Description logics for fuzzy ontologies on semantic web

To enable representation and reasoning for fuzzy ontologies with expressive fuzzy knowledge on the semantic web, a new fuzzy extension of description logics called the fuzzy description logics with comparison expressions （FCDLs） is presented. The syntax and semantics of FCDLs are formally defined, and the forms of axioms and assertions in FCDLs knowledge bases are specified. FCDLs combine both fuzzy concepts from the fuzzy description logics （FDLs） and cut concepts from the extended fuzzy description logics （EFDLs） in the same theory. Furthermore, cut concepts are extended into comparison cut concepts in FCDLs to represent comparison expressions between fuzzy membership degrees, which are often used in practice but not supported by the other fuzzy extensions of description logics. FCDLs have more expressive power than FDLs and EFDLs, and are able to represent expressive fuzzy knowledge and to perform reasoning tasks based on them. Therefore, FCDLs can enable representation and reasoning for fuzzy ontologies with expressive fuzzy knowledge on the semantic web.

Novel method for searching ontologies on semantic web

In order to solve the problem of information retrieval on the semantic web, a new semantic information retrieval （SIR） model for searching ontologies on the semantic web is proposed. First, SIR transformed domain ontologies into global ontologies. Then semantic index terms were extracted from these global ontologies. Based on semantic index terms, logical inferences can be performed and the logical views of the concept can be obtained. These logical views represent the expanded meaning of the concept. Using logical views, SIR can perform the information retrieval and inferences based on the semantic relationships in the documents, not only on the syntactic analysis of the documents. SIR can significantly enhance the recall and precision of the information retrieval by the semantic inference. Finally, the practicability of the SIR model is analyzed.

Kullback-Leibler distance based concepts mapping between web ontologies

A Kullback-Leibler（KL）distance based algorithm is presented to find the matches between concepts from different ontologies. First, each concept is represented as a specific probability distribution which is estimated from its own instances. Then, the similarity of two concepts from different ontologies is measured by the KL distance between the corresponding distributions. Finally, the concept-mapping relationship between different ontologies is obtained. Compared with other traditional instance-based algorithms, the computing complexity of the proposed algorithm is largely reduced. Moreover, because it proposes different estimation and smoothing methods of the concept distribution for different data types, it is suitable for various concepts mapping with different data types. The experimental results on real-world ontology mapping illustrate the effectiveness of the proposed algorithm.

Extend OWL: toward a clustering integration of collaborative ontologies and agents

In order to solve the problem of how to collaborate with foreign agents and ontologies, a restricted clustering integration approach is proposed. It differs from the traditional approaches in which web ontology language （OWL） is extended by adding some new collaborative interfaces （ i. e., agent-link and ontology-link） to it instead of owl： import. Syntaxes of the interface for foreign ontologies and foreign agents, respectively, and a meta-method of clustering integrated collaboration are discussed. The approach focuses on taking advantage of OWL itself to solve the collaborative problems, and it is feasible to track the contexts of newadded knowledge concerning ontological collaboration.

Approximate querying between heterogeneous ontologies based on association matrix

An approximate approach of querying between heterogeneous ontology-basedinformation systems based on an association matrix is proposed. First, the association matrix isdefined to describe relations between concepts in two ontologies. Then, a methodof rewriting queriesbased on the association matrix is presented to solve the ontology heterogeneity problem. Itrewrites the queries in one ontology to approximate queries in another ontology based on thesubsumption relations between concepts. The method also uses vectors to represent queries, and thencomputes the vectors with the association matrix; the disjoint relations between concepts can beconsidered by the results. It can get better approximations than the methods currently in use, whichdonot consider disjoint relations. The method can be processed by machines automatically. It issimple to implement and expected to run quite fast.

Method of creating ontologies for Prolog clauses

A method is proposed to build an ontology in the form of a conceptual graph for Prolog clauses, so that the Prolog reasoning engine can differentiate clauses semantically to some degree. The concept model of a clauses ontology is composed of predicate parameters and head sub-goals, and these sub-goals appear in the head of the rule body and precede any predicate calls. In the proposed method, a Prolog program can be transformed into a Prolog ＋ CG program that includes a clauses ontology. Some experiments show that, with a clauses ontology, some clauses which do not match current goals are not considered early enough, and, therefore, the size of the goal solution tree may be reduced. By the capability of conceptual graph, a clauses ontology makes the semantics of the Prolog program more clear and readable, and sometimes it speeds up the solution process obviously.

Bridge Ontology: A Multi-Ontologies-Based Approach for Semantic Annotation

Representing the relationships between ontologies is the key problem of semantic annotations based on multi-ontologies. Traditional approaches only had the ability of denoting the simple concept subsumption relations between ontologies. Through analyzing and classifying the relationships between ontologies, the idea of bridge ontology was proposed, which had the powerful capability of expressing the complex relationships between concepts and relationships between relations in multi-ontologies. Meanwhile, a new approach employing bridge ontology was proposed to deal with the multi-ontologies-based semantic annotation problem. The bridge ontology is a peculiar ontology, which can be created and maintained conveniently, and is effective in the multi-ontologies-based semantic annotation. The approach using bridge ontology has the advantages of low-cost, scalable, robust in the web circumstance, and avoiding the unnecessary ontology extending and integration. Key words semantic web - bridge ontology - multi-ontologies - semantic annotation CLC number TP 391 Foundation item: Supported by the National Natural Science Foundation of China (60373066, 60303024). National Grand Fundamental Research 973 Program of China (2002CB312000), National Re-search Foundation for the Doctoral Program of Higher Education of China (20020286004)Biography: WANG Peng (1977-), male, Ph.D candidate, research direction: semantic web, ontology, and knowledge representation on the Web.

Facilitating transparency in spinal cord injury studies using data standards and ontologies

Progress in developing robust therapies for spinal cord injury （SCI）, trau- matic brain injury （TBI） and peripheral nerve injury has been slow. A great deal has been learned over the past 30 years regarding both the intrinsic factors and the environmental factors that regulate axon growth, but this large body of information has not yet resulted in clinically available thera- peutics. This therapeutic bottleneck has many root causes, but a consensus is emerging that one contributing factor is a lack of standards for experi- mental design and reporting. The absence of reporting standards, and even of commonly accepted definitions of key words, also make data mining and bioinformatics analysis of neural plasticity and regeneration difficult, if not impossible. This short review will consider relevant background and poten- tial solutions to this problem in the axon regeneration domain.

Commentary on:“Facilitating transparency in spinal cord injury studies using data standards and ontologies”

Commentary Most would agree that providing comprehensive detail in scientific reporting is critical for the development of mean- ingful therapies and treatments for diseases. Such stellar practices 1） allow for reproduction of experiments to con- firm results, 2） promote thorough analyses of data, and 3） foster the incremental advancement of valid approaches. Unfortunately, most would also agree we have far to go to reach this vital goal （Hackam and Redelmeier, 2006; Prinz et al., 2011; Baker et al., 2014）.

Query Through Heterogeneous Ontologies Using Association Matrix

This paper introduces the definition and calculation of the association matrix between ontologies. It uses the association matrix to describe the relations between concepts in different ontologies and uses concept vectors to represent queries; then computes the vectors with the association matrix in order to rewrite queries. This paper proposes a simple method of querying through heterogeneous Ontology using association matrix. This method is based on the correctness of approximate information filtering theory; and it is simple to be implemented and expected to run quite fast. Key words semantic Web - information retrieval - ontology - query - association matrix CLC number TP 391 Foundation item: Supported by the National Natural Science Foundation of China (60373066, 60303024), National Grand Fundamental Research 973 Program of China (2002CB312000) and National Research Foundation for the Doctoral Program of Higher Education of China (20020286004)Biography: KANG Da-zhou (1980-), male, Master candidate, research direction: Semantic Web, knowledge representation on the Web.

Subsumption Checking between Concept Queries in Different Ontologies Based on Mutual Instances

This paper proposes a checking method based on mutual instances and discusses three key problems in the method： how to deal with mistakes in the mutual instances and how to deal with too many or too few mutual instances. It provides the checking based on the weighted mutual instances considering fault tolerance, gives a way to partition the large-scale mutual instances, and proposes a process greatly reducing the manual annotation work to get more mutual instances. Intension annotation that improves the checking method is also discussed. The method is practical and effective to check subsumption relations between concept queries in different ontologies based on mutual instances.

Constructing Product Ontologies with an Improved Conceptual Clustering Algorithm

In a distributed eMarketplace, recommended product ontologies are required for trading between buyers and sellers. Conceptual clustering can be employed to build dynamic recommended product ontologies. Traditional methods of conceptual clustering (e.g. COBWEB or Cluster/2) do not take heterogeneous attributes of a concept into account. Moreover, the result of these methods is clusters other than recommended concepts. A center recommendation clustering algorithm is provided. According to the values of heterogeneous attributes, recommended product names can be selected at the clusters, which are produced by this algorithm. This algorithm can also create the hierarchical relations between product names. The definitions of product names given by all participants are collected in a distributed eMarketplace. Recommended product ontologies are built. These ontologies include relations and definitions of product names, which come from different participants in the distributed eMarketplace. Finally a case is given to illustrate this method. The result shows that this method is feasible.

Concept Approximation between Fuzzy Ontologies

Fuzzy ontologics are efficient tools to handle fuzzy and uncertain knowledge on the semantic web; but there are heterogeneity problems when gaining interoperability among different fuzzy ontologies. This paper uses concept approximation between fuzzy ontologies based on instances to solve the heterogeneity problems. It firstly proposes an instance selection technology based on instance clustering and weighting to unify the fuzzy interpretation of different ontologies and reduce the number of instances to increase the efficiency. Then the paper resolves the problem of computing the approximations of concepts into the problem of computing the least upper approximations of atom concepts. It optimizes the search strategies by extending atom concept sets and defining the least upper bounds of concepts to reduce the searching space of the problem. An efficient algorithm for searching the least upper bounds of concept is given.

A Process for Extracting Non-Taxonomic Relationships of Ontologies from Text

Manual construction of ontologies by domain experts and knowledge engineers is an expensive and time consuming task so, automatic and/or semiautomatic approaches are needed. Ontology learning looks for identifying ontology elements like non-taxonomic relationships from information sources. These relationships correspond to slots in a frame-based ontology. This article proposes an initial process for semiautomatic extraction of non-taxonomic relationships of ontologies from textual sources. It uses Natural Language Processing (NLP) techniques to identify good candidates of non-taxonomic relationships and a data mining technique to suggest their possible best level in the ontology hierarchy. Once the extraction of these relationships is essentially a retrieval task, the metrics of this field like recall, precision and f-measure are used to perform evaluation.

Using ontology and rules to retrieve the semantics of disaster remote sensing data

Remote sensing data plays an important role in natural disaster management.However,with the increase of the variety and quantity of remote sensors,the problem of“knowledge barriers”arises when data users in disaster field retrieve remote sensing data.To improve this problem,this paper proposes an ontology and rule based retrieval(ORR)method to retrieve disaster remote sensing data,and this method introduces ontology technology to express earthquake disaster and remote sensing knowledge,on this basis,and realizes the task suitability reasoning of earthquake disaster remote sensing data,mining the semantic relationship between remote sensing metadata and disasters.The prototype system is built according to the ORR method,which is compared with the traditional method,using the ORR method to retrieve disaster remote sensing data can reduce the knowledge requirements of data users in the retrieval process and improve data retrieval efficiency.

An Algebra of Ontologies Approximation under Uncertainty

Ontologies are widely used in modeling the real world for the purpose of information sharing and reasoning. Traditional ontologies contain only concepts and relations that describe asserted facts about the world. Modeling in a dynamic world requires taking into consideration the uncertainty that may arise in the domain. In this paper, the concept of soft sets initiated by Molodtsov and the concept of rough sets introduced by Pawlack are used to define a way of instantiating ontologies of vague domains. We define ontological algebraic operations and their properties while taking into consideration the uncertain nature of domains. We show that, by doing so, intra ontological operations and their properties are preserved and formalized as operations in a vague set of objects and can be proved algebraically.

Converting Instance Checking to Subsumption: A Rethink for Object Queries over Practical Ontologies

Efficiently querying Description Logic (DL) ontologies is becoming a vital task in various data-intensive DL applications. Considered as a basic service for answering object queries over DL ontologies, instance checking can be realized by using the most specific concept (MSC) method, which converts instance checking into subsumption problems. This method, however, loses its simplicity and efficiency when applied to large and complex ontologies, as it tends to generate very large MSCs that could lead to intractable reasoning. In this paper, we propose a revision to this MSC method for DL SHI , allowing it to generate much simpler and smaller concepts that are specific enough to answer a given query. With independence between computed MSCs, scalability for query answering can also be achieved by distributing and parallelizing the computations. An empirical evaluation shows the efficacy of our revised MSC method and the significant efficiency achieved when using it for answering object queries.

Application of ontologies to traceability in the dairy supply chain

Systems for tracking products through supply chains range from paper-based records maintained by producers, processors, and suppliers to sophisticated ICT-based solutions. In addition to supporting product traceability, ICTs may also support data capture, recording, storage, and sharing of traceability attributes on processing, genetics, inputs, disease/pest tracking and measurement of environmental variables. A key success factor for a traceability system is the capability to integrate and share information along the supply chain. ICT represents a tool to overcome integration problems, data fusion and information dissemination. In this paper we illustrate the application of ontology as a tool to model business processes and rules within an agri- food chain. The business case is represented by the Bovlac project: a scientific and technologic platform to trace fresh cheese production.

BioBroker: Knowledge Discovery Framework for Heterogeneous Biomedical Ontologies and Data

A large number of ontologies have been introduced by the biomedical community in recent years. Knowledge discovery for entity identification from ontology has become an important research area, and it is always interesting to discovery how associations are established to connect concepts in a single ontology or across multiple ontologies. However, due to the exponential growth of biomedical big data and their complicated associations, it becomes very challenging to detect key associations among entities in an inefficient dynamic manner. Therefore, there exists a gap between the increasing needs for association detection and large volume of biomedical ontologies. In this paper, to bridge this gap, we presented a knowledge discovery framework, the BioBroker, for grouping entities to facilitate the process of biomedical knowledge discovery in an intelligent way. Specifically, we developed an innovative knowledge discovery algorithm that combines a graph clustering method and an indexing technique to discovery knowledge patterns over a set of interlinked data sources in an efficient way. We have demonstrated capabilities of the BioBroker for query execution with a use case study on a subset of the Bio2RDF life science linked data.

Ontologies for Software Project Management: A Review

Software Project Management is a knowledge intensive process that can benefit substantially from ontology development and ontology engineering. Ontology development could facilitate or improve substantially the software development process through the improvement of knowledge management, the increase of software and artefacts reusability, and the establishment of internal consistency within project management processes of various phases of software life cycle. A large number of ontologies have been developed attempting to address various software engineering aspects, such as requirements engineering, components reuse, domain modelling, etc. In this paper, we present a systematic literature review focusing on software project management ontologies. The literature review, among other, has identified lack of standardization in terminology and concepts, lack of systematic domain modelling and use of ontologies mainly in prototype ontology systems that address rather limited aspects of software project management processes.