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.

Data is integrated in a protein-centric manner by mapping all proteins and genes in the experimental results to UniProtKB (14) or UniParc (15) accession numbers using the id-mapping mechanism provided by the iProClass (16) system. In rare cases, RC created identifiers for gene(s)/protein(s) that could not be mapped to the existing databases. The original IDs used by the research centers are preserved. In this way every gene/protein is assigned a unique accession number which links the experimental results from the biodefense research centers to functional annotation and information from 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genome data, ontologies, literature and taxonomy. Data integration enhances the search functionality of the system, as protein attributes from all these other sources are made available in addition to those provided by the research centers, allowing complex searches across multiple experiments and data types. Hyperlinks to external data resources are provided.