Jingshan Huang

Service-Oriented Computing: Agents, Semantics, and Engineering

Executing Semantic Web Services with a Context-Aware Service Execution Agent.- An Effective Strategy for the Flexible Provisioning of Service Workflows.- Using Goals for Flexible Service Orchestration.- An Agent-Based Approach to User-Initiated Semantic Service Interconnection.- A Lightweight Agent Fabric for Service Autonomy.- Semantic Service Composition in Service-Oriented Multiagent Systems: A Filtering Approach.- Towards a Mapping from BPMN to Agents.- Associated Topic Extraction for Consumer Generated Media Analysis.- An MAS Infrastructure for Implementing SWSA Based Semantic Services.- A Role-Based Support Mechanism for Service Description and Discovery.- WS2JADE: Integrating Web Service with Jade Agents.- Z-Based Agents for Service Oriented Computing.

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

OMIT: A Domain-Specific Knowledge Base for MicroRNA Target Prediction

ABSTRACTIdentification and characterization of the important roles microRNAs (miRNAs) perform in human cancer is an increasingly active research area. Unfortunately, prediction of miRNA target genes remains a challenging task to cancer researchers. Current processes are time-consuming, error-prone, and subject to biologists’ limited prior knowledge. Therefore, we propose a domain-specific knowledge base built upon Ontology for MicroRNA Targets (OMIT) to facilitate knowledge acquisition in miRNA target gene prediction. We describe the ontology design, semantic annotation and data integration, and user-friendly interface and conclude that the OMIT system can assist biologists in unraveling the important roles of miRNAs in human cancer. Thus, it will help clinicians make sound decisions when treating cancer patients.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl.

Ontology-based knowledge discovery and sharing in bioinformatics and medical informatics: A brief survey

Worldwide health scientists are producing, accessing, analyzing, integrating, and storing massive amounts of digital medical data daily, through observation, experimentation, and simulation. If we were able to effectively transfer and integrate data from all possible resources, then a deeper understanding of all these data sets and better exposed knowledge, along with appropriate insights and actions, would be granted. Unfortunately, in many cases, the data users are not the data producers, and they thus face challenges in harnessing data in unforeseen and unplanned ways. In order to obtain the ability to integrate heterogeneous data, and thereby efficiently revolutionize the traditional medical and biological research, new methodologies built upon the increasingly pervasive cyberinfrastructure are required to conceptualize traditional medical and biological data, and acquire the “deep” knowledge out of original data thereafter. As formal knowledge representation models, ontologies can render invaluable help in this regard. In this paper, we summarize the state-of-the-art research in ontological techniques and their innovative application in medical and biological areas.

Use artificial neural network to align biological ontologies

BackgroundBeing formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics.ResultsIn this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others.ConclusionThe promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

OmniSeer: A Cognitive Framework for User Modeling, Reuse of Prior and Tacit Knowledge, and Collaborative Knowledge Services

This paper describes the current state of the OmniSeer system. OmniSeer supports intelligence analysts in the handling of massive amounts of data, the construction of scenarios, and the management of hypotheses. OmniSeer models analysts with dynamic user models that capture an analysts context, interests, and preferences, thus enabling more efficient and effective information retrieval. OmniSeer explicitly represents the prior and tacit knowledge of analysts, thus enabling transfer and reuse of such knowledge. Both the user and cognitive models employ a Bayesian network fragment representation, which supports principled probabilistic reasoning and analysis. An independent evaluation of OmniSeer was carried out at NIST and will be used to guide further development.

Knowledge Sharing and Reuse in Digital Forensics

Digital investigation involves examining large volumes of data from heterogeneous sources. We offer a framework forfacilitating examination and synthesis of this mountain of data using ontology matching and machine learning technology.

Ontology Reconciliation for Service-Oriented Computing

Service-oriented computing (SOC) is viewed as the computing paradigm of the near future, allowing for the dynamic interaction of services provided by distributed business partners. Being a declarative knowledge representation model, ontologies serve as a foundation for SOC. Due to the heterogeneous nature of independently designed ontologies, it is problematic for partners to understand the concepts adopted in ontologies from other sources. In order for partners to achieve seamless collaboration of services, they need to reconcile their ontologies with each other. During the alignment process and the following service interactions, compatibility is an important measurement that has been neglected in most research work. We extend a vector system to encode ontology compatibility. In addition, we present a new model - probabilistic center ontology - for better recording and maintenance of ontology alignment results. Our precise and efficient approach is verified by both theoretic proofs and experimental results

Reconciling agent ontologies for web service applications

Because there is still no agreed-upon global ontology, Web services supplied by different providers typically have individual and unique semantics, described by independently developed ontologies. The seamless connection of these distributed Web services for business-to-business applications depends heavily on reconciling the disparate semantics, possibly by integrating the ontologies. In this paper, we describe an approach to reconcile ontologies from distributed Web services. Our approach is totally automated, and features the following: i) alignment of the ontologies is performed without previous agreement on the semantics of the terminology in each ontology; ii) both linguistic and contextual features are considered; iii) the use of WordNet for linguistic analysis; iv) integration of heuristic knowledge for contextual analysis; and v) inference of new relationships by applying several rules based on domain-independent relationships and property lists. Experiments have been carried out to show the promising results of our system.