The problem of learning non-taxonomic relationships of ontologies from text

Manual construction of ontologies by domain experts and knowledge engineers is a costly task. Thus, automatic and/or semi-automatic approaches to their development are needed. Ontology Learning aims at identifying its constituent elements, such as non-taxonomic relationships, from textual information sources. This article presents a discussion of the problem of Learning Non-Taxonomic Relationships of Ontologies and defines its generic process. Four techniques representing the state of the art of Learning Non-Taxonomic Relationships of Ontologies are described and the solutions they provide are discussed along with their advantages and limitations

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

PARNT: A statistic based approach to extract non-taxonomic relationships of ontologies from text

Learning Non-Taxonomic Relationships is a subfield of Ontology learning that aims at automating the extraction of these relationships from text. This article proposes PARNT, a novel approach that supports ontology engineers in extracting these elements from corpora of plain English. PARNT is parametrized, extensible and uses original solutions that help to achieve better results when compared to other techniques for extracting non-taxonomic relationships from ontology concepts and English text. To evaluate the PARNT effectiveness, a comparative experiment with another state of the art technique was conducted.This work is supported by CNPq and CAPES, research funding agencies of the Brazilian government

Constructive Ontology Engineering

The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in literature have been used in creating ontologies from various data sources such as structured data in databases or unstructured text found in text documents or HTML documents. Various data mining techniques, natural language processing methods, syntactical analysis, machine learning methods, and other techniques have been used in building ontologies with automated and semi-automated processes. Due to the vast amount of unstructured text and its continued proliferation, the problem of constructing ontologies from text has attracted considerable attention for research. However, the constructed ontologies may be noisy, with missing and incorrect knowledge. Thus ontology construction continues to be a challenging research problem. The goal of this research is to investigate a new method for guiding a process of extracting and assembling candidate terms into domain specific concepts and relationships. The process is part of an overall semi automated system for creating ontologies from unstructured text sources and is driven by the user’s goals in an incremental process. The system applies natural language processing techniques and uses a series of syntactical analysis tools for extracting grammatical relations from a list of text terms representing the parts of speech of a sentence. The extraction process focuses on evaluating the subject predicate-object sequences of the text for potential concept-relation-concept triples to be built into an ontology. Users can guide the system by selecting seedling concept-relation-concept triples to assist building concepts from the extracted domain specific terms. As a result, the ontology building process develops into an incremental one that allows the user to interact with the system, to guide the development of an ontology, and to tailor the ontology for the user’s application needs. The main contribution of this work is the implementation and evaluation of a new semi- automated methodology for constructing domain specific ontologies from unstructured text corpus

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

Knowledge Search within a Company-WIKI

The usage of Wikis for the purpose of knowledge management within a business company is only of value if the stored information can be found easily. The fundamental characteristic of a Wiki, its easy and informal usage, results in large amounts of steadily changing, unstructured documents. The widely used full-text search often provides search results of insufficient accuracy. In this paper, we will present an approach likely to improve search quality, through the use of Semantic Web, Text Mining, and Case Based Reasoning (CBR) technologies. Search results are more precise and complete because, in contrast to full-text search, the proposed knowledge-based search operates on the semantic layer