Transformation From Semantic Data Model to Rdf

There have been several efforts to use relational model and database to store and manipulate Resource Description Framework (RDF). They have one general disadvantage, i.e. one is forced to map the model of semantics of RDF into relational model, which will end up in constraints and additional properties, such as, validating each assertion against the RDF schema which also stored as a triplets table. In this paper, we introduce Semantic Data Model as a proposed data model language to store and manipulate Resource Description Framework. This study also tries to prescribe the procedure on transforming a semantic data model into a RDF data model. Keyworsd: Semantic Data Model, Resource Description Framework

Storing RDF as a Graph

RDF is the first W3C standard for enriching information resources of the Web with detailed meta data. The semantics of RDF data is defined using a RDF schema. The most expressive language for querying RDF is RQL, which enables querying of semantics. In order to support RQL, a RDF storage system has to map the RDF graph model onto its storage structure. Several storage systems for RDF data have been developed, which store the RDF data as triples in a relational database. To evaluate an RQL query on those triple structures, the graph model has to be rebuilt from the triples. In this paper, we presented a new approach to store RDF data as a graph in a object-oriented database. Our approach avoids the costly rebuilding of the graph and efficiently queries the storage structure directly. The advantages of our approach have been shown by performance test on our prototype implementation OO-Store

Model Theory and Entailment Rules for RDF Containers, Collections and Reification

An RDF graph is, at its core, just a set of statements consisting of subjects, predicates and objects. Nevertheless, since its inception practitioners have asked for richer data structures such as containers (for open lists, sets and bags), collections (for closed lists) and reification (for quoting and provenance). Though this desire has been addressed in the RDF primer and RDF Schema specification, they are explicitely ignored in its model theory. In this paper we formalize the intuitive semantics (as suggested by the RDF primer, the RDF Schema and RDF semantics specifications) of these compound data structures by two orthogonal extensions of the RDFS model theory (RDFCC for RDF containers and collections, and RDFR for RDF reification). Second, we give a set of entailment rules that is sound and complete for the RDFCC and RDFR model theories. We show that complexity of RDFCC and RDFR entailment remains the same as that of simple RDF entailment

Processing SPARQL queries with regular expressions in RDF databases

Background: As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results: In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions: Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.X113sciescopu

UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web

The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework ("http://www.w3.org/RDF/":http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium's Semantic Web activities ("http://www.w3.org/2001/sw/":http://www.w3.org/2001/sw/) and is therefore well suited to work in a distributed and decentralized environment. The RDF data model represents arbitrary information as a set of simple statements of the form subject-predicate-object. To enable the linking of data on the Web, RDF requires that each resource must have a (globally) unique identifier. These identifiers allow everybody to make statements about a given resource and, together with the simple structure of the RDF data model, make it easy to combine the statements made by different people (or databases) to allow queries across different datasets. RDF is thus an industry standard that can make a major contribution to solve two important problems of bioinformatics: distributed annotation and data integration

Reconciliation of RDF* and Property Graphs

Both the notion of Property Graphs (PG) and the Resource Description Framework (RDF) are commonly used models for representing graph-shaped data. While there exist some system-specific solutions to convert data from one model to the other, these solutions are not entirely compatible with one another and none of them appears to be based on a formal foundation. In fact, for the PG model, there does not even exist a commonly agreed-upon formal definition. The aim of this document is to reconcile both models formally. To this end, the document proposes a formalization of the PG model and introduces well-defined transformations between PGs and RDF. As a result, the document provides a basis for the following two innovations: On one hand, by implementing the RDF-to-PG transformations defined in this document, PG-based systems can enable their users to load RDF data and make it accessible in a compatible, system-independent manner using, e.g., the graph traversal language Gremlin or the declarative graph query language Cypher. On the other hand, the PG-to-RDF transformation in this document enables RDF data management systems to support compatible, system-independent queries over the content of Property Graphs by using the standard RDF query language SPARQL. Additionally, this document represents a foundation for systematic research on relationships between the two models and between their query languages.Comment: slightly changed the definition of PGs and added the notion of property uniquenes