AUTH

Aristotle University of Thessaloniki AUTH (Greece, Zacharias G. Scouras)

Website: www.auth.gr

 

Contribution to CEREBRAD

The role of the AUTH team within the CEREBRAD project is the development of a light-weight data integration knowledge broker platform – codenamed InFlame – in collaboration with other teams active in WP4, namely “Biological consequences of Low-Dose Ionizing Radiation (LDIR) exposure of the Central Nervous System”. The principal aim is the integration of publicly available data from the literature and experimental resources and their coupling with -omics results obtained from other partners within CEREBRAD to support the detection of novel biomarkers in LDIR exposure within their molecular context and ultimately pathway discovery for LDIR research.

During the first phase of the CEREBRAD project, the group has scanned more than 1,000 relevant publications, identified -omics datasets reported therein, and extracted identifiers and links of these entries for incorporation into our data collections. These entries were linked to the following public data repositories: NCBI Resources, DAVID, IntAct, PCViz, Allen Brain Atlas and Euratom’s RBStore – covering more than 5,000 links already. Future releases will include Ingenuity®, GeneMania and others according to future needs and user specifications. These links, both within InFlame and across data resources mentioned above, were developed using the available REST APIs specific for each data repository. The final deployment is based on a Microsoft® platform: the IT infrastructure hosted on AUTH’s Data Center runs the Windows 2008 R2 Server operating system, a Microsoft® IIS Web and FTP server and Microsoft® SQL 2012 Server relational database management system. As InFlame is reaching its late-development phase, the plan will be to fork a public-domain software-driven version, as prototyping evolves towards a release version by the end of 2014.

 

Snapshot of the Gene Catalog menu from CEREBRAD's InFlame

 

Example of pathway discovery (From Pantzartzi et al., 2010. Promoter complexity and tissue-specific expression of stress response components in Mytilus galloprovincialis, a sessile marine invertebrate species. PLoS Comput. Biol. 6(7), e1000847.