Analysis of the human diseasome reveals phenotype modules across common, genetic, and infectious diseases

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text- mining approach to identify the phenotypes (signs and symptoms) associated with over 8,000 diseases. We demonstrate that our method generates phenotypes that correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that share signs and symptoms cluster together, and we use this network to identify phenotypic disease modules

Context and Keyword Extraction in Plain Text Using a Graph Representation

Document indexation is an essential task achieved by archivists or automatic indexing tools. To retrieve relevant documents to a query, keywords describing this document have to be carefully chosen. Archivists have to find out the right topic of a document before starting to extract the keywords. For an archivist indexing specialized documents, experience plays an important role. But indexing documents on different topics is much harder. This article proposes an innovative method for an indexing support system. This system takes as input an ontology and a plain text document and provides as output contextualized keywords of the document. The method has been evaluated by exploiting Wikipedia's category links as a termino-ontological resources