Semantic Infrastructure Research Articles

PSG: Peer-to-Peer semantic grid framework architecture

The grid vision, of sharing diverse resources in a flexible, coordinated and secure manner, strongly depends on metadata. Currently, grid metadata is generated and used in an ad-hoc fashion, much of it buried in the grid middleware code libraries and database schemas. This ad-hoc expression and use of metadata causes chronic dependency on human intervention during the operation of grid machinery. Therefore, the Semantic Grid is emerged as an extension of the grid in which rich resource metadata is exposed and handled explicitly, and shared and managed via grid protocols. The layering of an explicit semantic infrastructure over the grid infrastructure potentially leads to increase interoperability and flexibility. In this paper, we present PSG framework architecture that offers semantic-based grid services. PSG architecture allows the explicit use of semantics and defining the associated grid services. PSG architecture is originated from the integration of Peer-to-Peer (P2P) computing with semantics and agents. Ontologies are used in annotating each grid component, developing users/nodes profiles and organizing framework agents. While, P2P is responsible for organizing and coordinating the grid nodes and resources.

User-driven generation of semantic web content in Enterprise 2.0: a case study

The use of semantic web technologies in enterprise environments has been subject to lots of research and development since the end of the 1990s, with topics ranging from semantic middleware infrastructures to ontology-based knowledge management systems. In this paper, we focus on the particular issue of user-driven generation of semantic web content in Enterprise 2.0 environments, and demonstrate how we extended several already-deployed user-driven applications (such as blogs, wikis and tagging systems) to produce and use semantic annotations in such context. Especially, we discuss the technical aspects involved in the process as well as the incentives that have been provided to involve users in producing such data. In addition, we present how users reacted and accepted the tools and what are the lessons that we learnt during that project.

Algorithms and semantic infrastructure for mutation impact extraction and grounding

BackgroundMutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases.ResultsWe present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework.ConclusionWe address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

LIT: transcription, annotation, search and visualization tools for the Lexicon of the Italian Television

LIT (Lexicon of the Italian Television) is a project conceived by the Accademia della Crusca, the leading research institution on the Italian language, in collaboration with CLIEO (Center for theoretical and historical Linguistics: Italian, European and Oriental languages), with the aim of studying frequencies of the Italian vocabulary used in television. Approximately 170 hours of random television recordings acquired from the national broadcaster RAI (Italian Radio Television) during the year 2006 have been used to create the corpus of transcriptions. The principal outcome of the project is the design and implementation of an interactive system which combines a web-based video transcription and annotation tool, a full featured search engine, and a web application for data visualization with text-video syncing. Furthermore, the project is currently under deployment as a module of the larger national research funding FIRB 2009 VIVIT (Fondo di Investimento per la Ricerca di Base, Vivi l'Italiano), which will integrate its achievements and results within a semantic web infrastructure.

A Holistic Environment for the Design and Execution of Self-Adaptive Clinical Pathways

One of the main challenges to be confronted by modern health care, so as to increase treatment quality, is the personalization of treatment. The treatment personalization requires the continuous reconfiguration and adaptation of the selected treatment schemes according to the "current" clinical status of each patient and "current" circumstances inside a health care organization that change rapidly, as well as the updated medical knowledge. In this paper, we present an innovative software environment that provides an integrated IT solution concerning the adaptation of health care processes (clinical pathways) during execution time. The software comprises a health care process execution engine assisted by a semantic infrastructure for reconfiguring the clinical pathways. During the execution of clinical pathways, the system reasons over the rules and reconfigures the next steps of the treatment. A graphical designer interface is implemented for the definition of the rule-set for the clinical pathways adaptation in a user-friendly way.

Semantics-aware security policy specification for the semantic web data

The semantic web has been envisioned as a machine interpretable web, where data instances are described through concepts defined and related in ontologies. Though ontologies are publicly available as a crucial component of the semantic web infrastructure, many data instances are sensitive and should be kept confidential. Sensitive information can be illegally inferred from other seemingly unclassified information in combination with the underlying data semantics and interrelationships revealed by ontologies. In other words, the visibility of ontologies can pose inference threats to the security of data instances, and this requires that security policies be specified in such a way that the semantic relationships among data instances are taken into account. To protect the semantic web data or other semantics-rich data, this paper presents semantics-aware security policy specification. We propose concept-level, association-level and property-level access control models for different security objects, and that authorisations be propagated based on different inference patterns. These propagation policies can be used to generate safe and consistent access control authorisations.

Towards a semantic infrastructure for context-aware e-learning

Architectural supports, e.g., user context processing and learning content management are essential for facilitating the development and proliferation of context-aware e-learning services. In this ...

Data modeling and retrieval in semantic grid based on RDF

The data processed by semantic grid are often semi-structured data.Therefore,how to model and retrieve these semi-structured data is a key issue of semantic Web.The presenting model for semi-structured data base Resource Description Framework(RDF) and its information retrieval mechanism were proposed in this paper.Then a semantic grid infrastructure was described,which implemented knowledge sharing and retrieval in chemical engineering domain based on a chemical computing grid platform.

Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships

BackgroundDiscovering that drug entities already approved for one disease are effective treatments for other distinct diseases can be highly beneficial and cost effective. To do this predictively, our conjecture is that a semantic infrastructure linking mechanistic relationships between pharmacologic entities and multidimensional knowledge of biological systems and disease processes will be highly enabling.ResultsTo develop a knowledge framework capable of modeling and interconnecting drug actions and disease mechanisms across diverse biological systems contexts, we designed a Disease-Drug Correlation Ontology (DDCO), formalized in OWL, that integrates multiple ontologies, controlled vocabularies, and data schemas and interlinks these with diverse datasets extracted from pharmacological and biological domains. Using the complex disease Systemic Lupus Erythematosus (SLE) as an example, a high-dimensional pharmacome-diseasome graph network was generated as RDF XML, and subjected to graph-theoretic proximity and connectivity analytic approaches to rank drugs versus the compendium of SLE-associated genes, pathways, and clinical features. Tamoxifen, a current candidate therapeutic for SLE, was the highest ranked drug.ConclusionThis early stage demonstration highlights critical directions to follow that will enable translational pharmacotherapeutic research. The uniform application of Semantic Web methodology to problems in data integration, knowledge representation, and analysis provides an efficient and potentially powerful means to allow mining of drug action and disease mechanism relationships. Further improvements in semantic representation of mechanistic relationships will provide a fertile basis for accelerated drug repositioning, reasoning, and discovery across the spectrum of human disease.

Faceted infrastructure for semantic digital libraries

PurposeThe paper aims to argue that digital library retrieval should be based on semantic representations and propose a semantic infrastructure for digital libraries.Design/methodology/approachThe approach taken is formal model based on subject representation for digital libraries.FindingsSearch engines and search techniques have fallen short of user expectations as they do not give context based retrieval. Deploying semantic web technologies would lead to efficient and more precise representation of digital library content and hence better retrieval. Though digital libraries often have metadata of information resources which can be accessed through OAI‐PMH, much remains to be accomplished in making digital libraries semantic web compliant. This paper presents a semantic infrastructure for digital libraries, that will go a long way in providing them and web based information services with products highly customised to users needs.Research limitations/implicationsHere only a model for semantic infrastructure is proposed. This model is proposed after studying current user‐centric, top‐down models adopted in digital library service architectures.Originality/valueThis paper gives a generic model for building semantic infrastructure for digital libraries. Faceted ontologies for digital libraries is just one approach. But the same may be adopted by groups working with different approaches in building ontologies to realise efficient retrieval in digital libraries.

Semantic web infrastructure for fungal enzyme biotechnologists

The FungalWeb Ontology seeks to support various data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the FungalWeb Ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter, we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) presenting application scenarios (ii) presenting the conceptualizations of the ontological frame able to support these scenarios and (iii) suggesting semantic queries typical of a fungal enzymologist involved in product development. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontoligent Interactive Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns and ontology content. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.

An overview of S-OGSA: A Reference Semantic Grid Architecture

The Grid's vision, of sharing diverse resources in a flexible, coordinated and secure manner through dynamic formation and disbanding of virtual communities, strongly depends on metadata. Currently, Grid metadata is generated and used in an ad hoc fashion, much of it buried in the Grid middleware's code libraries and database schemas. This ad hoc expression and use of metadata causes chronic dependency on human intervention during the operation of Grid machinery, leading to systems which are brittle when faced with frequent syntactic changes in resource coordination and sharing protocols. The Semantic Grid is an extension of the Grid in which rich resource metadata is exposed and handled explicitly, and shared and managed via Grid protocols. The layering of an explicit semantic infrastructure over the Grid Infrastructure potentially leads to increased interoperability and greater flexibility. In recent years, several projects have embraced the Semantic Grid vision. However, the Semantic Grid lacks a Reference Architecture or any kind of systematic framework for designing Semantic Grid components or applications. The Open Grid Service Architecture (OGSA) aims to define a core set of capabilities and behaviours for Grid systems. We propose a Reference Architecture that extends OGSA to support the explicit handling of semantics, and defines the associated knowledge services to support a spectrum of service capabilities. Guided by a set of design principles, Semantic-OGSA (S-OGSA) defines a model, the capabilities and the mechanisms for the Semantic Grid. We conclude by highlighting the commonalities and differences that the proposed architecture has with respect to other Grid frameworks.

DartGrid: a semantic infrastructure for building database Grid applications

AbstractIn the presence of a Database Grid where a huge number of highly diverse, widely distributed, autonomously managed databases can be involved in a sharing cycle, database tools and middleware should be well suited for schema mediation and query processing in a semantically meaningful way. In this paper, an implemented system called DartGrid is presented. DartGrid is intended to provide a semantic infrastructure for building database grid applications. We explore the essential and fundamental roles played by Resource Description Framework (RDF) semantics for database grids and implement a set of semantically enabled tools and grid services such as semantic browser, semantic mapping tools, ontology service, semantic query service and semantic registration service. We propose an RDF‐View‐based approach for relational schema mediation and describe the view‐based semantic query rewriting algorithm implemented in DartGrid. DartGrid has been used to build a real database grid application for Traditional Chinese Medicine in China. Copyright © 2006 John Wiley & Sons, Ltd.

Milestones and requirements for introducing semantic web concepts in information systems programmes

The Semantic Web as a vision for a machine-readable, metadata-intensive Web has resulted in an evolving collection of technologies and tools that deserve attention from the viewpoint of education. Nonetheless, existing approaches to curriculum design for this topic that emphasise on knowledge representation or technical issues should be complemented with an organisational vision that focuses on the value provided by Semantic Web infrastructure as a corporate asset and also by Semantic Web tools built on top of it. This paper addresses the conceptual framework that justifies Semantic Web technology in the context of information systems (IS), and provides an account of some of the main requirements and milestones needed to integrate the Semantic Web as a topic in IS programmes. Concretely, an existing IS model curricula is used to provide some tentative guidelines for such integration.

Semantic Web Infrastructure for Fungal Enzyme Biotechnologists

The FungalWeb Ontology aims to support the data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the Fungal Web ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) suggesting semantic queries typical of a fungal enzymologist involved in product development, (ii) presenting application scenarios, and (iii) presenting the conceptualizations of the ontological frame able to support these scenarios. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontologent Interative Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic and automated reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.

An Overview of S-OGSA: A Reference Semantic Grid Architecture

The Grid's vision, of sharing diverse resources in a flexible, coordinated and secure manner through dynamic formation and disbanding of virtual communities, strongly depends on metadata. Currently, Grid metadata is generated and used in an ad hoc fashion, much of it buried in the Grid middleware's code libraries and database schemas. This ad hoc expression and use of metadata causes chronic dependency on human intervention during the operation of Grid machinery, leading to systems which are brittle when faced with frequent syntactic changes in resource coordination and sharing protocols. The Semantic Grid is an extension of the Grid in which rich resource metadata is exposed and handled explicitly, and shared and managed via Grid protocols. The layering of an explicit semantic infrastructure over the Grid Infrastructure potentially leads to increased interoperability and greater flexibility. In recent years, several projects have embraced the Semantic Grid vision. However, the Semantic Grid lacks a reference architecture or any kind of systematic framework for designing Semantic Grid components or applications. The Open Grid Service Architecture (OGSA) aims to define a core set of capabilities and behaviours for Grid systems. We propose a Reference Architecture that extends OGSA to support the explicit handling of semantics, and defines the associated knowledge services to support a spectrum of service capabilities. Guided by a set of design principles, Semantic-OGSA (S-OGSA) defines a model, the capabilities and the mechanisms for the Semantic Grid. We conclude by highlighting the commonalities and differences that the proposed architecture has with respect to other Grid frameworks.

SemWebDL: A privacy-preserving Semantic Web infrastructure for digital libraries

Recent advances in digital libraries have been closely intertwined with advances in Internet technologies. With the advent of the Web, digital libraries have been able to reach constituencies previously unanticipated. Because of the wide deployability of Web-accessible digital libraries, the potential for privacy violations has also grown tremendously. The much touted Semantic Web, with its agent, service, and ontology technologies, is slated to take the Web to another qualitative level in advances. Unfortunately, these advances may also open doors for privacy violations in ways never seen before. We propose a Semantic Web infrastructure, called SemWebDL, that enables the dynamic composition of disparate and autonomous digital libraries while preserving user privacy. In the proposed infrastructure, users will be able to pose more qualitative queries that may require the ad hoc collaboration of multiple digital libraries. In addition to the Semantic Web-based infrastructure, the quality of the response would rest on extraneous information in the form of a profile. We introduce the concept of communities to enable subject-based cooperation and search speedup. Further, digital libraries’ heterogeneity and autonomy are transcended by a layered Web-service-based infrastructure. Semantic Web-based digital library providers would advertise to Web services, which in turn are organized in communities accessed by users. For the purpose of privacy preservation, we devise a three-tier privacy model consisting of user privacy, Web service privacy, and digital library privacy that offers autonomy of perspectives for privacy definition and violation. We propose an approach that seamlessly interoperates with potentially conflicting privacy definitions and policies at the different levels of the Semantic Web-based infrastructure. A key aspect in the approach is the use of reputations for outsourcing Web services. A Web service reputation is associated with its behavior with regard to privacy preservation. We developed a technique that uses attribute ontologies and information flow difference to collect, evaluate, and disseminate the reputation of Web services.

Schemas and Ontologies: Building a Semantic Infrastructure for the Grid and Digital Libraries Workshop Report from E-Science Institute, Edinburgh

This article discusses building a semantic infrastructure for the grid and digital libraries. It is a workshop report from E-Science institute, Edinburgh

Augmented Intensional Reasoning in Knowledge-Based Accounting Systems

A limitation of existing accounting systems is their lack of knowledge sharing and knowledge reuse, which makes the design and implementation of new accounting systems time-consuming and expensive. An important requirement for knowledge sharing and reuse is the existence of a common semantic infrastructure. In this article we use McCarthy's (1982) Resource-Event-Agent (REA) model as a common semantic infrastructure in an accounting context. The objective is to make knowledge-intensive use of REA to share accounting concepts across functional boundaries and to reuse these concepts in different applications and different systems, an approach we call augmented intensional reasoning. Intensional reasoning is the active use of conceptual structures in information systems operations such as design and information retrieval. For augmented intensional reasoning, the conceptual structures are extended with domain-specific REA knowledge. Sections II and III describe different dimensions of augmented intensional reasoning: the REA primitives, the technological features needed to support augmented intensional reasoning, the need for epistemologically adequate representations to make augmented intensional reasoning feasible, and the practical necessity of implementation compromises. Sections IV and V explore two uses of augmented intensional reasoning: design and operation of knowledge-based accounting systems. The example in Section V explains how augmented intensional reasoning works: (1) define the conceptual schema, (2) structure the conceptual schema in terms of REA (knowledge augmentation), (3) define a shareable and reusable accounting concept (claim), and (4) use the concept (claim) to derive information in different accounting cycles (revenue and acquisition).