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

A silicon model of auditory localization

The barn owl accurately localizes sounds in the azimuthal plane, using interaural time difference as a cue. The time-coding pathway in the owl's brainstem encodes a neural map of azimuth, by processing interaural timing information. We have built a silicon model of the time-coding pathway of the owl. The integrated circuit models the structure as well as the function of the pathway; most subcircuits in the chip have an anatomical correlate. The chip computes all outputs in real time, using analog, continuous-time processing

Permanent generic relatedness and silent change

Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level ontology that allows expressing these modes

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

Semantic Modeling of Analytic-based Relationships with Direct Qualification

Successfully modeling state and analytics-based semantic relationships of documents enhances representation, importance, relevancy, provenience, and priority of the document. These attributes are the core elements that form the machine-based knowledge representation for documents. However, modeling document relationships that can change over time can be inelegant, limited, complex or overly burdensome for semantic technologies. In this paper, we present Direct Qualification (DQ), an approach for modeling any semantically referenced document, concept, or named graph with results from associated applied analytics. The proposed approach supplements the traditional subject-object relationships by providing a third leg to the relationship; the qualification of how and why the relationship exists. To illustrate, we show a prototype of an event-based system with a realistic use case for applying DQ to relevancy analytics of PageRank and Hyperlink-Induced Topic Search (HITS).Comment: Proceedings of the 2015 IEEE 9th International Conference on Semantic Computing (IEEE ICSC 2015

A Semantic Grid Service for Experimentation with an Agent-Based Model of Land-Use Change

Agent-based models, perhaps more than other models, feature large numbers of parameters and potentially generate vast quantities of results data. This paper shows through the FEARLUS-G project (an ESRC e-Social Science Initiative Pilot Demonstrator Project) how deploying an agent-based model on the Semantic Grid facilitates international collaboration on investigations using such a model, and contributes to establishing rigorous working practices with agent-based models as part of good science in social simulation. The experimental workflow is described explicitly using an ontology, and a Semantic Grid service with a web interface implements the workflow. Users are able to compare their parameter settings and results, and relate their work with the model to wider scientific debate.Agent-Based Social Simulation, Experiments, Ontologies, Replication, Semantic Grid

Design Research and Domain Representation

While diverse theories about the nature of design research have been proposed, they are rarely considered in relation to one another across the broader disciplinary field. Discussions of design research paradigms have tended to use overarching binary models for understanding differing knowledge frameworks. This paper focuses on an analysis of theories of design research and the use of Web 3 and open content systems to explore the potential of building more relational modes of conceptual representation. The nature of this project is synthetic, building upon the work of other design theorists and researchers. A number of theoretical frameworks will be discussed and examples of the analysis and modelling of key concepts and information relationships, using concept mapping software, collaborative ontology building systems and semantic wiki technologies will be presented. The potential of building information structures from content relationships that are identified by domain specialists rather than the imposition of formal, top-down, information hierarchies developed by information scientists, will be considered. In particular the opportunity for users to engage with resources through their own knowledge frameworks, rather than through logically rigorous but largely incomprehensible ontological systems, will be explored in relation to building resources for emerging design researchers. The motivation behind this endeavour is not to create a totalising meta-theory or impose order on the ‘ill structured’ and ‘undisciplined’, domain of design. Nor is it to use machine intelligence to ‘solve design problems’. It seeks to create dynamic systems that might help researchers explore design research theories and their various relationships with one another. It is hoped such tools could help novice researchers to better locate their own projects, find reference material, identify knowledge gaps and make new linkages between bodies of knowledge by enabling forms of data-poesis - the freeing of data for different trajectories. Keywords: Design research; Design theory; Methodology; Knowledge systems; Semantic web technologies.</p

An Enhanced Spatial Reasoning Ontology for Maritime Anomaly Detection

International audienceAlthough originally conceived as a conceptual object for modelling knowledge, current ontologies do not make it possible to manipulate spatial knowledge. However, spatial knowledge is an essential component of any modelling specification. This problem provided the motivation for the creation of an expert system driven by an ontology. The system enables experts in the maritime domain to characterise abnormal ship behaviour based on formal semantic properties. Users are able to specify and execute spatial rules that are directly integrated into the ontology and a map interface linked to the ontology displays the results of the inferences obtained