An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B.

The advent of bioinformatics, genome-sequencing and high-throughput genome-wide experimentation (e.g. proteomics, transcriptomics) has lead to characterization of complex components pathosystems. Systemwide studies of interactions between components of biological systems and how these interactions give rise to the function and behavior of that system are becoming increasingly possible (23) (24) (25) . The available data in the RC [e.g. transcriptional and proteomics data of pathogen B. anthracis and of host mouse macrophages response (Use case 2)], greatly facilitates the analysis of the host and pathogen interaction using the framework of cyberinfrastructure built at the RC (26) (27) (28) (29) (30) . For example, a researcher can query all proteins that have been experimentally demonstrated to interact with secretion system chaperones and further refine that list by choosing those proteins that have been annotated as having signal peptide characteristics and are conserved among a list of pathogens. This use case is illustrated in Figure 3 . After entering the word 'chaperone' combined with the 'protein name' category, and 'signal' combined with the 'feature' category, as shown in the Figure 3A , and submitting the search, the system returns one chaperone protein in which the signal feature is represented ( Figure 3A) . Following the iProClass image (green at the left side), the user can review this chaperone protein summary information stored in the RC system ( Figure 3B ). Again clicking the UniProtKB ID hyperlink in Figure 3B , the user will obtain the most comprehensive annotation data regarding this chaperone protein ( Figure 3C ). More sophisticated search can be carried out by the experienced users.