A Multiagent-Based Framework for Integrating Biological Data

A Multiagent-Based Framework for Integrating Biological Data

Faheema Maghrabi (Ain Shams University, Egypt), Hossam M. Faheem (Ain Shams University, Egypt), Taysir Soliman (Asuit University, Egypt) and Zaki Taha Fayed (Ain Shams University, Egypt)
DOI: 10.4018/978-1-60566-970-0.ch002
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Abstract

Biological data has been rapidly increasing in volume in different Web data sources. To query multiple data sources manually on the internet is time consuming for biologists. Therefore, systems and tools that facilitate searching multiple biological data sources are needed. Traditional approaches to build distributed or federated systems do not scale well to the large, diverse, and the growing number of biological data sources. Internet search engines allow users to search through large numbers of data sources, but provide very limited capabilities for locating, combining, processing, and organizing information. A promising approach to this problem is to provide access to the large number of biological data sources through a multiagent-based framework where a set of agents can cooperate with each other to retrieve relevant information from different biological Web databases. The proposed system uses a mediator-based integration approach with domain ontology, which uses as a global schema. In this paper we propose a multiagent-based framework that responds to biological queries according to its biological domain ontology.
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Introduction

“We could not employ a workflow system that is not adaptable to changes.” states a chip design expert from Silicon Image GmbH, Hannover (S. Rackow, personal interview, October 25, 2006). Chip designers are used to dealing with the dynamics that result from the evolution of technology as well as from changes in the market. The increasing dynamics of the workflow is a phenomenon that affects the production processes within the high-tech industry: Software developers have to be flexible when the customer requirements change. Healthcare professionals must react to side-effects and to other complications during the treatment of patients. What these examples from various domains have in common is that they cause major deviations from the usual business processes at run time. Furthermore, the ongoing processes need refinement after several weeks or months of running. Workflow technology supports business processes (Workflow Management Coalition, 1999). However, traditional workflow management systems, those described in Leymann and Roller (2000), are not able to deal with adaptable processes. Consequently, there is a need for agile workflow technology (Weber & Wild, 2005), that is, a workflow technology that allows the late-modeling and structural adaptation of ongoing workflows. Change reuse is essential to these difficult modeling tasks.

Workflows are “the automation of a business process, in whole or part, during which documents, information or tasks are passed from one participant to another for action, according to a set of procedural rules” (Workflow Management Coalition, 1999). A workflow management system “defines, creates and manages the execution of workflows through the use of software, running on one or more workflow engines, which is able to interpret the process definition, interact with workflow participants and, where required, invoke the use of IT tools and applications” (Workflow Management Coalition, 1999). A workflow enactment service is “a software service that may consist of one or more workflow engines” (Workflow Management Coalition, 1999).

All agile workflow approaches require the application of changes concurrently to normal process execution. In contrast to the existing approaches, very large process graphs are dealt with. They require a suspension mechanism in case of delayed decisions as they do occur in practise. Due to the highly dynamic environments of the workflows, the approach is aware of the context of influence factors. As other agile approaches, reusing experience from the changes of workflows in the past for the adaptation of an ongoing workflow are aimed at. In contrast to existing change reuse approaches, the retrieval of past workflows should consider the workflows’ structure directly rather than solely operating on additional information. In this article, a new approach of agile workflow technology which includes new basic methods for the representation, execution, and partial suspension of adaptable workflows as well as more sophisticated methods for the support of change reuse by means of case-based reasoning is described. It is an extension of previous work described in the literature (Minor, Schmalen, Tartakovsky, & Bergmann, 2008). The following hypothesis that will be investigated empirically in this article is stated: The evaluation of structural differences of workflows provides a good approximation for the usability of past modifications for current change requests. The purpose of our work is to contribute new workflow concepts and methods to solving the practical but difficult problem of handling business processes in very dynamic, long-term scenarios.

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Literature Review

The workflows to be interpreted in conventional workflow management systems have a fixed structure. In the literature, a number of approaches exist that aim at making workflows more flexible. Some work on flexible workflows in the broader sense are first discussed and then the literature on agile workflows in the actual sense are briefly reviewed. The latter is closely related to the work. The literature on similarity assessment of workflows is also discussed and the position on context-awareness during change reuse is defined.

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