11/12/2017

Thesis lecture of Oriol López Massaguer: "Development of informatic tools for extracting biomedical data from open and proprietary data sources with predictive purposes"

Next thursday 14th of December at 11.30, Oriol López Massaguer from the PharmacoInformatics group of GRIB will defense his thesis: "Development of informatic tools for extracting biomedical data from open and proprietary data sources with predictive purposes" at the Classroom number 61.346-348, placed at the third floor of the Doctor Aiguader building (Dr. Aiguader 80, Barcelona).

Abstract: we developed new software tools to obtain information from public and private data sources to develop in silico toxicity models. The first of these tools is Collector, an Open Source application that generates "QSAR-ready" series of compounds annotated with bioactivities, extracting the data from the Open PHACTS platform using semantic web technologies. Collector was applied in the framework of the eTOX project to develop predictive models for toxicity endpoints.

Additionally, we conceived, designed, implemented and tested a method to derive toxicity scorings suitable for predictive modelling starting from in vivo preclinical repeated-dose studies generated by the pharmaceutical industry.

This approach was tested by generating scorings for three hepatotoxicity endpoints: 'degenerative lesions', 'inflammatory liver changes' and 'non-neoplasic proliferative lesions'. The suitability of these scores was tested by comparing them with experimentally obtained point of departure doses as well as by developing tentative QSAR models, obtaining acceptable results.

Our method relies on ontology-based inference to extract information from our ontology annotated data stored in a relational database. Our method, as a whole, can be applied to other preclinical toxicity databases to generate toxicity scorings. Moreover, the ontology-based inference method on its own is applicable to any relational databases annotated with ontologies