Using RDF to Model the Structure and Process of Systems

Using RDF to Model the Structure and Process of Systems∗ Marko A. Rodriguez Jennifer H. Watkins Johan Bollen Los Alamos National Laboratory {marko,jhw,jbollen}@lanl.gov Carlos Gershenson New England Complex Systems Institute carlos@necsi.org October 28, 2018 Abstract Many systems can be described in terms of networks of discrete el- ements and their various relationships to one another. A semantic net- work, 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 net- work models. First, the Resource Description Framework (RDF) offers a standardized semantic network data model that can be further formal- ized 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 109 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. ∗Rodriguez, M.A., Watkins, J.H., Bollen, J., Gershenson, C., “Using RDF to Model the Structure and Process of Systems”, International Conference on Complex Systems, Boston, Massachusetts, October 2007. 1 arXiv:0709.1167v2 [cs.AI] 15 Oct 2007 1 Introduction The figurehead of the Semantic Web initiative, Tim Berners-Lee, describes the Semantic Web as ... an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation [2]. However, Berners-Lee’s definition assumes an application space that is specific to the “web” and to the interaction between humans and ma- chines. More generally, the Semantic Web is actually a conglomeration of standards and technologies that can be used in various disparate applica- tion spaces. The Semantic Web is simply a highly-distributed, standard- ized semantic network (i.e. directed labeled network) data model and a set of tools to operate on that data model. With respect to the purpose of this article, the Semantic Web and its associated technologies can be leveraged to model and manipulate any system that can be represented as a heterogeneous set of discrete elements connected to one another by a set of heterogeneous relationships whether those elements are web pages, automata, cells, people, cities, etc. This article will introduce complexity science researchers to a collection of standards designed for modeling the heterogeneous relationships that compose systems and technologies that support large-scale data sets on the order to 109 edges. This article has the following outline. Section 2 presents a review of the Resource Description Framework (RDF). RDF is the standardized data model for representing a semantic network and is the foundational technology of the Semantic Web. Section 3 presents a review of both RDF Schema (RDFS) and the Web Ontology Language (OWL). RDFS and OWL are languages for abstractly defining the topological features of an RDF network and are analogous, in some ways, to the database schemas of relational databases (e.g. MySQL and Oracle). Section 4 presents a review of triple-store technology and its similarities and differences with the relational database. Finally, Section 5 presents the semantic network programming language Neno and the RDF virtual machine Fhat. 2 The Resource Description Framework The Resource Description Framework (RDF) is a standardized data model for representing a semantic network [5]. RDF is not a syntax (i.e. data format). There exist various RDF syntaxes and depending on the ap- plication space one syntax may be more appropriate than another. An RDF-based semantic network is called an RDF network. An RDF network differs from the directed network of common knowledge because the edges in the network are qualified. For instance, in a directed network, an edge is represented as an ordered pair (i, j). This relationship states that i is related to j by some unspecified type of relationship. Because edges are not qualified, all edges have a homogenous meaning in a directed network (e.g. a coauthorship network, a friendship network, a transportation net- work). On the other hand, in an RDF network, edges are qualified such that a relationship is represented by an ordered triple ⟨i, ω, j⟩. A triple 2 can be interpreted as a statement composed of a subject, a predicate, and an object. The subject i is related to the object j by the predicate ω. For instance, a scholarly network can be represented as an

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