Description : An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry. Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.
Description : The Digital Library Approach. Manual Annotations. Wrapping. Information Extraction & Linguistics. Graphics. Usage of Annotations.
Description : Did you ever read something on a book, felt the need to comment, took up a pencil and scribbled something on the books’ text’? If you did, you just annotated a book. But that process has now become something fundamental and revolutionary in these days of computing. Annotation is all about adding further information to text, pictures, movies and even to physical objects. In practice, anything which can be identified either virtually or physically can be annotated. In this book, we will delve into what makes annotations, and analyse their significance for the future evolutions of the web. We will explain why it was thought to be unreasonable to annotate documents manually and how Web 2.0 is making us rethink our beliefs. We will have a look at tools which make use of Artificial Intelligence techniques to support people in the annotation task. Behind these tools, there exists an important property of the web known as redundancy; we will explain what it is and show how it can be exploited. Finally we will gaze into the crystal ball and see what we might expect to see in the future. Until people understand what the web is all about and its grounding in annotation, people cannot start appreciating it. And until they do so, they cannot start creating the web of the future.
Description : Create your own natural language training corpus for machine learning. Whether you’re working with English, Chinese, or any other natural language, this hands-on book guides you through a proven annotation development cycle—the process of adding metadata to your training corpus to help ML algorithms work more efficiently. You don’t need any programming or linguistics experience to get started. Using detailed examples at every step, you’ll learn how the MATTER Annotation Development Process helps you Model, Annotate, Train, Test, Evaluate, and Revise your training corpus. You also get a complete walkthrough of a real-world annotation project. Define a clear annotation goal before collecting your dataset (corpus) Learn tools for analyzing the linguistic content of your corpus Build a model and specification for your annotation project Examine the different annotation formats, from basic XML to the Linguistic Annotation Framework Create a gold standard corpus that can be used to train and test ML algorithms Select the ML algorithms that will process your annotated data Evaluate the test results and revise your annotation task Learn how to use lightweight software for annotating texts and adjudicating the annotations This book is a perfect companion to O’Reilly’s Natural Language Processing with Python.
Description : This book constitutes the revised selected papers of the 5th International Provenance and Annotation Workshop, IPAW 2014, held in Cologne, Germany in June 2014. The 14 long papers, 20 short papers and 4 extended abstracts presented were carefully reviewed and selected from 53 submissions. The papers include tools that enable provenance capture from software compilers, from web publications and from scripts, using existing audit logs and employing both static and dynamic instrumentation.
Description : formats using XSLT transformations. The two main text analytics architectures, GATE and UIMA, are then described and compared, with practical exercises showing how to configure and customize them. The final chapter is an introduction to text analytics, describing the main applications and functions including named entity recognition, coreference resolution and information extraction, with practical examples using both open source and commercial tools." --Book Jacket.
Description : The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis. The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data. Each chapter includes references and pointers to relevant tools. As very few existing genome annotation pipelines are capable of dealing with the staggering amount of DNA sequence information, new strategies must be developed to accommodate the needs of today’s genome researchers. Covering this topic in detail, Genome Annotation provides you with the foundation and tools to tackle this challenging and evolving area. Suitable for both students new to the field and professionals who deal with genomic information in their work, the book offers two genome annotation systems on an accompanying CD-ROM.
Description : Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.
Description : This book constitutes the thoroughly refereed post-conference proceedings of the Second International Provenance and Annotation Workshop, IPAW 2008, held in Salt Lake City, UT, USA, in June 2007. The 14 revised full papers and 15 revised short and demo papers presented together with 2 keynote lectures were carefully reviewed and selected from 40 submissions. The paper are organized in topical sections on provenance: models and querying; provenance: visualization, failures, identity; provenance and workflows; provenance for streams and collaboration; and applications.