Towards an Ontology-Based Phenotypic Query Model

Clinical research based on data from patient or study data management systems plays an important role in transferring basic findings into the daily practices of physicians. To support study recruitment, diagnostic processes, and risk factor evaluation, search queries for such management systems can be used. Typically, the query syntax as well as the underlying data structure vary greatly between different data management systems. This makes it difficult for domain experts (e.g., clinicians) to build and execute search queries. In this work, the Core Ontology of Phenotypes is used as a general model for phenotypic knowledge. This knowledge is required to create search queries that determine and classify individuals (e.g., patients or study participants) whose morphology, function, behaviour, or biochemical and physiological properties meet specific phenotype classes. A specific model describing a set of particular phenotype classes is called a Phenotype Specification Ontology. Such an ontology can be automatically converted to search queries on data management systems. The methods described have already been used successfully in several projects. Using ontologies to model phenotypic knowledge on patient or study data management systems is a viable approach. It allows clinicians to model from a domain perspective without knowing the actual data structure or query language

Tools for conversion, analysis, and annotation of histology images

Research presented in this thesis is aimed at making significant contributions in the field of computational pathology through the development of TIAToolbox, an open-source comprehensive Python library for computational pathology image analysis. The toolbox provides functionalities for tasks such as WSI reading, patch extraction, model inference, and visualization, with pre-trained models available for patch classification, semantic segmentation, and nucleus instance segmentation and classification. Additionally, the thesis explores the utility of alternative representations, including self-supervised and pooled multi-level wavelet representations, for histology image analysis. Moreover, the research addresses the challenges in annotation storage and querying, with the development of efficient storage systems capable of handling millions of annotations. These tools and techniques contribute to advancing computational pathology and provide valuable resources for future research, enabling more accurate and efficient analysis of histopathology images, thus having the potential to improve outcomes for patients

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward