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Biological Data Integration : Computer and Statistical Approaches / / coordinated by Christine Froidevaux, Marie-Laure Martin-Magniette, and Guillem Rigaill
| Biological Data Integration : Computer and Statistical Approaches / / coordinated by Christine Froidevaux, Marie-Laure Martin-Magniette, and Guillem Rigaill |
| Edizione | [First edition.] |
| Pubbl/distr/stampa | London, England : , : ISTE Ltd, , [2023] |
| Descrizione fisica | 1 online resource (276 pages) |
| Disciplina | 570.113 |
| Soggetto topico | Systems biology |
| ISBN |
1-394-25731-7
1-394-25729-5 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover -- Title Page -- Copyright Page -- Contents -- Preface -- Part 1. Knowledge Integration -- Chapter 1. Clinical Data Warehouses -- 1.1. Introduction to clinical information systems and biomedical warehousing: data warehouses for what purposes? -- 1.1.1. Warehouse history -- 1.1.2. Using data warehouses today -- 1.2. Challenge: widely scattered data -- 1.3. Data warehouses and clinical data -- 1.3.1. Warehouse structures -- 1.3.2. Warehouse construction and supply -- 1.3.3. Uses -- 1.4. Warehouses and omics data: challenges -- 1.4.1. Challenges of data volumetry and structuring omic data -- 1.4.2. Attempted solutions -- 1.5. Challenges and prospects -- 1.5.1. Toward general-purpose warehouses -- 1.5.2. Ethical dimension of the implementation and the use of warehouses -- 1.5.3. Origin and reproducibility -- 1.5.4. Data quality -- 1.5.5. Data warehousing federation and data sharing -- 1.6. References -- Chapter 2. Semantic Web Methods for Data Integration in Life Sciences -- 2.1. Data-related requirements in life sciences -- 2.1.1. Databases for the life sciences -- 2.1.2. Requirements -- 2.1.3. Common approaches: InterMine and BioMart -- 2.2. Semantic Web -- 2.2.1. Techniques -- 2.2.2. Implementation -- 2.3. Perspectives -- 2.3.1. Facilitating appropriation to users -- 2.3.2. Facilitating the appropriation by software programs: FAIR data -- 2.3.3. Federated queries -- 2.4. Conclusion -- 2.5. References -- Chapter 3. Workflows for Bioinformatics Data Integration -- 3.1. Introduction -- 3.2. Bioinformatics data processing chains: difficulties -- 3.2.1. Designing a data processing chain -- 3.2.2. Analysis execution and reproducibility -- 3.2.3. Maintenance, sharing and reuse -- 3.3. Solutions provided by scientific workflow systems -- 3.3.1. Fundamentals of workflow systems -- 3.3.2. Workflow systems -- 3.4. Use case: RNA-seq data analysis.
3.4.1. Study description -- 3.4.2. From data processing chain to workflows -- 3.4.3. Data processing chains implemented as workflows: conclusion -- 3.5. Challenges, open problems and research opportunities -- 3.5.1. Formalizing workflow development -- 3.5.2. Workflow testing -- 3.5.3. Discovering and sharing workflows -- 3.6. Conclusion -- 3.7. References -- Part 2. Integration and Statistics -- Chapter 4. Variable Selection in the General Linear Model: Application to Multiomic Approaches for the Study of Seed Quality -- 4.1. Introduction -- 4.2. Methodology -- 4.2.1. Estimation of the covariance matrix ƒ°q -- 4.2.2. Estimation of B -- 4.3. Numerical experiments -- 4.3.1. Statistical performance -- 4.3.2. Numerical performance -- 4.4. Application to the study of seed quality -- 4.4.1. Metabolomics data -- 4.4.2. Proteomics data -- 4.5. Conclusion -- 4.6. Appendices -- 4.6.1. Example of using the package MultiVarSel for metabolomic data analysis -- 4.6.2. Example of using the package MultiVarSel for proteomic data analysis -- 4.7. Acknowledgments -- 4.8. References -- Chapter 5. Structured Compression of Genetic Information and Genome-Wide Association Study by Additive Models -- 5.1. Genome-wide association studies -- 5.1.1. Introduction to genetic mapping and linkage analysis -- 5.1.2. Principles of genome-wide association studies -- 5.1.3. Single nucleotide polymorphism -- 5.1.4. Disease penetrance and odds ratio -- 5.1.5. Single marker analysis -- 5.1.6. Multi-marker analysis -- 5.2. Structured compression and association study -- 5.2.1. Context -- 5.2.2. New structured compression approach -- 5.3. Application to ankylosing spondylitis (AS) -- 5.3.1. Data -- 5.3.2. Predictive power evaluation -- 5.3.3. Manhattan diagram -- 5.3.4. Estimation for the most significant SNP aggregates -- 5.4. Conclusion -- 5.5. References -- Chapter 6. Kernels for Omics. 6.1. Introduction -- 6.2. Relational data -- 6.2.1. Data described by the kernel -- 6.2.2. Data described by a general (dis)similarity measure -- 6.3. Exploratory analysis for relational data -- 6.3.1. Kernel clustering -- 6.3.2. Kernel principal component analysis -- 6.3.3. Kernel self-organizing maps -- 6.3.4. Limitations of relational methods -- 6.4. Combining relational data -- 6.4.1. Data integration in systems biology -- 6.4.2. Kernel approaches in data integration -- 6.4.3. A consensual kernel -- 6.4.4. A parsimonious kernel that preserves the topology of the initial data -- 6.4.5. A complete kernel preserving the topology of the initial data -- 6.5. Application -- 6.5.1. Loading Tara Ocean data -- 6.5.2. Data integration by kernel approaches -- 6.5.3. Exploratory analysis: kernel PCA -- 6.6. Session information for the results of the example -- 6.7. References -- Chapter 7. Multivariate Models for Data Integration and Biomarker Selection in 'Omics Data -- 7.1. Introduction -- 7.2. Background -- 7.2.1. Mathematical notations -- 7.2.2. Terminology -- 7.2.3. Multivariate projection-based approaches -- 7.2.4. A criterion to maximize specific to each methodology -- 7.2.5. A linear combination of variables to reduce the dimension of the data -- 7.2.6. Identifying a subset of relevant molecular features -- 7.2.7. Summary -- 7.3. From the biological question to the statistical analysis -- 7.3.1. Exploration of one dataset: PCA -- 7.3.2. Classify samples: projection to latent structure discriminant analysis -- 7.3.3. Integration of two datasets: projection to latent structure and related methods -- 7.3.4. Integration of several datasets: multi-block approaches -- 7.4. Graphical outputs -- 7.4.1. Individual plots -- 7.4.2. Variable plots -- 7.5. Overall summary -- 7.6. Liver toxicity study -- 7.6.1. The datasets. 7.6.2. Biological questions and statistical methods -- 7.6.3. Single dataset analysis -- 7.6.4. Integrative analysis -- 7.7. Conclusion -- 7.8. Acknowledgments -- 7.9. Appendix: reproducible R code -- 7.9.1. Toy examples -- 7.9.2. Liver toxicity -- 7.10. References -- List of Authors -- Index -- EULA. |
| Record Nr. | UNINA-9910830623303321 |
| London, England : , : ISTE Ltd, , [2023] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Data Integration in the Life Sciences [[electronic resource] ] : 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008, Proceedings / / edited by Amos Bairoch, Sarah Cohen-Boulakia, Christine Froidevaux
| Data Integration in the Life Sciences [[electronic resource] ] : 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008, Proceedings / / edited by Amos Bairoch, Sarah Cohen-Boulakia, Christine Froidevaux |
| Edizione | [1st ed. 2008.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2008 |
| Descrizione fisica | 1 online resource (XIII, 209 p.) |
| Disciplina | 610 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Medicine
Data mining Health informatics Database management Application software Bioinformatics Medicine/Public Health, general Data Mining and Knowledge Discovery Health Informatics Database Management Information Systems Applications (incl. Internet) Computational Biology/Bioinformatics |
| Soggetto genere / forma |
Evry (2008)
Kongress. |
| ISBN | 3-540-69828-0 |
| Classificazione |
BIO 110f
SS 4800 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Keynote Presentations -- Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues -- BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats -- Data Integration in the Life Sciences: Fun, Findings and Frustrations -- Semantic Web for the Life Sciences -- Analyzing the Evolution of Life Science Ontologies and Mappings -- Ontology Design Principles and Normalization Techniques in the Web -- Exploiting Ontology Structure and Patterns of Annotation to Mine Significant Associations between Pairs of Controlled Vocabulary Terms -- Designing and Evaluating Architectures to Integrate Biological Data -- Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System -- VisGenome and Ensembl: Usability of Integrated Genome Maps -- An Entity Resolution Framework for Deduplicating Proteins -- New Architectures and Experience on Using Systems -- Semantic Representation and Querying of caBIG Data Services -- SisGen: A CORBA–Based Data Management Program for DNA Sequencing Projects -- Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species -- ENFIN - An Integrative Structure for Systems Biology -- Systems Using Technologies from the Semantic Web for the Life Sciences -- A System for Ontology-Based Annotation of Biomedical Data -- Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse -- OMIE: Ontology Mapping within an Interactive and Extensible Environment -- Chemical Knowledge for the Semantic Web -- Mining Integrated Biological Data -- Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions -- Semi Supervised Spectral Clustering for Regulatory Module Discovery -- New Features of Major Resources for Biomolecular Data -- UniProtKB/Swiss-Prot: New and Future Developments -- EBI Proteomics Services -- DILS 2008 Tutorial -- Bio-ontologies Tutorial. |
| Record Nr. | UNISA-996465841303316 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Data Integration in the Life Sciences : 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008, Proceedings / / edited by Amos Bairoch, Sarah Cohen-Boulakia, Christine Froidevaux
| Data Integration in the Life Sciences : 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008, Proceedings / / edited by Amos Bairoch, Sarah Cohen-Boulakia, Christine Froidevaux |
| Edizione | [1st ed. 2008.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2008 |
| Descrizione fisica | 1 online resource (XIII, 209 p.) |
| Disciplina | 610 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Medicine
Data mining Health informatics Database management Application software Bioinformatics Medicine/Public Health, general Data Mining and Knowledge Discovery Health Informatics Database Management Information Systems Applications (incl. Internet) Computational Biology/Bioinformatics |
| Soggetto genere / forma |
Evry (2008)
Kongress. |
| ISBN | 3-540-69828-0 |
| Classificazione |
BIO 110f
SS 4800 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Keynote Presentations -- Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues -- BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats -- Data Integration in the Life Sciences: Fun, Findings and Frustrations -- Semantic Web for the Life Sciences -- Analyzing the Evolution of Life Science Ontologies and Mappings -- Ontology Design Principles and Normalization Techniques in the Web -- Exploiting Ontology Structure and Patterns of Annotation to Mine Significant Associations between Pairs of Controlled Vocabulary Terms -- Designing and Evaluating Architectures to Integrate Biological Data -- Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System -- VisGenome and Ensembl: Usability of Integrated Genome Maps -- An Entity Resolution Framework for Deduplicating Proteins -- New Architectures and Experience on Using Systems -- Semantic Representation and Querying of caBIG Data Services -- SisGen: A CORBA–Based Data Management Program for DNA Sequencing Projects -- Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species -- ENFIN - An Integrative Structure for Systems Biology -- Systems Using Technologies from the Semantic Web for the Life Sciences -- A System for Ontology-Based Annotation of Biomedical Data -- Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse -- OMIE: Ontology Mapping within an Interactive and Extensible Environment -- Chemical Knowledge for the Semantic Web -- Mining Integrated Biological Data -- Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions -- Semi Supervised Spectral Clustering for Regulatory Module Discovery -- New Features of Major Resources for Biomolecular Data -- UniProtKB/Swiss-Prot: New and Future Developments -- EBI Proteomics Services -- DILS 2008 Tutorial -- Bio-ontologies Tutorial. |
| Record Nr. | UNINA-9910768199103321 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 2008 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Symbolic and Quantitative Approaches to Reasoning and Uncertainty [[electronic resource] ] : European Conference, ECSQARU '95, Fribourg, Switzerland, July 3-5, 1995. Proceedings / / edited by Christine Froidevaux, Juerg Kohlas
| Symbolic and Quantitative Approaches to Reasoning and Uncertainty [[electronic resource] ] : European Conference, ECSQARU '95, Fribourg, Switzerland, July 3-5, 1995. Proceedings / / edited by Christine Froidevaux, Juerg Kohlas |
| Edizione | [1st ed. 1995.] |
| Pubbl/distr/stampa | Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 1995 |
| Descrizione fisica | 1 online resource (X, 438 p.) |
| Disciplina | 006.3 |
| Collana | Lecture Notes in Artificial Intelligence |
| Soggetto topico |
Artificial intelligence
Mathematical logic Artificial Intelligence Mathematical Logic and Formal Languages |
| ISBN | 3-540-49438-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | For all typical -- A posteriori knowledge: from ambiguous knowledge and undefined information to knowledge -- Modeling uncertain relational knowledge: the AV-quantified production rules approach -- Multiple database logic -- A local approach to reasoning under inconsistency in stratified knowledge bases -- Quasi-classical logic: Non-trivializable classical reasoning from inconsistent information -- A cost bounded possibilistic ATMS -- A substructural connective for possibilistic logic -- Chain graphs: Semantics and expressiveness -- Axiomatic treatment of possibilistic independence -- Parametric structure of probabilities in Bayesian networks -- From non-monotonic syntax-based entailment to preference-based argumentation -- Non-monotonic syntax-based entailment: A classification of consequence relations -- Local Möbius transforms of monotone capacities -- Automated reasoning with merged contradictory information whose reliability depends on topics -- Linking transition-based update and base revision -- Prioritized transitions for updates -- Probabilistic satisfiability and decomposition -- Update postulates without inertia -- Similarity-based consequence relations -- Epistemic approach to actions with typical effects -- Nonmonotonic belief state frames and reasoning frames -- A Bayesian network based learning system: — Architecture and performance comparison with other methods -- Specificity by default -- Constructing flexible dynamic belief networks from first-order probabilistic knowledge bases -- On the formalism of stochastic logic -- Using default logic in information retrieval -- Sensitivity analysis in Bayesian networks -- Bayesian approximation and invariance of Bayesian belief functions -- Model-based diagnostics using hints -- An axiomatic approach to extensional probability measures -- The dynamics of default reasoning -- Lemma handling in default logic theorem provers -- Uncertain reasoning in concept lattices -- A theorem prover for default logic based on prioritized conflict resolution and an extended resolution principle -- A theorem prover for lukaszewicz open default theory -- Two different types of discontinuity of bayesian learning in causal probabilistic networks -- Revision in extended propositional calculus -- Using qualitative uncertainty in protein topology prediction -- Circumscribing features and fluents: Reasoning about action with default effects -- Using Maximum Entropy to compute marginal probabilities in a causal binary tree need not take exponential time -- Yet some more considerations on cumulativity in default logics -- A two-stage approach to first order default reasoning -- A reduction of the theory of confirmation to the notions of distance and measure -- Cluster-based specification techniques in Dempster-Shafer theory -- And/or trees for knowledge representation -- Why defeasible deontic logic needs a multi preference semantics -- Numeric defaults. |
| Record Nr. | UNISA-996466131603316 |
| Berlin, Heidelberg : , : Springer Berlin Heidelberg : , : Imprint : Springer, , 1995 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||