Raul Rodriguez-Esteban

Learn More
Functional areas of mammalian cerebral cortex seem positioned to minimize costs of their interconnections, down to a best-in-a-billion optimality level. The optimization problem here, originating in microcircuit design, is: Given connections among components, what is the physical placement of the components on a surface that minimizes total length of(More)
Text-mining algorithms make mistakes in extracting facts from natural-language texts. In biomedical applications, which rely on use of text-mined data, it is critical to assess the quality (the probability that the message is correctly extracted) of individual facts--to resolve data conflicts and inconsistencies. Using a large set of almost 100,000 manually(More)
We have generated and made publicly available two very large networks of molecular interactions: 49,493 mouse-specific and 52,518 human-specific interactions. These networks were generated through automated analysis of 368,331 full-text research articles and 8,039,972 article abstracts from the PubMed database, using the GeneWays system. Our networks cover(More)
A pattern of widespread connection optimization in the nervous system has become evident: deployment of some neural interconnections attains optimality, sometimes without detectable limits. New results for optimization of layout of connected areas of rat olfactory cortex and of rat amygdala are reported here. One larger question concerns mechanisms-how such(More)
Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic applications, do not offer sufficient flexibility for a wide range of(More)
Molecular perturbations provide a powerful toolset for biomedical researchers to scrutinize the contributions of individual molecules in biological systems. Perturbations qualify the context of experimental results and, despite their diversity, share properties in different dimensions in ways that can be formalized. We propose a formal framework to describe(More)
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to(More)