Ontology Generation Framework Research Articles

Semi-automated ontology development scheme via text mining of scientific records

PurposeThe purpose of this study is to develop a domain independent, cost-effective, time-saving and semi-automated ontology generation framework that could extract taxonomic concepts from unstructured text corpus. In the human disease domain, ontologies are found to be extremely useful for managing the diversity of technical expressions in favour of information retrieval objectives. The boundaries of these domains are expanding so fast that it is essential to continuously develop new ontologies or upgrade available ones.Design/methodology/approachThis paper proposes a semi-automated approach that extracts entities/relations via text mining of scientific publications. Text mining-based ontology (TmbOnt)-named code is generated to assist a user in capturing, processing and establishing ontology elements. This code takes a pile of unstructured text files as input and projects them into high-valued entities or relations as output. As a semi-automated approach, a user supervises the process, filters meaningful predecessor/successor phrases and finalizes the demanded ontology-taxonomy. To verify the practical capabilities of the scheme, a case study was performed to drive glaucoma ontology-taxonomy. For this purpose, text files containing 10,000 records were collected from PubMed.FindingsThe proposed approach processed over 3.8 million tokenized terms of those records and yielded the resultant glaucoma ontology-taxonomy. Compared with two famous disease ontologies, TmbOnt-driven taxonomy demonstrated a 60%–100% coverage ratio against famous medical thesauruses and ontology taxonomies, such as Human Disease Ontology, Medical Subject Headings and National Cancer Institute Thesaurus, with an average of 70% additional terms recommended for ontology development.Originality/valueAccording to the literature, the proposed scheme demonstrated novel capability in expanding the ontology-taxonomy structure with a semi-automated text mining approach, aiming for future fully-automated approaches.

Linked open data-based framework for automatic biomedical ontology generation

BackgroundFulfilling the vision of Semantic Web requires an accurate data model for organizing knowledge and sharing common understanding of the domain. Fitting this description, ontologies are the cornerstones of Semantic Web and can be used to solve many problems of clinical information and biomedical engineering, such as word sense disambiguation, semantic similarity, question answering, ontology alignment, etc. Manual construction of ontology is labor intensive and requires domain experts and ontology engineers. To downsize the labor-intensive nature of ontology generation and minimize the need for domain experts, we present a novel automated ontology generation framework, Linked Open Data approach for Automatic Biomedical Ontology Generation (LOD-ABOG), which is empowered by Linked Open Data (LOD). LOD-ABOG performs concept extraction using knowledge base mainly UMLS and LOD, along with Natural Language Processing (NLP) operations; and applies relation extraction using LOD, Breadth first Search (BSF) graph method, and Freepal repository patterns.ResultsOur evaluation shows improved results in most of the tasks of ontology generation compared to those obtained by existing frameworks. We evaluated the performance of individual tasks (modules) of proposed framework using CDR and SemMedDB datasets. For concept extraction, evaluation shows an average F-measure of 58.12% for CDR corpus and 81.68% for SemMedDB; F-measure of 65.26% and 77.44% for biomedical taxonomic relation extraction using datasets of CDR and SemMedDB, respectively; and F-measure of 52.78% and 58.12% for biomedical non-taxonomic relation extraction using CDR corpus and SemMedDB, respectively. Additionally, the comparison with manually constructed baseline Alzheimer ontology shows F-measure of 72.48% in terms of concepts detection, 76.27% in relation extraction, and 83.28% in property extraction. Also, we compared our proposed framework with ontology-learning framework called “OntoGain” which shows that LOD-ABOG performs 14.76% better in terms of relation extraction.ConclusionThis paper has presented LOD-ABOG framework which shows that current LOD sources and technologies are a promising solution to automate the process of biomedical ontology generation and extract relations to a greater extent. In addition, unlike existing frameworks which require domain experts in ontology development process, the proposed approach requires involvement of them only for improvement purpose at the end of ontology life cycle.

Automated ontology generation framework powered by linked biomedical ontologies for disease-drug domain

Objective and background: The exponential growth of the unstructured data available in biomedical literature, and Electronic Health Record (EHR), requires powerful novel technologies and architectures to unlock the information hidden in the unstructured data. The success of smart healthcare applications such as clinical decision support systems, disease diagnosis systems, and healthcare management systems depends on knowledge that is understandable by machines to interpret and infer new knowledge from it. In this regard, ontological data models are expected to play a vital role to organize, integrate, and make informative inferences with the knowledge implicit in that unstructured data and represent the resultant knowledge in a form that machines can understand. However, constructing such models is challenging because they demand intensive labor, domain experts, and ontology engineers. Such requirements impose a limit on the scale or scope of ontological data models. We present a framework that will allow mitigating the time-intensity to build ontologies and achieve machine interoperability.Methods: Empowered by linked biomedical ontologies, our proposed novel Automated Ontology Generation Framework consists of five major modules: a) Text Processing using compute on demand approach. b) Medical Semantic Annotation using N-Gram, ontology linking and classification algorithms, c) Relation Extraction using graph method and Syntactic Patterns, d), Semantic Enrichment using RDF mining, e) Domain Inference Engine to build the formal ontology.Results: Quantitative evaluations show 84.78% recall, 53.35% precision, and 67.70% F-measure in terms of disease-drug concepts identification; 85.51% recall, 69.61% precision, and F-measure 76.74% with respect to taxonomic relation extraction; and 77.20% recall, 40.10% precision, and F-measure 52.78% with respect to biomedical non-taxonomic relation extraction.Conclusion: We present an automated ontology generation framework that is empowered by Linked Biomedical Ontologies. This framework integrates various natural language processing, semantic enrichment, syntactic pattern, and graph algorithm based techniques. Moreover, it shows that using Linked Biomedical Ontologies enables a promising solution to the problem of automating the process of disease-drug ontology generation.

Comparative Analysis of Data Mining Tools and Techniques for Information Retrieval

Background/Objectives: There are a lot of information retrieval techniques available for getting information from different kinds of sources. Main aim of this paper is to improve information retrieval activities to a higher level. Different methods for information retrieval have been studied and discussed. It involves use of Fuzzy Ontology Generation framework (FOGA) framework along with Formal Concept Analysis (FCA) based clustering and keyword matching approach. Hidden Markov Model has been used for retrieval of data from search engines in an intelligent and efficient way for correct identification and retrieval from the database. Classification algorithm has been used for detection of community and conversion of large community graph to sub community graph for its better study and usage. Findings: It has been found that fuzzy ontology generation framework can automatically generate the fuzzy ontology which is very hard and time consuming task otherwise. Clustering of data can be done using the technique of formal concept analysis along with keyword matching method. There is a large amount of data available under similar words but with different meanings. So there has been a lot of problem in retrieval of exact data as required in a very short amount of time. In this case Hidden Markov Model can be used which can find the non-observable or hidden stochastic process from the observable stochastic process. Application/Improvements: Generalized Expectation-Maximization algorithm used with Hidden Markov Model can find unknown parameters. By adding frequency tracking algorithm along with Hidden Markov Model, we can also track audible data from a large database. Community detection algorithm along with Informap and Bigclam algorithms used with Hidden Markov Model will increase the modularity of data. Its applications include use of information retrieval of different types of data in an extremely faster and efficient way.

A Fuzzy Ontology Generation Framework from Fuzzy Relational Databases

Ontology is an important part of the W3C standards for the Semantic Web used to specify standard conceptual vocabularies to exchange data among systems, provide reusable knowledge bases, and facilitate interoperability across multiple heterogeneous systems and databases. However, current ontology is not sufficient for handling vague information that is commonly found in many application domains. A feasible solution is to import the fuzzy ability to extend the classical ontology. In this article, we propose a fuzzy ontology generation framework from the fuzzy relational databases, in which the fuzzy ontology consists of fuzzy ontology structure and instances. We simultaneously consider the schema and instances of the fuzzy relational databases, and respectively transform them to fuzzy ontology structure and fuzzy RDF data model. This can ensure the integrality of the original structure as well as the completeness and consistency of the original instances in the fuzzy relational databases.

A citation-based document retrieval system for finding research expertise

Current citation-based document retrieval systems generally offer only limited search facilities, such as author search. In order to facilitate more advanced search functions, we have developed a significantly improved system that employs two novel techniques: Context-based Cluster Analysis (CCA) and Context-based Ontology Generation frAmework (COGA). CCA aims to extract relevant information from clusters originally obtained from disparate clustering methods by building relationships between them. The built relationships are then represented as formal context using the Formal Concept Analysis (FCA) technique. COGA aims to generate ontology from clusters relationship built by CCA. By combining these two techniques, we are able to perform ontology learning from a citation database using clustering results. We have implemented the improved system and have demonstrated its use for finding research domain expertise. We have also conducted performance evaluation on the system and the results are encouraging.

Automatic fuzzy ontology generation for semantic Web

Ontology is an effective conceptualism commonly used for the semantic Web. Fuzzy logic can be incorporated to ontology to represent uncertainty information. Typically, fuzzy ontology is generated from a predefined concept hierarchy. However, to construct a concept hierarchy for a certain domain can be a difficult and tedious task. To tackle this problem, this paper proposes the FOGA (fuzzy ontology generation framework) for automatic generation of fuzzy ontology on uncertainty information. The FOGA framework comprises the following components: fuzzy formal concept analysis, concept hierarchy generation, and fuzzy ontology generation. We also discuss approximating reasoning for incremental enrichment of the ontology with new upcoming data. Finally, a fuzzy-based technique for integrating other attributes of database to the ontology is proposed.