Ontology-based data integration

About: Ontology-based data integration is a research topic. Over the lifetime, 11065 publications have been published within this topic receiving 216888 citations.

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

Abstract: Background: The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description: Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions: In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

OntoShare - An Ontology-based Knowledge Sharing System for virtual Communities of Practice.

Abstract: An ontology-based knowledge sharing system OntoShare and its evaluation as part of a case study is described. RDF(S) is are used to specify and populate an ontology, based on information shared between users in virtual communities. We begin by discussing the advantages that use of Semantic Web technology afford in the area of knowledge management tools. The way in which OntoShare supports WWW-based communities of practice is described. Usage of OntoShare semi-automatically builds an RDF-annotated information resource for the community (and potentially for others also). Observing that in practice the meanings of and relationships between concepts evolve over time, OntoShare supports a degree of ontology evolution based on usage of the system - that is, based on the kinds of information users are sharing and the con- cepts (ontological classes) to which they assign this information. A case study involving OntoShare was carried out. The evaluation exercise for this case study and its results are described. We conclude by describing avenues of ongoing and future research.

Document annotation and ontology population from linguistic extractions

Abstract: In this paper, we present a workbench for semi-automatic ontology population from textual documents It provides an environment for mapping the linguistic extractions with the domain ontology thanks to knowledge acquisition rules Those rules are activated when a pertinent linguistic tag is reached Those linguistic tags are then mapped to a concept, one of its attributes or even a semantic relation between several concepts The rules instantiate these concepts, attributes and relations in the knowledge base constrained by the domain ontology This paper deals with the underlying knowledge capture process and presents the first experiments realized on a real client application from the legal publishing domain

Personal ontologies

Abstract: Corporations can suffer from too much information, and it is often inaccessible, inconsistent, and incomprehensible. The corporate solution entails knowledge management techniques and data warehouses. The paper discusses the use of the personal ontology. The promising approach is an organization scheme based on a model of an office and its information, an ontology, coupled with the proper tools for using it.

An ontology-based support for product conceptual design

Abstract: The research presented in this paper is a follow-up of our prior work involving the development of a graphical modeling tool to support designers at the conceptual design stage. To close the loop for supporting designers in generating design concepts flexibly, fast, and easily, an ontology-based approach for knowledge management that works along with the graphical modeling tool is discussed. Ontology and databases for the tool are developed to promote the systematic capture of design knowledge and efficient reuse of the design knowledge selection. In order to locate the proper information and query the data from the databases, the relationship between the ontology and databases, the data analysis process, ontology enrichment, and the ontology-based query engine are built to offer users multiple design results according to users' requirements. A tire design example is presented to demonstrate the proposed approach. The ontology-based method described in this paper can help retrieve and save the complex relations, support the reasoning, integrate heterogeneous data resources and offer users more accurate, proper and comprehensive data.