Semantic Web Ontologies Research Articles

Context-dependent views to axioms and consequences of Semantic Web ontologies

The framework developed in this paper can deal with scenarios where selected sub-ontologies of a large ontology are offered as views to users, based on contexts like the access rights of a user, the trust level required by the application, or the level of detail requested by the user. Instead of materializing a large number of different sub-ontologies, we propose to keep just one ontology, but equip each axiom with a label from an appropriate context lattice. The different contexts of this ontology are then also expressed by elements of this lattice. For large-scale ontologies, certain consequences (like the subsumption hierarchy) are often pre-computed. Instead of pre-computing these consequences for every context, our approach computes just one label (called a boundary) for each consequence such that a comparison of the user label with the consequence label determines whether the consequence follows from the sub-ontology determined by the context. We describe different black-box approaches for computing boundaries, and present first experimental results that compare the efficiency of these approaches on large real-world ontologies. Black-box means that, rather than requiring modifications of existing reasoning procedures, these approaches can use such procedures directly as sub-procedures, which allows us to employ existing highly-optimized reasoners. Similar to designing ontologies, the process of assigning axiom labels is error-prone. For this reason, we also address the problem of how to repair the labelling of an ontology in case the knowledge engineer notices that the computed boundary of a consequence does not coincide with her intuition regarding in which context the consequence should or should not be visible.

Unintended consequences of existential quantifications in biomedical ontologies.

BackgroundThe Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.ResultsWe analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom), from which we examined a random sample of 2,836 clauses.According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.ConclusionsThe current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.

Computerization of workflows, guidelines, and care pathways: a review of implementation challenges for process-oriented health information systems.

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation 'challenge' themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying 'challenge' themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings.

Innovation in Stem Cell Advocacy: You Only Get What You Can Measure

We propose that stem cell advocacy must engage in self-analysis to determine how to be maximally effective. For this analysis, eight advocacy elements can be measured: agitation, legislation, regulation, litigation, policy development, collaboration, education and innovation. For several of these elements, we show that stem cell advocates, particularly advocates for human embryonic stem cell research, have been matched by their opponents. This demonstrates the need for combining innovation and collaboration with advocacy-oriented education. To pursue innovative and collaborative education, we propose a 'bench-to-public knowledge' model and present some preliminary observations made with this model for different stem cell types. We also propose development of a semantic web information system to be operated within Internet Cloud/Apps/Social Media. We call this system the 'Stem Cell Information Technology Accelerator Platform'. Toward its construction, we propose formation of a working group to conceive semantic web ontology for stem cell science and its clinical translation into medicine. This ontology would function as a map of the relationships between and among the various informational components comprising discourse on stem cell research and its clinical translation, and would allow various stakeholders to contribute to evolving models of that science and translation. These models could, in turn, support an innovative and collaborative approach to education in furtherance of stem cell advocacy.

Folksonomies in the library: their impact on user experience, and their implications for the work of librarians

Folksonomies (‘bottom-up’, user-generated categorisations) are an integral part of ‘Web 2.0’ technologies, and have been employed in a wide variety of online contexts, including businesses (such as Amazon), social networking sites, photo and music sharing, blogs, and OPAC ‘discovery layers’. These unstructured knowledge organisation systems will also have an important role in future Semantic Web ontologies. Despite many shortcomings, the use of tags and folksonomies has become standard practice in indexing the Social Web. This conceptual paper poses four questions: 1. How have folksonomies been incorporated into libraries? 2. Does the use of tag clouds and folksonomies add value to the user’s experience of the library catalogue? 3. Is it possible for folksonomies to supplant traditional ‘top-down’ taxonomies? 4. What implications does the use of folksonomies have for the work of librarians? These are addressed through reference to the literature, as well as surveying examples of folksonomies in library catalogues.

S3QL: A distributed domain specific language for controlled semantic integration of life sciences data

BackgroundThe value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control.We have previously described the Simple Sloppy Semantic Database (S3DB) as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL), to operate on its underlying core model and facilitate management of Linked Data.ResultsReflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA) and molecular epidemiology of infectious diseases.ConclusionsS3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms.

Using provenance to debug changing ontologies

On the Semantic Web ontologies evolve and are managed in a distributed setting, e.g. in biomedical databases. Changes are contributed by multiple persons or organizations at various points in time. Often, changes differ by certainty or trustworthiness. When judging changes of automatically inferred knowledge and when debugging such evolving ontologies, the provenance of axioms (e.g. agent, trust degree and modification time) needs to be taken into account. Providing and reasoning with rich provenance data for expressive ontology languages, however, is a non-trivial task. In this paper we propose a formalization of provenance, which allows for the computation of provenance for inferences and inconsistencies. It allows us to answer questions such as “When has this inconsistency been introduced and who is responsible for this change?” as well as “Can I trust this inference?”. We propose a black box algorithm for reasoning with provenance, which is based on general pinpointing, and an optimization, which enables the use of provenance for debugging in real time even for very large and expressive ontologies, such as used in biomedical portals.

Constructing Domain Ontology Based on Fuzzy Set and Concept Lattice

The major content in FCA is to extract formal concepts and connections between them from data in form of formal context so as to form a lattice structure of formal concepts. Fuzzy set theory and fuzzy logic are acknowledged as an appropriate formalism for capturing imprecise and vague knowledge. The paper offers a methodology for building ontology for knowledge sharing and reusing based on fuzzy concept lattices union. This paper makes up these defects by applying formal concept analysis theory and fuzzy sets to construct concept hierarchies of ontology, and the experiments shows the CPU Time in the attribute numbers, indicating that FFCA is superior to FCA in building the ontology of semantic web.

Framework of integrated Semantic Web Services and Ontology Development for Telecommunication Industry

The concept of web services is loosely coupled, location transparent, and protocol-independent software system for distributed platform. Literature review indicates that existing web services content is composed for humans to read whereas Semantic Web Services (SWS) have emerged as a new paradigm for meaningful data retrieval in a distributed environment. SWS have automated the information processing by interpreting human and machines content comprehensively. Telecommunications industry with its increasing demand of services and adapting nature of frequent changes forces service providers to support automated service discovery for cutting cost and response time. The objective of this paper is not only to overcome the existing limitation of automated discovery for heterogeneous and homogenous services in one model for industrial application as discussed in this paper but also to provide a way for an integrated enhancement of semantic web services. The proposed framework is an integrated approach for enhancement for goal based services discovery for telecommunication industry. We have developed domain and billing application ontologies and a prototype to validate the proposed framework by integrating Web Service Execution Environment (WSMX) and Internet Reasoning Service (IRS-III).

Secure and Intelligent Decision making in Semantic web mining

With the huge amount of information available online the World Wide Web is a fertile area for data mining research. The Web has become a major vehicle in performing research and education related activities for researches and students. Web mining is the use of data mining technologies to automatically interact and discover information from web documents, which can be in structured, unstructured or semistructured form. We present an enterprise framework regarding semantic web mining in distance learning, which can be used to not only improve the quality of web mining results but also enhances the functions and services and the interoperability of long distance educational information systems and standards in the educational field. For on line distance education system we propose an Ontology-based approach to share online data and retrieve all relevant data about students and their courses. Thus semantic web ontology help build better web mining analysis in educational institute and web mining in-turns helps contract basis more powerful ontology in distance learning. Since the majority of the online data considered as private data we need various mechanism for privacy preservation and control over the online presence data. We propose privacy protection in semantic web mining using role back access control.

CREATING CONTEXT-AWARE COLLABORATIVE WORKING ENVIRONMENTS

Context-aware systems are intended for providing services adapted to the needs of people, by taking into account their state and the information related to their environment. One alternative to represent this context information resides in the use of Semantic Web ontologies. They provide a formal vocabulary which allows to easily express and share knowledge. Additionally, several types of automatic knowledge manipulation and reasoning processes become available thanks to the formal features of such ontologies. The inclusion of context information through ontologies in Collaborative Working Environments (CWEs) may bring important benefits to team work inside an organization, such as an automatic selection between different collaborative services according to the team members' preferences and their current state. This paper describes the design and implementation of a context-reasoning system which has been integrated into a CWE architecture to take advantage of context-awareness.

The Development Process of the Semantic Web and Web Ontology

This paper deals with the semantic web and web ontology. The existing ontology development processes are not catered towards casual web ontology development, a notion analogous to standard web page development. Ontologies have become common on the World-Wide Web[2]. Key features of this process include easy and rapid creation of ontological skeletons, searching and linking to existing ontologies and a natural language-based technique to improve presentation of ontologies[6]. Ontologies, however, vary greatly in size, scope and semantics. They can range from generic upper-level ontologies to domain-specific schemas. The success of the Semantic Web is based on the existance of numerous distributed ontologies, using which users can annotate their data, thereby enabling shared machine readable content. This paper elaborates the stages in a casual ontology development process.

Using Provenance to Debug Changing Ontologies

On the Semantic Web ontologies evolve and are managed in a distributed setting, e.g. in biomedical databases. Changes are contributed by multiple persons or organizations at various points in time. Often, changes differ by certainty or trustworthiness. When judging changes of automatically inferred knowledge and when debugging such evolving ontologies, the provenance of axioms (e.g. agent, trust degree and modification time) needs to be taken into account. Providing and reasoning with rich provenance data for expressive ontology languages, however, is a non-trivial task. In this paper we propose a formalization of provenance, which allows for the computation of provenance for inferences and inconsistencies. It allows us to answer questions such as “When has this inconsistency been introduced and who is responsible for this change?” as well as “Can I trust this inference?”. We propose a black box algorithm for reasoning with provenance, which is based on general pinpointing, and an optimization, which enables the use of provenance for debugging in real time even for very large and expressive ontologies, such as used in biomedical portals.

SPARQL Assist Language Neutral Query Composer

AbstractSPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.

SPARQL Assist Language Neutral Query Composer

SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.

Semantic wiki for quality management in software development projects

Quality management has become a strategic issue for organisations and is very valuable to produce quality software. However, quality management systems (QMS) are not easy to implement and maintain. The authors' experience shows the benefits of developing a QMS by first formalising it using semantic web ontologies and then putting them into practice through a semantic wiki. The QMS ontology that has been developed captures the core concepts of a traditional QMS and combines them with concepts coming from the MPIu+a development process model, which is geared towards obtaining usable and accessible software products. Then, the ontology semantics is directly put into play by a semantics-aware tool, the Semantic MediaWiki. The developed QMS tool is being used for 2 years by the GRIHO research group, where it has manages almost 50 software development projects taking into account the quality management issues. It has also been externally audited by a quality certification organisation. Its users are very satisfied with their daily work with the tool, which manages all the documents created during project development and also allows them to collaborate, thanks to the wiki features.

Methodology Research of Ontology Building in Semantic Web

This paper describes two concepts on the Semantic Web and Ontology and points out the core role of Ontology in Semantic Web. Moreover, the writer gives a Double-Channel Helix Methodology and expounds its advantages at the structure and the task-flow.

Concepts and semantic relations in information science

AbstractConcept‐based information retrieval and knowledge representation are in need of a theory of concepts and semantic relations. Guidelines for the construction and maintenance of knowledge organization systems (KOS) (such as ANSI/NISO Z39.19‐2005 in the U.S.A. or DIN 2331:1980 in Germany) do not consider results of concept theory and theory of relations to the full extent. They are not able to unify the currently different worlds of traditional controlled vocabularies, of the social web (tagging and folksonomies) and of the semantic web (ontologies). Concept definitions as well as semantic relations are based on epistemological theories (empiricism, rationalism, hermeneutics, pragmatism, and critical theory). A concept is determined via its intension and extension as well as by definition. We will meet the problem of vagueness by introducing prototypes. Some important definitions are concept explanations (after Aristotle) and the definition of family resemblances (in the sense of Wittgenstein). We will model concepts as frames (according to Barsalou). The most important paradigmatic relation in KOS is hierarchy, which must be arranged into different classes: Hyponymy consists of taxonomy and simple hyponymy, meronymy consists of many different part‐whole‐relations. For practical application purposes, the transitivity of the given relation is very important. Unspecific associative relations are of little help to our focused applications and should be replaced by generalizable and domain‐specific relations. We will discuss the reflexivity, symmetry, and transitivity of paradigmatic relations as well as the appearance of specific semantic relations in the different kinds of KOS (folksonomies, nomenclatures, classification systems, thesauri, and ontologies). Finally, we will pick out KOS as a central theme of the Semantic Web.

A context-aware adaptive learning system using agents

Evolution of Web technologies has made e-learning a popular common way of education and training. As an outcome, learning content adaptation has been the subject of many research projects lately. This paper suggests a framework for building an adaptive Learning Management System (LMS). The proposed architecture is based upon multi-agent systems and uses both Sharable Content Object Reference Model (SCORM) 2004 and semantic Web ontology for learning content storage, sequencing and adaptation. This system has been implemented upon a well known open-source LMS and its functionalities are demonstrated through the simulation of a scenario mimicing the real life conditions. The result reveals the system effectiveness for which it appears that the proposed approach may be very promising.

An Investigation on Semantic Web-based Business Support: Ontology development and inference framework for the course recommendation

As a fundamental knowledge source in a global learning environment, it is feasible to apply the relational database management systems (RDBMS), object-oriented database management systems (OODBMS), and other traditional DBMS. However, the traditional DBMSs are not feasible in semantic knowledge/ontology representation and inference. One of the reasonable ways to overcome the limitations is the semantic web-based business support framework. Especially, in this study, we focused on the development of semantic web ontology and natural language (NL)-based inference framework. To validate the efficiency of the proposed framework, we considered a reasonable scenario for course recommendation in a university.