Using RDF to Model the Structure and Process of Systems

Many systems can be described in terms of networks of discrete elements and their various relationships to one another. A semantic network, or multi-relational network, is a directed labeled graph consisting of a heterogeneous set of entities connected by a heterogeneous set of relationships. Semantic networks serve as a promising general-purpose modeling substrate for complex systems. Various standardized formats and tools are now available to support practical, large-scale semantic network models. First, the Resource Description Framework (RDF) offers a standardized semantic network data model that can be further formalized by ontology modeling languages such as RDF Schema (RDFS) and the Web Ontology Language (OWL). Second, the recent introduction of highly performant triple-stores (i.e. semantic network databases) allows semantic network models on the order of $10^9$ edges to be efficiently stored and manipulated. RDF and its related technologies are currently used extensively in the domains of computer science, digital library science, and the biological sciences. This article will provide an introduction to RDF/RDFS/OWL and an examination of its suitability to model discrete element complex systems.Comment: International Conference on Complex Systems, Boston MA, October 200

AMaχoS—Abstract Machine for Xcerpt

Web query languages promise convenient and efficient access to Web data such as XML, RDF, or Topic Maps. Xcerpt is one such Web query language with strong emphasis on novel high-level constructs for effective and convenient query authoring, particularly tailored to versatile access to data in different Web formats such as XML or RDF. However, so far it lacks an efficient implementation to supplement the convenient language features. AMaχoS is an abstract machine implementation for Xcerpt that aims at efficiency and ease of deployment. It strictly separates compilation and execution of queries: Queries are compiled once to abstract machine code that consists in (1) a code segment with instructions for evaluating each rule and (2) a hint segment that provides the abstract machine with optimization hints derived by the query compilation. This article summarizes the motivation and principles behind AMaχoS and discusses how its current architecture realizes these principles

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description