Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
نویسندگان
چکیده
منابع مشابه
Prediction of Human Gene - Phenotype Associations by Exploiting the Hierarchical Structure of the Human Phenotype Ontology
The Human Phenotype Ontology (HPO) provides a conceptualization of phenotype information and a tool for the computational analysis of human diseases. It covers a wide range of phenotypic abnormalities encountered in human diseases and its terms (classes) are structured according to a directed acyclic graph. In this context the prediction of the phenotypic abnormalities associated to human genes...
متن کاملApplication of gene ontology to gene identification.
Candidate gene identification deals with associating genes to underlying biological phenomena, such as diseases and specific disorders. It has been shown that classes of diseases with similar phenotypes are caused by functionally related genes. Currently, a fair amount of knowledge about the functional characterization can be found across several public databases; however, functional descriptor...
متن کاملDISEASES: text mining and data integration of disease-gene associations.
Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrenc...
متن کاملPrediction of Essential Genes by Mining Gene Ontology Semantics
Essential genes are indispensable for an organism’s living. These genes are widely discussed, and many researchers proposed prediction methods that not only find essential genes but also assist pathogens discovery and drug development. However, few studies utilized the relationship between gene functions and essential genes for essential gene prediction. In this paper, we explore the topic of e...
متن کاملStoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link betwe...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Database
سال: 2019
ISSN: 1758-0463
DOI: 10.1093/database/baz019