Centralizing Discovery Information: From Logistics to Knowledge at a Public Organization

Manuel      Urbano-Cuadrado; Obdulia      Rabal; Julen      Oyarzabal

Abstract

Due to the huge amount of data generated in drug discovery programs, their success strongly depends on both the workflows and platforms to manage and, more importantly, to integrate different chemical and biological data sources. At Experimental Therapeutics Program in the Spanish National Cancer Research Center (CNIO), we have addressed our efforts in the design and optimal implementation of those key processes that enable dynamic workflows and interfaces between the different information blocks. Our approach focuses on the development of a common chemical and biological repository (CCBR) that gathers all data that pass quality control criteria. An integral web application (WACBIP) was designed to query against CCBR while providing decision making tools. Currently, our CCBR contains more than 43,000 unique structures as well as experimental data from more than 350 different biological assays. As input sources of the CCBR, we federated a series of Laboratory Information Management Systems (LIMS) which cover sections as follows: chemical synthesis, analytical department, compound logistics, biochemical and cellular data (including high throughput and high-content screenings; HTS and HCS), computational chemistry (in silico chemogenomics and physico-chemical profiling) and in vivo pharmacology. With regard to the last section, an integral In vivo Management e-Biobook (IVMB) that handles the entire workflow of in vivo labs was designed and implemented. Herein we describe the processes and tools that we have developed and implemented, balancing purchase and development, for centralizing discovery information as well as providing decision-making and project management tools – a clear unmet need in public organizations and networks.

Keywords: Data integration, chemical biology information, database, discovery LIMSs federation, e-chembook, logistics, HCS, HTS, in vivo e-biobook, data visualization, decision-making tools, project management platform, drug discovery workflow