Automatically changing modules in modular ontology development and management

Modularity has been proposed as a solution to deal with large ontologies. This requires, various module management tasks, such as swapping an outdated module for a new one or a computationally costly one for a leaner fragment. No mechanism exists to exchange an arbitrary module automatically. To solve this manual task, we modify the SUGOI algorithm into SUGOI-Gen; with SUGOI-Gen, one can swap any module within a modular system, implemented it, and wrapped a GUI around it. We carried out an experimental evaluation with six ontologies covering three different use-cases to determine whether arbitrary interchangeability is practically doable, and to what extent such changes affect the quality of the module and automated reasoning over it. The results are positive, with the success rate varying between 22-100% depending on the number of mappings between the source and target module. The evaluation also revealed that the interchangeability does indeed have an impact on a module’s metrics. Regarding reasoning, when comparing an original ontology to one where a module has been swapped, the processing time is greatly improved for all except one of the swapped modules in the set

Git4Voc: Git-based Versioning for Collaborative Vocabulary Development

Collaborative vocabulary development in the context of data integration is the process of finding consensus between the experts of the different systems and domains. The complexity of this process is increased with the number of involved people, the variety of the systems to be integrated and the dynamics of their domain. In this paper we advocate that the realization of a powerful version control system is the heart of the problem. Driven by this idea and the success of Git in the context of software development, we investigate the applicability of Git for collaborative vocabulary development. Even though vocabulary development and software development have much more similarities than differences there are still important differences. These need to be considered within the development of a successful versioning and collaboration system for vocabulary development. Therefore, this paper starts by presenting the challenges we were faced with during the creation of vocabularies collaboratively and discusses its distinction to software development. Based on these insights we propose Git4Voc which comprises guidelines how Git can be adopted to vocabulary development. Finally, we demonstrate how Git hooks can be implemented to go beyond the plain functionality of Git by realizing vocabulary-specific features like syntactic validation and semantic diffs

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

Reconfigurability Function Deployment in Software Development

In the forthcoming highly dynamic and complex business environment high-speed and cost-effective development of software applications for targeting a precise, unique and momentary set of requirements (no more-no less) associated to a customized business case will bring sig-nificant benefits both for producers and users. This requires a life cycle change-oriented ap-proach in software development. In this respect, designing software with intrinsic evolutionary resources for reconfiguration represents the sound approach. A methodology for concurrent deployment of reconfigurability characteristics in software applications is introduced in this paper. Its potential is exemplified in a case study dealing with web-based software tools to support systematic product innovation projects.Reconfigurability, Software Development, Innovation, TRIZ, RAD

Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence Community

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

Design, Application and Evaluation of a Multi Agent System in the Logistics Domain

The increasing demand for flexibility of automated production systems also affects the automated material flow systems (aMFS) they contain and demands reconfigurable systems. However, the centralized control concept usually applied in aMFS hinders an easy adaptation, as the entire control software has to be re-tested, when manually changing sub-parts of the control. As adaption and subsequent testing are a time-consuming task, concepts for splitting the control from one centralized to multiple, decentralized control nodes are required. Therefore, this paper presents a holistic agent-based control concept for aMFS, whereby the system is divided into so-called automated material flow modules (aMFM), each being controlled by a dedicated module agent. The concept allows the reconfiguration of aMFS, consisting of heterogeneous, stationary aMFM, during runtime. Furthermore, it includes aspects such as uniform agent knowledge bases through metamodel-based development, a communication ontology considering different information types and properties, strategic route optimization in decentralized control architecture and a visualization concept to make decisions of the module agents comprehensible to operators and maintenance staff. The evaluation of the concept is performed by means of material flow simulations as well as a prototypical implementation on a lab-sized demonstrator.Comment: 13 pages, https://ieeexplore.ieee.org/abstract/document/9042827

A knowledge based approach to integration of products, processes and reconfigurable automation resources

The success of next generation automotive companies will depend upon their ability to adapt to ever changing market trends thus becoming highly responsive. In the automotive sector, the assembly line design and reconfiguration is an especially critical and extremely complex job. The current research addresses some of the aspects of this activity under the umbrella of a larger ongoing research project called Business Driven Automation (BDA) project. The BDA project aims to carry out complete virtual 3D modeling-based verifications of the assembly line for new or revised products in contrast to the prevalent practice of manual evaluation of effects of product change on physical resources. [Continues.