Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

A Way to Automatically Enrich Biomedical Ontologies

International audienceBiomedical ontologies play an important role for information extraction in the biomedical domain. We present a workflow for updating automatically biomedical ontologies, composed of four steps. We detail two contributions concerning the concept extraction and semantic linkage of extracted terminology

Enhanced image annotations based on spatial information extraction and ontologies

Current research on image annotation often represents images in terms of labelled regions or objects, but pays little attention to the spatial positions or relationships between those regions or objects. To be effective, general purpose image retrieval systems require images with comprehensive annotations describing fully the content of the image. Much research is being done on automatic image annotation schemes but few authors address the issue of spatial annotations directly. This paper begins with a brief analysis of real picture queries to librarians showing how spatial terms are used to formulate queries. The paper is then concerned with the development of an enhanced automatic image annotation system, which extracts spatial information about objects in the image. The approach uses region boundaries and region labels to generate annotations describing absolute object positions and also relative positions between pairs of objects. A domain ontology and spatial information ontology are also used to extract more complex information about the relative closeness of objects to the viewer

Current status of biomedical ontologies: developments in 2007

The goal of this paper is to survey existing biomedical ontologies and their developments in 2007. This paper discusses features of biomedical ontologies that allow true information integration in biomedical domain. The paper is a compilation of several biomedical ontologies like Gene Ontology, Protein Ontology, etc. that have developed serving primarily the purposes of information extraction from on-line biomedical literature and databases

Current status of biomedical ontologies: developments in 2006

The goal of this paper is to survey existing biomedical ontologies and their developments in 2007. This paper discusses features of biomedical ontologies that allow true information integration in biomedical domain. The paper is a compilation of several biomedical ontologies like Gene Ontology, Protein Ontology, etc. that have developed serving primarily the purposes of information extraction from on-line biomedical literature and databases

AQUA: an ontology driven question answering system

This paper describes AQUA our question answering over the Web. AQUA was designed to work over heterogeneous sources. This means that AQUA is equipped to work as closed domain and in addition to open-domain question answering. As a first instance, AQUA tries to answer a question using a Knowledge base. If a query cannot be satisfied over a knowledge base/database. Then, AQUA tries to find an answer on web pages (i.e. it uses as corpus the internet as resource). Our system uses NLP (Natural Language Processing), First order logic and Information Extraction technologies. AQUA has been tested using an ontology which describes academic life. Keywords Ontologies, Information Extraction, Machine Learnin

Ontología y Procesamiento de Lenguaje Natural

At present, the convergence of several areas of knowledge has led to the design and implementation of ICT systems that support the integration of heterogeneous tools, such as artificial intelligence (AI), statistics and databases (BD), among others. Ontologies in computing are included in the world of AI and refer to formal representations of an area of knowledge or domain. The discipline that is in charge of the study and construction of tools to accelerate the process of creation of ontologies from the natural language is the ontological engineering. In this paper, we propose a knowledge management model based on the clinical histories of patients (HC) in Panama, based on information extraction (EI), natural language processing (PLN) and the development of a domain ontology.Keywords: Knowledge, information extraction, ontology, automatic population of ontologies, natural language processing