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Record Nr. |
UNINA9910770265603321 |
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Autore |
Bernasconi Anna |
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Titolo |
Model, Integrate, Search... Repeat : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi |
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Pubbl/distr/stampa |
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Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
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ISBN |
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Edizione |
[1st ed. 2023.] |
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Descrizione fisica |
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1 online resource (277 pages) |
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Collana |
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Lecture Notes in Business Information Processing, , 1865-1356 ; ; 496 |
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Disciplina |
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Soggetti |
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Application software |
Bioinformatics |
Quantitative research |
Artificial intelligence - Data processing |
Computer and Information Systems Applications |
Data Analysis and Big Data |
Data Science |
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Lingua di pubblicazione |
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Formato |
Materiale a stampa |
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Livello bibliografico |
Monografia |
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Nota di contenuto |
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Intro -- Foreword -- Preface -- Acknowledgements -- Contents -- Acronyms -- Introduction -- Genomic Data Integration -- Thesis Contribution within the GeCo Project -- The Recent COVID-19 Pandemic -- Thesis Structure -- Part I Human Genomic Data Integration -- Genomic Data Players and Processes -- Technological Pipeline of Genomic Data -- Production -- Integration -- Services and Access -- Taxonomy of Players Involved in Data Production and Integration -- Main Genomic Data Players -- Contributors -- Repository Hosts -- Consortia -- Integrators -- Modeling Genomic Data -- The Genomic Data Model -- The Genomic Conceptual Model -- Analysis of Metadata Attributes -- Model Design -- Validation: Source-Specific Views of GCM -- Related Works -- Integrating Genomic Data -- Theoretical Rationale -- Approach Overview -- Data Download -- Data Transformation -- Data Cleaning -- Data Mapping -- Data Normalization and Enrichment -- Search Service and Ontology Selection -- Enrichment Process -- Data Constraint Checking -- Architecture Implementation -- Data Persistence -- Architecture Validation -- |
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Lossless Integration -- Semantic Enrichment -- User Evaluation -- Related Works -- Snapshot of the Data Repository -- Included Data Sources -- OpenGDC: Integrating Cancer Genomic Data and Metadata -- Towards Automated Integration of Unstructured Metadata -- Experiments -- Related Works -- Searching Genomic Data -- Issues in Exploiting Semantic Knowledge in Genomics -- Inference Explanation -- GeKnowGraph: Exploration-Based Interface -- Exploration Interaction -- GenoSurf: a Web-Based Search Server for Genomic Datasets -- Data Search -- Key-Value Search -- Query Sessions -- Result Visualization -- Additional Functionalities -- Use Cases -- Validation of GenoSurf -- Related Works -- Future Directions of the Data Repository -- Including New Data Sources. |
Improving Genomic Data Quality Dimensions -- Towards Better Interoperability -- Simplifying Data and Tools for End Users -- Monitoring Integration and Search Value -- Part II Viral Sequence Data Integration -- Viral Sequences Data Management Resources -- Landscape of Data Resources for Viral Sequences -- Fully Open-Source Resources -- GISAID and its Resources -- Integration of Sources of Viral Sequences -- Metadata Integration -- Value Harmonization and Ontological Efforts -- Replicated Sequences in Multiple Sources -- SARS-CoV-2 Search Systems -- Portals to NCBI and GISAID Resources -- Integrative Search Systems -- Comparison -- Discussion -- GISAID Restrictions -- Metadata Quality -- (Un)Willingness to Share Sequence Data -- Modeling Viral Sequence Data -- Conceptual Modeling for Viral Genomics -- Answering Complex Biological Queries -- Related Works -- Integrating Viral Sequence Data -- Database Content -- Relational Schema -- Data Import -- Annotation and Variant Calling -- Data Curation -- Searching Viral Sequence Data -- Requirements Analysis -- Lessons Learnt -- Web Interface -- Example Queries -- Discussion -- Related Works -- Future Directions of the Viral Sequence Repository -- Research Agenda -- ViruSurf Extensions -- Visualization Support: VirusViz -- Active Monitoring of SARS-CoV-2 Variations -- Integrating Host-Pathogen Information -- The Virus Genotype - Host Phenotype Connection -- The Host Genotype - Host Phenotype Connection -- Part III Epilogue -- Conclusions and Vision -- Summary of Thesis Contributions -- Achievements within GeCo Project -- Outlook -- META-BASE tool configuration -- User Manual -- Process Configuration -- Mapper Configuration -- Experimental setup GEO metadata extraction -- Mappings of viral sources attributes into ViruSurf -- References. |
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Sommario/riassunto |
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This book is a revised version of the PhD dissertation written by the author to receive her PhD from the Department of Electronics, Information and Bioengineering at Politecnico di Milano, Italy. The work deals with one of the central objectives of the European Research Council project “Data-Driven Genomic Computing”, i.e., building an integrated repository for genomic data. It reflects the research adventure that starts from modeling biological data, goes through the challenges of integrating complex data and their describing metadata and finally builds tools for searching the data empowered by a semantic layer. The results of this thesis are part of a broad vision: the availability of conceptual models, related databases, and search systems for both humans and viruses genomics will provide important opportunities for research, especially if virus data will be connected to its host, the human being, who is the provider of genomic and phenotype information. In 2023,the PhD dissertation won the CAiSE PhD Award, granted to outstanding PhD theses in the field of information systems engineering. |
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2. |
Record Nr. |
UNINA9910483208503321 |
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Titolo |
Advances in Computational Intelligence : 12th International Work-Conference on Artificial Neural Networks, IWANN 2013, Puerto de la Cruz, Tenerife, Spain, June 12-14, 2013, Proceedings, Part II / / edited by Ignacio Rojas, Gonzalo Joya, Joan Cabestany |
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Pubbl/distr/stampa |
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Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2013 |
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ISBN |
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Edizione |
[1st ed. 2013.] |
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Descrizione fisica |
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1 online resource (XXVIII, 517 p. 180 illus.) |
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Collana |
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Theoretical Computer Science and General Issues, , 2512-2029 ; ; 7903 |
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Disciplina |
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Soggetti |
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Bioinformatics |
Pattern recognition systems |
Artificial intelligence |
Data mining |
Computer science |
Computational and Systems Biology |
Automated Pattern Recognition |
Artificial Intelligence |
Data Mining and Knowledge Discovery |
Models of Computation |
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Lingua di pubblicazione |
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Formato |
Materiale a stampa |
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Livello bibliografico |
Monografia |
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Note generali |
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Bibliographic Level Mode of Issuance: Monograph |
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Nota di contenuto |
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It’s as Easy as ABC: Introducing Anthropology-Based Computing -- Extreme Learning Machine: A Robust Modeling Technique? Yes! -- A Novel Framework to Design Fuzzy Rule-Based Ensembles Using Diversity Induction and Evolutionary Algorithms-Based Classifier Selection and Fusion -- Using Nonlinear Dimensionality Reduction to Visualize Classifiers -- Which Dissimilarity Is to Be Used When Extracting Typologies in Sequence Analysis? A Comparative Study -- Implementation of the C-Mantec Neural Network Constructive Algorithm in an Arduino Uno Microcontroller -- A Constructive Neural Network to Predict Pitting Corrosion Status of Stainless Steel -- Robust Sensor and Actuator Fault Diagnosis with GMDH Neural Networks -- |
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Diffusion Methods for Wind Power Ramp Detection -- Computational Study Based on Supervised Neural Architectures for Fluorescence Detection of Fungicides -- Study of Alternative Strategies to Selection of Peer in P2P Wireless Mesh Networks -- A Cloud-Based Neural Network Simulation Environment -- Performance Evaluation over Indoor Channels of an Unsupervised Decision-Aided Method for OSTBC Systems -- On Second Language Tutoring through Womb Grammars -- Simulated Annealing for Real-Time Vertical-Handoff in Wireless Networks -- Ant Colony Optimization Inspired Algorithm for 3D Object Segmentation -- Alternative OVA Proposals for Cooperative Competitive RBFN Design in Classification Tasks -- A Genetic Algorithms-Based Approach for Optimizing Similarity Aggregation in Ontology Matching -- Self-organized Learning by Self-Enforcing Networks. |
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Sommario/riassunto |
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This two-volume set LNCS 7902 and 7903 constitutes the refereed proceedings of the 12th International Work-Conference on Artificial Neural Networks, IWANN 2013, held in Puerto de la Cruz, Tenerife, Spain, in June 2013. The 116 revised papers were carefully reviewed and selected from numerous submissions for presentation in two volumes. The papers explore sections on mathematical and theoretical methods in computational intelligence, neurocomputational formulations, learning and adaptation emulation of cognitive functions, bio-inspired systems and neuro-engineering, advanced topics in computational intelligence and applications. |
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