Revising the UMLS Semantic Network

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration

Business Process Retrieval Based on Behavioral Semantics

This paper develops a framework for retrieving business processes considering search requirements based on behavioral semantics properties; it presents a framework called "BeMantics" for retrieving business processes based on structural, linguistics, and behavioral semantics properties. The relevance of the framework is evaluated retrieving business processes from a repository, and collecting a set of relevant business processes manually issued by human judges. The "BeMantics" framework scored high precision values (0.717) but low recall values (0.558), which implies that even when the framework avoided false negatives, it prone to false positives. The highest pre- cision value was scored in the linguistic criterion showing that using semantic inference in the tasks comparison allowed to reduce around 23.6 % the number of false positives. Using semantic inference to compare tasks of business processes can improve the precision; but if the ontologies are from narrow and specific domains, they limit the semantic expressiveness obtained with ontologies from more general domains. Regarding the perform- ance, it can be improved by using a filter phase which indexes business processes taking into account behavioral semantics propertie

A formal verification framework and associated tools for enterprise modeling : application to UEML

The aim of this paper is to propose and apply a verification and validation approach to Enterprise Modeling that enables the user to improve the relevance and correctness, the suitability and coherence of a model by using properties specification and formal proof of properties

Comprehensive Security Framework for Global Threats Analysis

Cyber criminality activities are changing and becoming more and more professional. With the growth of financial flows through the Internet and the Information System (IS), new kinds of thread arise involving complex scenarios spread within multiple IS components. The IS information modeling and Behavioral Analysis are becoming new solutions to normalize the IS information and counter these new threads. This paper presents a framework which details the principal and necessary steps for monitoring an IS. We present the architecture of the framework, i.e. an ontology of activities carried out within an IS to model security information and User Behavioral analysis. The results of the performed experiments on real data show that the modeling is effective to reduce the amount of events by 91%. The User Behavioral Analysis on uniform modeled data is also effective, detecting more than 80% of legitimate actions of attack scenarios

On relating functional modeling approaches: abstracting functional models from behavioral models

This paper presents a survey of functional modeling approaches and describes a strategy to establish functional knowledge exchange between them. This survey is focused on a comparison of function meanings and representations. It is argued that functions represented as input-output flow transformations correspond to behaviors in the approaches that characterize functions as intended behaviors. Based on this result a strategy is presented to relate the different meanings of function between the approaches, establishing functional knowledge exchange between them. It is shown that this strategy is able to preserve more functional information than the functional knowledge exchange methodology of Kitamura, Mizoguchi, and co-workers. The strategy proposed here consists of two steps. In step one, operation-on-flow functions are translated into behaviors. In step two, intended behavior functions are derived from behaviors. The two-step strategy and its benefits are demonstrated by relating functional models of a power screwdriver between methodologies

Conceptual Model-Based Systems Biology: Mapping Knowledge and Discovering Gaps in the mRNA Transcription Cycle

We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure—the objects that comprise the system, and behavior—how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point—the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model