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

Coping with lists in the ifcOWL ontology

Over the past few years, several suggestions have been made of how to convert an EXPRESS schema into an OWL ontology. The conversion from EXPRESS to OWL is of particular use to architectural design and construction industry, because one of the key data models in architectural design and construction industry, namely the Industry Foundation Classes (IFC) is represented using the EXPRESS information modelling language. In each of these conversion options, the way in which lists are converted (e.g. lists of coordinates, lists of spaces in a floor) is key to the structure and eventual strength of the resulting ontology. In this article, we outline and discuss the main decisions that can be made in converting LIST concepts in EXPRESS to equivalent OWL expressions. This allows one to identify which conversion option is appropriate to support proper and efficient information reuse in the domain of architecture and construction

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

Reasoning & Querying – State of the Art

Various query languages for Web and Semantic Web data, both for practical use and as an area of research in the scientific community, have emerged in recent years. At the same time, the broad adoption of the internet where keyword search is used in many applications, e.g. search engines, has familiarized casual users with using keyword queries to retrieve information on the internet. Unlike this easy-to-use querying, traditional query languages require knowledge of the language itself as well as of the data to be queried. Keyword-based query languages for XML and RDF bridge the gap between the two, aiming at enabling simple querying of semi-structured data, which is relevant e.g. in the context of the emerging Semantic Web. This article presents an overview of the field of keyword querying for XML and RDF

Successful new product development by optimizing development process effectiveness in highly regulated sectors: the case of the Spanish medical devices sector

Rapid development and commercialization of new products is of vital importance for small and medium sized enterprises (SME) in regulated sectors. Due to strict regulations, competitive advantage can hardly be achieved through the effectiveness of product concepts only. If an SME in a highly regulated sector wants to excell in new product development (NPD) performance, the company should focus on the flexibility, speed, and productivity of its NPD function: i.e. the development process effectiveness. Our main research goals are first to explore if SMEs should focus on their their development process effectiveness rather than on their product concept effectiveness to achieve high NPD performance; and second, to explore whether a shared pattern in the organization of the NPD function can be recognized to affect NPD performance positively. The medical devices sector in Spain is used as an example of a\ud highly regulated sector. A structured survey among 11 SMEs, of which 2 were studied also as in in-depth case studies, led to the following results. First of all, indeed the companies in the dataset which focused on the effectiveness of their development process, stood out in NPD performance. Further, the higher performing companies did have a number of commonalities in the organisation of their NPD function: 1) The majority of the higher performing firms had an NPD strategy characterized by a predominantly incremental project portfolio.\ud 2) a) Successful firms with an incremental project portfolio combined this with a functional team structure b) Successful firms with a radical project portfolio combined this with a heavyweight or autonomous team structure.\ud 3) A negative reciprocal relationship exists between formalization of the NPD processes and the climate of the NPD function, in that a formalized NPD process and an innovative climate do not seem to reinforce each other. Innovative climate combined with an informal NPD process does however contribute positively to NPD performance. This effect was stronger in combination with a radical project portfolio. The highest NPD performance was measured for companies focusing mainly on incremental innovation. It is argued that in highly regulated sectors, companies with an incremental product portfolio would benefit from employing a functional structure. Those companies who choose for a more radical project portfolio in highly regulated sectors should be aware\ud that they are likely to excell only in the longer term by focusing on strategic flexibility. In their NPD organization, they might be well advised to combine informal innovation processes with an innovative climate

Globally reasoning about localised security policies in distributed systems

In this report, we aim at establishing proper ways for model checking the global security of distributed systems, which are designed consisting of set of localised security policies that enforce specific issues about the security expected. The systems are formally specified following a syntax, defined in detail in this report, and their behaviour is clearly established by the Semantics, also defined in detail in this report. The systems include the formal attachment of security policies into their locations, whose intended interactions are trapped by the policies, aiming at taking access control decisions of the system, and the Semantics also takes care of this. Using the Semantics, a Labelled Transition System (LTS) can be induced for every particular system, and over this LTS some model checking tasks could be done. We identify how this LTS is indeed obtained, and propose an alternative way of model checking the not-yet-induced LTS, by using the system design directly. This may lead to over-approximation thereby producing imprecise, though safe, results. We restrict ourselves to finite systems, in the sake of being certain about the decidability of the proposed method. To illustrate the usefulness and validity of our proposal, we present 2 small case-study-like examples, where we show how the system can be specified, which policies could be added to it, and how to decide if the desired global security property is met. Finally, an Appendix is given for digging deeply into how a tool for automatically performing this task is being built, including some implementation issues. The tool takes advantage of the proposed method, and given some system and some desired global security property, it safely (i.e. without false positives) ensures satisfaction of it

Preliminary Concepts for Economic Systems Analysis

In preparing theoretical tools to analyze economic systems we need several fundamental concepts that are often applied in various scientific investigations outside economic studies. Amongst others, the concept of autopoiesis, which was introduced by Niklas Luhmann into his sociological systems theory, is the most important in constructing a theoretical model to explain the working of economic systems. An autopoietic system may be regarded as the functional core by which other elementary concepts such as homeostasis, machinery, corporate system and social entropy can be logically connected. In conclusion, all economic systems are contained in distinct social systems of autopoietic character and incorporated with them as a subsystem or partially independent system.system, autopoiesis