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

The transaction pattern through automating TrAM

Transaction Agent Modelling (TrAM) has demonstrated how the early requirements of complex enterprise systems can be captured and described in a lucid yet rigorous way. Using Geerts and McCarthy’s REA (Resource-Events-Agents) model as its basis, the TrAM process manages to capture the ‘qualitative’ dimensions of business transactions and business processes. A key part of the process is automated model-checking, which CG has revealed to be beneficial in this regard. It enables models to retain the high-level business concepts yet providing a formal structure at that high-level that is lacking in Use Cases. Using a conceptual catalogue informed by transactions, we illustrate the automation of a transaction pattern from which further specialisations impart a tested specification for system implementation, which we envisage as a multi-agent system in order to reflect the dynamic world of business activity. It would furthermore be able to interoperate across business domains as they would share the generalised TM as a pattern.</p

Generic unified modelling process for developing semantically rich, dynamic and temporal models

Models play a vital role in supporting a range of activities in numerous domains. We rely on models to support the design, visualisation, analysis and representation of parts of the world around us, and as such significant research effort has been invested into numerous areas of modelling; including support for model semantics, dynamic states and behaviour, temporal data storage and visualisation. Whilst these efforts have increased our capabilities and allowed us to create increasingly powerful software-based models, the process of developing models, supporting tools and /or data structures remains difficult, expensive and error-prone. In this paper we define from literature the key factors in assessing a model’s quality and usefulness: semantic richness, support for dynamic states and object behaviour, temporal data storage and visualisation. We also identify a number of shortcomings in both existing modelling standards and model development processes and propose a unified generic process to guide users through the development of semantically rich, dynamic and temporal models

Including widespread geometry formats in semantic graphs using RDF literals

The exchange of building data involves both geometric and non-geometric data. A promising Linked Data approach is to embed data from existing geometry formats inside Resource Description Framework (RDF) literals. Based on a study of relevant specifications and related work, this toolset-independent approach was found suitable for the exchange of geometric construction data. To implement the approach in practice, the File Ontology for Geometry formats (FOG) and accompanying modelling method is developed. In a proof-of-concept web application that uses FOG, is demonstrated how geometry descriptions of different existing formats are automatically recognised and parsed

mPower: A component-based development framework for multi-agent systems to support business processes

One of the obstacles preventing the widespread adoption of multi-agent systems in industry is the difficulty of implementing heterogeneous interactions among participating agents via asynchronous messages. This difficulty arises from the need to understand how to combine elements of various content languages, ontologies, and interaction protocols in order to construct meaningful and appropriate messages. In this paper mPower, a component-based layered framework for easing the development of multi-agent systems, is described, and the facility for customising the components for reuse in similar domains is explained. The framework builds on the JADE-LEAP platform, which provides a homogeneous layer over diverse operating systems and hardware devices, and allows ubiquitous deployment of applications built on multi-agent systems both in wired and wireless environments. The use of the framework to develop mPowermobile , a multi-agent system to support mobile workforces, is reported

Programming patterns and development guidelines for Semantic Sensor Grids (SemSorGrid4Env)

The web of Linked Data holds great potential for the creation of semantic applications that can combine self-describing structured data from many sources including sensor networks. Such applications build upon the success of an earlier generation of 'rapidly developed' applications that utilised RESTful APIs. This deliverable details experience, best practice, and design patterns for developing high-level web-based APIs in support of semantic web applications and mashups for sensor grids. Its main contributions are a proposal for combining Linked Data with RESTful application development summarised through a set of design principles; and the application of these design principles to Semantic Sensor Grids through the development of a High-Level API for Observations. These are supported by implementations of the High-Level API for Observations in software, and example semantic mashups that utilise the API