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This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.
Book Synopsis The Gene Ontology Handbook by : Christophe Dessimoz
Download or read book The Gene Ontology Handbook written by Christophe Dessimoz and published by . This book was released on 2020-10-08 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.
Artificial Intelligence federates numerous scientific fields in the aim of developing machines able to assist human operators performing complex treatments---most of which demand high cognitive skills (e.g. learning or decision processes). Central to this quest is to give machines the ability to estimate the likeness or similarity between things in the way human beings estimate the similarity between stimuli. In this context, this book focuses on semantic measures: approaches designed for comparing semantic entities such as units of language, e.g. words, sentences, or concepts and instances defined into knowledge bases. The aim of these measures is to assess the similarity or relatedness of such semantic entities by taking into account their semantics, i.e. their meaning---intuitively, the words tea and coffee, which both refer to stimulating beverage, will be estimated to be more semantically similar than the words toffee (confection) and coffee, despite that the last pair has a higher syntactic similarity. The two state-of-the-art approaches for estimating and quantifying semantic similarities/relatedness of semantic entities are presented in detail: the first one relies on corpora analysis and is based on Natural Language Processing techniques and semantic models while the second is based on more or less formal, computer-readable and workable forms of knowledge such as semantic networks, thesauri or ontologies. Semantic measures are widely used today to compare units of language, concepts, instances or even resources indexed by them (e.g., documents, genes). They are central elements of a large variety of Natural Language Processing applications and knowledge-based treatments, and have therefore naturally been subject to intensive and interdisciplinary research efforts during last decades. Beyond a simple inventory and categorization of existing measures, the aim of this monograph is to convey novices as well as researchers of these domains toward a better understanding of semantic similarity estimation and more generally semantic measures. To this end, we propose an in-depth characterization of existing proposals by discussing their features, the assumptions on which they are based and empirical results regarding their performance in particular applications. By answering these questions and by providing a detailed discussion on the foundations of semantic measures, our aim is to give the reader key knowledge required to: (i) select the more relevant methods according to a particular usage context, (ii) understand the challenges offered to this field of study, (iii) distinguish room of improvements for state-of-the-art approaches and (iv) stimulate creativity toward the development of new approaches. In this aim, several definitions, theoretical and practical details, as well as concrete applications are presented.
Book Synopsis Semantic Similarity from Natural Language and Ontology Analysis by : Sébastien Harispe
Download or read book Semantic Similarity from Natural Language and Ontology Analysis written by Sébastien Harispe and published by Springer Nature. This book was released on 2022-05-31 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: Artificial Intelligence federates numerous scientific fields in the aim of developing machines able to assist human operators performing complex treatments---most of which demand high cognitive skills (e.g. learning or decision processes). Central to this quest is to give machines the ability to estimate the likeness or similarity between things in the way human beings estimate the similarity between stimuli. In this context, this book focuses on semantic measures: approaches designed for comparing semantic entities such as units of language, e.g. words, sentences, or concepts and instances defined into knowledge bases. The aim of these measures is to assess the similarity or relatedness of such semantic entities by taking into account their semantics, i.e. their meaning---intuitively, the words tea and coffee, which both refer to stimulating beverage, will be estimated to be more semantically similar than the words toffee (confection) and coffee, despite that the last pair has a higher syntactic similarity. The two state-of-the-art approaches for estimating and quantifying semantic similarities/relatedness of semantic entities are presented in detail: the first one relies on corpora analysis and is based on Natural Language Processing techniques and semantic models while the second is based on more or less formal, computer-readable and workable forms of knowledge such as semantic networks, thesauri or ontologies. Semantic measures are widely used today to compare units of language, concepts, instances or even resources indexed by them (e.g., documents, genes). They are central elements of a large variety of Natural Language Processing applications and knowledge-based treatments, and have therefore naturally been subject to intensive and interdisciplinary research efforts during last decades. Beyond a simple inventory and categorization of existing measures, the aim of this monograph is to convey novices as well as researchers of these domains toward a better understanding of semantic similarity estimation and more generally semantic measures. To this end, we propose an in-depth characterization of existing proposals by discussing their features, the assumptions on which they are based and empirical results regarding their performance in particular applications. By answering these questions and by providing a detailed discussion on the foundations of semantic measures, our aim is to give the reader key knowledge required to: (i) select the more relevant methods according to a particular usage context, (ii) understand the challenges offered to this field of study, (iii) distinguish room of improvements for state-of-the-art approaches and (iv) stimulate creativity toward the development of new approaches. In this aim, several definitions, theoretical and practical details, as well as concrete applications are presented.
"This book shows systems analysts and business analysts how ontological thinking can help them clarify requirements analysis tasks in business systems"--Provided by publisher.
Book Synopsis Business Systems Analysis with Ontologies by : Green, Peter F.
Download or read book Business Systems Analysis with Ontologies written by Green, Peter F. and published by IGI Global. This book was released on 2005-03-31 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book shows systems analysts and business analysts how ontological thinking can help them clarify requirements analysis tasks in business systems"--Provided by publisher.
It is the aim of the present study to introduce the reader to the ways of thinking of those contemporary philosophers who apply the tools of symbolic logic to classical philosophical problems. Unlike the "conti nental" reader for whom this work was originally written, the English speaking reader will be more familiar with most of the philosophers dis cussed in this book, and he will in general not be tempted to dismiss them indiscriminately as "positivists" and "nominalists". But the English version of this study may help to redress the balance in another respect. In view of the present emphasis on ordinary language and the wide spread tendency to leave the mathematical logicians alone with their technicalities, it seems not without merit to revive the interest in formal ontology and the construction of formal systems. A closer look at the historical account which will be given here, may convince the reader that there are several points in the historical develop ment whose consequences have not yet been fully assessed: I mention, e. g. , the shift from the traditional three-level semantics of sense and deno tation to the contemporary two-level semantics of representation; the relation of extensional structure and intensional content in the extensional systems of Wittgenstein and Carnap; the confusing changes in labelling the different kinds of analytic and apriori true sentences; etc. Among the philosophically interesting tools of symbolic logic Lesniewski's calculus of names deserves special attention.
Book Synopsis Ontology and the Logistic Analysis of Language by : Guido Küng
Download or read book Ontology and the Logistic Analysis of Language written by Guido Küng and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is the aim of the present study to introduce the reader to the ways of thinking of those contemporary philosophers who apply the tools of symbolic logic to classical philosophical problems. Unlike the "conti nental" reader for whom this work was originally written, the English speaking reader will be more familiar with most of the philosophers dis cussed in this book, and he will in general not be tempted to dismiss them indiscriminately as "positivists" and "nominalists". But the English version of this study may help to redress the balance in another respect. In view of the present emphasis on ordinary language and the wide spread tendency to leave the mathematical logicians alone with their technicalities, it seems not without merit to revive the interest in formal ontology and the construction of formal systems. A closer look at the historical account which will be given here, may convince the reader that there are several points in the historical develop ment whose consequences have not yet been fully assessed: I mention, e. g. , the shift from the traditional three-level semantics of sense and deno tation to the contemporary two-level semantics of representation; the relation of extensional structure and intensional content in the extensional systems of Wittgenstein and Carnap; the confusing changes in labelling the different kinds of analytic and apriori true sentences; etc. Among the philosophically interesting tools of symbolic logic Lesniewski's calculus of names deserves special attention.
Describes the origins, structure, and meaning of the leading philosophic work by the Jewish religious scholar.
Book Synopsis Martin Buber's Ontology by : Robert E. Wood
Download or read book Martin Buber's Ontology written by Robert E. Wood and published by Northwestern University Press. This book was released on 1969 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: Describes the origins, structure, and meaning of the leading philosophic work by the Jewish religious scholar.
This book constitutes the proceedings of the International Conference on ENTERprise information systems, held Viana do Castelo, Portugal, in October 2010.
Book Synopsis ENTERprise Information Systems, Part II by : Joao Eduardo Quintela Varajao
Download or read book ENTERprise Information Systems, Part II written by Joao Eduardo Quintela Varajao and published by Springer. This book was released on 2010-12-02 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the International Conference on ENTERprise information systems, held Viana do Castelo, Portugal, in October 2010.
With the advancements of semantic web, ontology has become the crucial mechanism for representing concepts in various domains. For research and dispersal of customized healthcare services, a major challenge is to efficiently retrieve and analyze individual patient data from a large volume of heterogeneous data over a long time span. This requirement demands effective ontology-based information retrieval approaches for clinical information systems so that the pertinent information can be mined from large amount of distributed data. This unique and groundbreaking book highlights the key advances in ontology-based information retrieval techniques being applied in the healthcare domain and covers the following areas: Semantic data integration in e-health care systems Keyword-based medical information retrieval Ontology-based query retrieval support for e-health implementation Ontologies as a database management system technology for medical information retrieval Information integration using contextual knowledge and ontology merging Collaborative ontology-based information indexing and retrieval in health informatics An ontology-based text mining framework for vulnerability assessment in health and social care An ontology-based multi-agent system for matchmaking patient healthcare monitoring A multi-agent system for querying heterogeneous data sources with ontologies for reducing cost of customized healthcare systems A methodology for ontology based multi agent systems development Ontology based systems for clinical systems: validity, ethics and regulation
Book Synopsis Ontology-Based Information Retrieval for Healthcare Systems by : Vishal Jain
Download or read book Ontology-Based Information Retrieval for Healthcare Systems written by Vishal Jain and published by John Wiley & Sons. This book was released on 2020-07-29 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the advancements of semantic web, ontology has become the crucial mechanism for representing concepts in various domains. For research and dispersal of customized healthcare services, a major challenge is to efficiently retrieve and analyze individual patient data from a large volume of heterogeneous data over a long time span. This requirement demands effective ontology-based information retrieval approaches for clinical information systems so that the pertinent information can be mined from large amount of distributed data. This unique and groundbreaking book highlights the key advances in ontology-based information retrieval techniques being applied in the healthcare domain and covers the following areas: Semantic data integration in e-health care systems Keyword-based medical information retrieval Ontology-based query retrieval support for e-health implementation Ontologies as a database management system technology for medical information retrieval Information integration using contextual knowledge and ontology merging Collaborative ontology-based information indexing and retrieval in health informatics An ontology-based text mining framework for vulnerability assessment in health and social care An ontology-based multi-agent system for matchmaking patient healthcare monitoring A multi-agent system for querying heterogeneous data sources with ontologies for reducing cost of customized healthcare systems A methodology for ontology based multi agent systems development Ontology based systems for clinical systems: validity, ethics and regulation
Domain analysis is the process of studying the actions, knowledge production, knowledge dissemination, and knowledge-base of a community of commonality, such as an academic discipline or a professional community. The products of domain analysis range from controlled vocabularies and other knowledge organization systems, to scientific evidence about the growth and sharing of knowledge and the evolution of communities of discourse and practice.In the field of knowledge organization- both the science and the practice domain analysis is the basic research method for identifying the concepts that will be critical building blocks for knowledge organization systems. This book will survey the theoretical rationale for domain analysis, present tutorials in the specific methods of domain analysis, especially with regard to tools for visualizing knowledge domains. Focuses on the science and practice of organizing knowledge Includes step-by-step instructions to enable the book to be used as a textbook or a manual for researchers
Book Synopsis Domain Analysis for Knowledge Organization by : Richard Smiraglia
Download or read book Domain Analysis for Knowledge Organization written by Richard Smiraglia and published by Chandos Publishing. This book was released on 2015-06-15 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt: Domain analysis is the process of studying the actions, knowledge production, knowledge dissemination, and knowledge-base of a community of commonality, such as an academic discipline or a professional community. The products of domain analysis range from controlled vocabularies and other knowledge organization systems, to scientific evidence about the growth and sharing of knowledge and the evolution of communities of discourse and practice.In the field of knowledge organization- both the science and the practice domain analysis is the basic research method for identifying the concepts that will be critical building blocks for knowledge organization systems. This book will survey the theoretical rationale for domain analysis, present tutorials in the specific methods of domain analysis, especially with regard to tools for visualizing knowledge domains. Focuses on the science and practice of organizing knowledge Includes step-by-step instructions to enable the book to be used as a textbook or a manual for researchers
This unique book succinctly summarizes the need to measure how ontologies (one of the building blocks of the Semantic Web) are currently being utilized, providing insights for various stakeholders. Where possible it improves and reuses terms in existing vocabularies/ontologies, as recommended by the Linked Data community. Recent advances in the Semantic Web have led to a proliferation of Resource Description Framework (RDF) data, which employ ontologies to semantically describe the information on the Web making it equally understandable for both humans and machines. However, to create a network effect, it is important that selective ontologies are used by more data publishers to improve the value of that ontology. For this to happen, it is vital to discover what is being used from an ontology to semantically annotate the information on the Web specific to a given domain. Answers to such basic but crucial questions can only be achieved by ascertaining how ontologies in the current semantic web are being utilized and adopted. The proposed frameworks to obtain such insights are explained with real-world examples to provide a clear and detailed description of ontology usage analysis. Both theoretical and practical, the book is of value to academics and professionals working in industry. Specifically, it is of primary interest to researchers, graduate students and practitioners in the area of the Semantic Web and its various real-world applications.
Book Synopsis Measuring and Analysing the Use of Ontologies by : Jamshaid Ashraf
Download or read book Measuring and Analysing the Use of Ontologies written by Jamshaid Ashraf and published by Springer. This book was released on 2018-03-16 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book succinctly summarizes the need to measure how ontologies (one of the building blocks of the Semantic Web) are currently being utilized, providing insights for various stakeholders. Where possible it improves and reuses terms in existing vocabularies/ontologies, as recommended by the Linked Data community. Recent advances in the Semantic Web have led to a proliferation of Resource Description Framework (RDF) data, which employ ontologies to semantically describe the information on the Web making it equally understandable for both humans and machines. However, to create a network effect, it is important that selective ontologies are used by more data publishers to improve the value of that ontology. For this to happen, it is vital to discover what is being used from an ontology to semantically annotate the information on the Web specific to a given domain. Answers to such basic but crucial questions can only be achieved by ascertaining how ontologies in the current semantic web are being utilized and adopted. The proposed frameworks to obtain such insights are explained with real-world examples to provide a clear and detailed description of ontology usage analysis. Both theoretical and practical, the book is of value to academics and professionals working in industry. Specifically, it is of primary interest to researchers, graduate students and practitioners in the area of the Semantic Web and its various real-world applications.
Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.
Book Synopsis Environmental Genomics by : C. Cristofre Martin
Download or read book Environmental Genomics written by C. Cristofre Martin and published by Springer Science & Business Media. This book was released on 2008-01-18 with total page 363 pages. Available in PDF, EPUB and Kindle. Book excerpt: Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.
