A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Switching Partners: Dancing with the Ontological Engineers

Ontologies are today being applied in almost every field to support the alignment and retrieval of data of distributed provenance. Here we focus on new ontological work on dance and on related cultural phenomena belonging to what UNESCO calls the “intangible heritage.” Currently data and information about dance, including video data, are stored in an uncontrolled variety of ad hoc ways. This serves not only to prevent retrieval, comparison and analysis of the data, but may also impinge on our ability to preserve the data that already exists. Here we explore recent technological developments that are designed to counteract such problems by allowing information to be retrieved across disciplinary, cultural, linguistic and technological boundaries. Software applications such as the ones envisaged here will enable speedier recovery of data and facilitate its analysis in ways that will assist both archiving of and research on dance

CAMILA formal software engineering supported by functional programming

This paper describes two experiences in teaching a formal approach to software engineering at undergraduate level supported by Camila a functional programming based tool Carried on in di erent institutions each of them addresses a particular topic in the area requirement analysis and generic systems design in the rst case speci cation and implementation development in the second Camila the common framework to both experiences animates a set based language extended with a mild use of category theory which can be reasoned upon for program calculation and classi cation purposes The project a liates itself to but is not restricted to the research in exploring Functional Programming as a rapid prototyping environment for formal software models Its kernel is fully connectable to external applications and equipped with a component repository and distribution facilities The paper explains how Camila is being used in the educational practice as a tool to think with providing a kind of cross fertilization between students under standing of di erent parts of the curriculum Furthermore it helps in developing a number of engineering skills namely the ability to analyze and classify infor mation problems and models and to resort to the combined use of di erent programming frameworks in approaching them.Eje: Conferencia latinoamericana de programación funcionalRed de Universidades con Carreras en Informática (RedUNCI

Designing Service-Oriented Chatbot Systems Using a Construction Grammar-Driven Natural Language Generation System

Service oriented chatbot systems are used to inform users in a conversational manner about a particular service or product on a website. Our research shows that current systems are time consuming to build and not very accurate or satisfying to users. We find that natural language understanding and natural language generation methods are central to creating an e�fficient and useful system. In this thesis we investigate current and past methods in this research area and place particular emphasis on Construction Grammar and its computational implementation. Our research shows that users have strong emotive reactions to how these systems behave, so we also investigate the human computer interaction component. We present three systems (KIA, John and KIA2), and carry out extensive user tests on all of them, as well as comparative tests. KIA is built using existing methods, John is built with the user in mind and KIA2 is built using the construction grammar method. We found that the construction grammar approach performs well in service oriented chatbots systems, and that users preferred it over other systems

CleanGraph - Graph viewing and editing for family trees and UML class diagrams

Traditionally, different types of diagrams are used to represent varying types of data in a fast and easy way to read. Their usage includes describing systems, understanding their features and presenting how different parts are interconnected, making them useful for many applications. Unfortunately, as the complexity of the data showed increases, so does the complexity of the diagram, making it more difficult to read and interpret. Since interactions are usually limited to panning and zooming, there is room for improvement with more interaction and different input methods. The goal is to tackle these issues in two types of diagrams -- Family Trees (FT) and Universal Modeling Language (UML) class diagrams. To achieve this, a new platform will be created, capable of generating diagrams and displaying them in a way where overlapping and unrelated data is minimised alongside having better methods for interacting with and manipulating information. These diagrams will prioritise visual clarity by grouping together elements with relevant or important information, as well as having new ways of interaction, such as selecting elements to receive more information and manually grouping them to better explore the data. Guaranteeing the viability of the solution will require two main issues to be addressed: (1) Defining a fitting diagram disposition and why it is the more advantageous; (2) Understanding the best way to create interactions with diagrams while making it intuitive and keeping them readable. Finding the best platform for the solution to reach its intended audience while providing the desired ease of use is one of the priorities. The evaluation of this work will be attained through previously defined metrics, to ensure that the generated diagram is adequate. The quality of the diagrams will be defined by characteristics such as overlapping connections between elements, related or unrelated data of adjacent elements to the selected one and the amount of displayed data at once. The result of the proposal aims to give a better tool to users seeking improved methods to view their ancestry data, as well as software architects, project managers and system analysts, who would benefit from a better platform for system representation. The developed features can help them convey their ideas easily to developers or anyone interested in the data represented, improving simplicity, workflow and potentially bringing new and improved methods of viewing and displaying information in these areas

Complex adaptive systems based data integration : theory and applications

Data Definition Languages (DDLs) have been created and used to represent data in programming languages and in database dictionaries. This representation includes descriptions in the form of data fields and relations in the form of a hierarchy, with the common exception of relational databases where relations are flat. Network computing created an environment that enables relatively easy and inexpensive exchange of data. What followed was the creation of new DDLs claiming better support for automatic data integration. It is uncertain from the literature if any real progress has been made toward achieving an ideal state or limit condition of automatic data integration. This research asserts that difficulties in accomplishing integration are indicative of socio-cultural systems in general and are caused by some measurable attributes common in DDLs. This research’s main contributions are: (1) a theory of data integration requirements to fully support automatic data integration from autonomous heterogeneous data sources; (2) the identification of measurable related abstract attributes (Variety, Tension, and Entropy); (3) the development of tools to measure them. The research uses a multi-theoretic lens to define and articulate these attributes and their measurements. The proposed theory is founded on the Law of Requisite Variety, Information Theory, Complex Adaptive Systems (CAS) theory, Sowa’s Meaning Preservation framework and Zipf distributions of words and meanings. Using the theory, the attributes, and their measures, this research proposes a framework for objectively evaluating the suitability of any data definition language with respect to degrees of automatic data integration. This research uses thirteen data structures constructed with various DDLs from the 1960\u27s to date. No DDL examined (and therefore no DDL similar to those examined) is designed to satisfy the law of requisite variety. No DDL examined is designed to support CAS evolutionary processes that could result in fully automated integration of heterogeneous data sources. There is no significant difference in measures of Variety, Tension, and Entropy among DDLs investigated in this research. A direction to overcome the common limitations discovered in this research is suggested and tested by proposing GlossoMote, a theoretical mathematically sound description language that satisfies the data integration theory requirements. The DDL, named GlossoMote, is not merely a new syntax, it is a drastic departure from existing DDL constructs. The feasibility of the approach is demonstrated with a small scale experiment and evaluated using the proposed assessment framework and other means. The promising results require additional research to evaluate GlossoMote’s approach commercial use potential