Ontology construction from online ontologies

One of the main hurdles towards a wide endorsement of ontologies is the high cost of constructing them. Reuse of existing ontologies offers a much cheaper alternative than building new ones from scratch, yet tools to support such reuse are still in their infancy. However, more ontologies are becoming available on the web, and online libraries for storing and indexing ontologies are increasing in number and demand. Search engines have also started to appear, to facilitate search and retrieval of online ontologies. This paper presents a fresh view on constructing ontologies automatically, by identifying, ranking, and merging fragments of online ontologies

Some Issues on Ontology Integration

The word integration has been used with different meanings in the ontology field. This article aims at clarifying the meaning of the word “integration” and presenting some of the relevant work done in integration. We identify three meanings of ontology “integration”: when building a new ontology reusing (by assembling, extending, specializing or adapting) other ontologies already available; when building an ontology by merging several ontologies into a single one that unifies all of them; when building an application using one or more ontologies. We discuss the different meanings of “integration”, identify the main characteristics of the three different processes and proposethree words to distinguish among those meanings:integration, merge and use

Ontology Population for Open-Source Intelligence

We present an approach based on GATE (General Architecture for Text Engineering) for the automatic population of ontologies from text documents. We describe some experimental results, which are encouraging in terms of extracted correct instances of the ontology. We then focus on a phase of our pipeline and discuss a variant thereof, which aims at reducing the manual effort needed to generate pre-defined dictionaries used in document annotation. Our additional experiments show promising results also in this case

Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology

Ontology Construction from Online Ontologies

One of the main hurdles towards a wide endorsement of ontologies is the high cost of constructing them. Reuse of existing ontologies offers a much cheaper alternative than building new ones from scratch, yet tools to support such reuse are still in their infancy. However, more ontologies are becoming available on the web, and online libraries for storing and indexing ontologies are increasing in number and demand. Search engines have also started to appear, to facilitate search and retrieval of online ontologies. This paper presents a fresh view on constructing ontologies automatically, by identifying, ranking, and merging fragments of online ontologies

A Generic library of problem-solving methods for scheduling applications

In this paper we describe a generic library of problem-solving methods (PSMs) for scheduling applications. Although, some attempts have been made in the past at developing libraries of scheduling methods, these only provide limited coverage: in some cases they are specific to a particular scheduling domain; in other cases they simply implement a particular scheduling technique; in other cases they fail to provide the required degree of depth and precision. Our library is based on a structured approach, whereby we first develop a scheduling task ontology, and then construct a task-specific but domain independent model of scheduling problem-solving, which generalises from specific approaches to scheduling problem-solving. Different PSMs are then constructed uniformly by specialising the generic model of scheduling problem-solving. Our library has been evaluated on a number of real-life and benchmark applications to demonstrate its generic and comprehensive nature

Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species. Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories. A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database. To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection. A large collection of new genetic markers was provided by this ESTs collection. This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation. (Résumé d'auteur

Improving Knowledge Retrieval in Digital Libraries Applying Intelligent Techniques

Nowadays an enormous quantity of heterogeneous and distributed information is stored in the digital University. Exploring online collections to find knowledge relevant to a user’s interests is a challenging work. The artificial intelligence and Semantic Web provide a common framework that allows knowledge to be shared and reused in an efficient way. In this work we propose a comprehensive approach for discovering E-learning objects in large digital collections based on analysis of recorded semantic metadata in those objects and the application of expert system technologies. We have used Case Based-Reasoning methodology to develop a prototype for supporting efficient retrieval knowledge from online repositories. We suggest a conceptual architecture for a semantic search engine. OntoUS is a collaborative effort that proposes a new form of interaction between users and digital libraries, where the latter are adapted to users and their surroundings