An information retrieval approach to ontology mapping

In this paper, we present a heuristic mapping method and a prototype mapping system that support the process of semi-automatic ontology mapping for the purpose of improving semantic interoperability in heterogeneous systems. The approach is based on the idea of semantic enrichment, i.e., using instance information of the ontology to enrich the original ontology and calculate similarities between concepts in two ontologies. The functional settings for the mapping system are discussed and the evaluation of the prototype implementation of the approach is reported. \ud \u

BIM semantic-enrichment for built heritage representation

In the built heritage context, BIM has shown difficulties in representing and managing the large and complex knowledge related to non-geometrical aspects of the heritage. Within this scope, this paper focuses on a domain-specific semantic-enrichment of BIM methodology, aimed at fulfilling semantic representation requirements of built heritage through Semantic Web technologies. To develop this semantic-enriched BIM approach, this research relies on the integration of a BIM environment with a knowledge base created through information ontologies. The result is knowledge base system - and a prototypal platform - that enhances semantic representation capabilities of BIM application to architectural heritage processes. It solves the issue of knowledge formalization in cultural heritage informative models, favouring a deeper comprehension and interpretation of all the building aspects. Its open structure allows future research to customize, scale and adapt the knowledge base different typologies of artefacts and heritage activities

Evaluating the semantic web: a task-based approach

The increased availability of online knowledge has led to the design of several algorithms that solve a variety of tasks by harvesting the Semantic Web, i.e. by dynamically selecting and exploring a multitude of online ontologies. Our hypothesis is that the performance of such novel algorithms implicity provides an insight into the quality of the used ontologies and thus opens the way to a task-based evaluation of the Semantic Web. We have investigated this hypothesis by studying the lessons learnt about online ontologies when used to solve three tasks: ontology matching, folksonomy enrichment, and word sense disambiguation. Our analysis leads to a suit of conclusions about the status of the Semantic Web, which highlight a number of strengths and weaknesses of the semantic information available online and complement the findings of other analysis of the Semantic Web landscape

An Ontology-Based Method for Semantic Integration of Business Components

Building new business information systems from reusable components is today an approach widely adopted and used. Using this approach in analysis and design phases presents a great interest and requires the use of a particular class of components called Business Components (BC). Business Components are today developed by several manufacturers and are available in many repositories. However, reusing and integrating them in a new Information System requires detection and resolution of semantic conflicts. Moreover, most of integration and semantic conflict resolution systems rely on ontology alignment methods based on domain ontology. This work is positioned at the intersection of two research areas: Integration of reusable Business Components and alignment of ontologies for semantic conflict resolution. Our contribution concerns both the proposal of a BC integration solution based on ontologies alignment and a method for enriching the domain ontology used as a support for alignment.Comment: IEEE New Technologies of Distributed Systems (NOTERE), 2011 11th Annual International Conference; ISSN: 2162-1896 Print ISBN: 978-1-4577-0729-2 INSPEC Accession Number: 12122775 201

htsint: a Python library for sequencing pipelines that combines data through gene set generation

Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. Conclusion: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint