide flexibility to users and user applications by allowing them to extract and elaborate data from the stored data sources. Conversely, since the introduction of Extensible Markup Language (XML), it is fast emerging as the dominant standard for storing, describing, and interchanging data among various web and heterogeneous data sources. In combination with XML Schema, XML provides rich facilities for defining and constraining user-defined data semantics and properties, a feature that is unique to XML. In this context, it is interesting to investigate traditional database features, such as view models and view design techniques for XML. However, traditional view formalisms are strongly coupled to the data language and its syntax, thus it proves to be a difficult task to support views in the case of semi-structured data models. Therefore, in this paper we propose a Layered View Model (LVM) for XML with conceptual and schemata extensions. Here our work is three-fold; first we propose an approach to separate the implementation and conceptual aspects of the views that provides a clear separation of concerns, thus, allowing analysis and design of views to be separated from their implementation. Secondly, we define representations to express and construct these views at the conceptual level. Thirdly, we define a view transformation methodology for XML views in the LVM, which carries out automated transformation to a view schema and a view query expression in an appropriate query language. Also, to validate and apply the LVM concepts, methods and transformations developed, we propose a view-driven application development framework with the flexibility to develop web and database applications for XML, at varying levels of abstraction

The Foundational Model of Anatomy Ontology

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data

Temporal Representation and Reasoning in OWL 2

The representation of temporal information has been in the center of intensive research activities over the years in the areas of knowledge representation, databases and more recently, the Semantic Web. The proposed approach extends the existing framework of representing temporal information in ontologies by allowing for representation of concepts evolving in time (referred to as “dynamic” information) and of their properties in terms of qualitative descriptions in addition to quantitative ones (i.e., dates, time instants and intervals). For this purpose, we advocate the use of natural language expressions, such as “before” or “after”, for temporal entities whose exact durations or starting and ending points in time are unknown. Reasoning over all types of temporal information (such as the above) is also an important research problem. The current work addresses all these issues as follows: The representation of dynamic concepts is achieved using the “4D-fluents” or, alternatively, the “N-ary relations” mechanism. Both mechanisms are thoroughly explored and are expanded for representing qualitative and quantitative temporal information in OWL. In turn, temporal information is expressed using either intervals or time instants. Qualitative temporal information representation in particular, is realized using sets of SWRL rules and OWL axioms leading to a sound, complete and tractable reasoning procedure based on path consistency applied on the existing relation sets. Building upon existing Semantic Web standards (OWL), tools and member submissions (SWRL), as well as integrating temporal reasoning support into the proposed representation, are important design features of our approach

Ontologias para Manutenção Preditiva com Dados sensíveis ao tempo

As empresas de fabrico industrial devem assegurar um processo produtivo contínuo para serem competitivas e fornecer os produtos fabricados no prazo e com a qualidade exigida pelos clientes. A quebra da cadeia de fabrico pode ter desfechos graves, resultando numa redução da produção e na interrupção da cadeia de abastecimento. Estes processos são compostos por cadeias de máquinas que executam tarefas em etapas. Cada máquina tem uma tarefa específica a executar, e o resultado de cada etapa é fornecido à próxima etapa. Uma falha imprevista numa das máquinas tende a interromper toda a cadeia produtiva. A manutenção preventiva agendada tem como objetivo evitar a ocorrência de falhas, tendo como base o tempo médio antes da falha (MTBF), que representa a expectativa média de vida de componentes individuais com base em dados históricos. As tarefas de manutenção podem implicar um período de paralisação e a interrupção da produção. Esta manutenção é executada rotineiramente e a substituição de componentes não considera a necessidade premente da sua substituição, sendo os mesmos substituídos com base no ciclo do agendamento. É aqui que a manutenção preditiva é aplicável. Efetuando a recolha de dados de sensores dos equipamentos, é possível detetar irregularidades nos dados recolhidos, através da aplicação de processos de raciocínio e inferência, conduzindo à atempada previsão e deteção de falhas. Levando este cenário à otimização do tempo de manutenção, evitando falhas inesperadas, à redução de custos e ao aumento da produtividade em comparação com a manutenção preventiva. Os dados fornecidos pelos sensores são sensíveis ao tempo, variações e flutuações ocorrem ao longo do tempo e devem ser analisados em relação ao período em que ocorrem. Esta dissertação tem como objetivo o desenvolvimento de uma ontologia para a manutenção preditiva que descreva a sua abrangência e o campo da sua aplicação. A aplicabilidade da ontologia será demonstrada com uma ferramenta, igualmente desenvolvida, que transforma dados sensíveis ao tempo recolhidos em tempo real a partir de sensores de máquinas industriais, fornecidos por WebServices, em indivíduos dessa mesma ontologia, considerando a representação do fator temporal dos dados.Manufacturing companies must ensure a continuous production process to be competitive and supply the manufactured goods in time and with the desired quality the customers expect. Any disruption in the manufacturing chain may have disastrous consequences, representing a shortage of production and the interruption of the supply chain. The manufacturing processes are composed of a chain of industrial machines operating in stages. Each machine has a specific task to complete, and the result of each stage is forwarded to the next stage. An unpredicted malfunction of one of the machines tends to interrupt the whole production chain. Scheduled Preventive maintenance intends to avoid causes leading to faults, but relies on parameters such as Mean Time Before Failure (MTBF), which represents the average expected life span of individual components based on statistical data. A maintenance task may lead to a period of downtime and consequently to a production halt. Being the maintenance scheduled and executed routinely, the replacement of components, does not consider the effective need of its replacement, they are replaced based on the scheduling cycle. This is where predictive maintenance is applicable. By collecting sensor data of industrial equipment, anomalies can be determined through reasoning and inference processes applied to the data, leading to an early fault and time to failure prediction. This scenario leads to maintenance timing optimization, avoidance of unexpected failures, cost savings and improved productivity when compared to preventive maintenance. Data supplied by sensors is timesensitive, as variations and fluctuations occur over periods of time and must be analysed concerning the period they occur. This dissertation aims to develop an ontology for predictive maintenance that describes the scope and field of application. The applicability of the ontology will be demonstrated with a tool, also to be developed, that transforms time-sensitive data collected in real time from sensors of industrial machines, provided by a WebServices, into individuals of the same ontology, considering the representation of the temporal factor of the data

Knowledge-based support in Non-Destructive Testing for health monitoring of aircraft structures

Maintenance manuals include general methods and procedures for industrial maintenance and they contain information about principles of maintenance methods. Particularly, Non-Destructive Testing (NDT) methods are important for the detection of aeronautical defects and they can be used for various kinds of material and in different environments. Conventional non-destructive evaluation inspections are done at periodic maintenance checks. Usually, the list of tools used in a maintenance program is simply located in the introduction of manuals, without any precision as regards to their characteristics, except for a short description of the manufacturer and tasks in which they are employed. Improving the identification concepts of the maintenance tools is needed to manage the set of equipments and establish a system of equivalence: it is necessary to have a consistent maintenance conceptualization, flexible enough to fit all current equipment, but also all those likely to be added/used in the future. Our contribution is related to the formal specification of the system of functional equivalences that can facilitate the maintenance activities with means to determine whether a tool can be substituted for another by observing their key parameters in the identified characteristics. Reasoning mechanisms of conceptual graphs constitute the baseline elements to measure the fit or unfit between an equipment model and a maintenance activity model. Graph operations are used for processing answers to a query and this graph-based approach to the search method is in-line with the logical view of information retrieval. The methodology described supports knowledge formalization and capitalization of experienced NDT practitioners. As a result, it enables the selection of a NDT technique and outlines its capabilities with acceptable alternatives

Ontology patterns for the representation of quality changes of cells in time

Background: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical information from these data. This information can be used to develop process models of cellular dynamics. However, so far there has been no structured, standardized way of annotating and storing the tracking results, which is critical for comparative analysis and data integration. The key requirement to be satisfied by an ontology is the representation of a cell’s change over time. Unfortunately, popular ontology languages, such as Web Ontology Language (OWL), have limitations for the representation of temporal information. The current paper addresses the fundamental problem of modeling changes of qualities over time in biomedical ontologies specified in OWL. Results: The presented analysis is a result of the lessons learned during the development of an ontology, intended for the annotation of cell tracking experiments. We present, discuss and evaluate various representation patterns for specifying cell changes in time. In particular, we discuss two patterns of temporally changing information: n-ary relation reification and 4d fluents.These representation schemes are formalized within the ontology language OWL and are aimed at the support for annotation of cell tracking experiments. We analyze the performance of each pattern with respect to standard criteria used in software engineering and data modeling, i.e. simplicity, scalability, extensibility and adequacy. We further discuss benefits, drawbacks, and the underlying design choices of each approach. Conclusions: We demonstrate that patterns perform differently depending on the temporal distribution of modeled information. The optimal model can be constructed by combining two competitive approaches. Thus, we demonstrate that both reification and 4d fluents patterns can work hand in hand in a single ontology. Additionally, we have found that 4d fluents can be reconstructed by two patterns well known in the computer science community, i.e. state modeling and actor-role pattern