proteome [54]. One needs to be careful in choosing the diagnostic targets that these two non-pathogenic organisms are not being detected. The initial list of 327 was refined to identify ‘‘core unique’’ proteins that are 100 amino acids or more in length. The 100 residue cutoff was used to ensure that the target list consisted of proteins that are real (short proteins might not be real) and are unique, as identification of homologs for short proteins is not trivial [55]. This resulted in a list of 21 ‘‘core unique’’ proteins in the pathogenic strains. It is possible that the proteins found may have homologs in other organisms which were undetected by CUPID because the genes were not annotated as open reading frames To confirm their uniqueness, the 21 proteins were screened for significant regions of similarity at the DNA level (either pseudogenes or unannotated genes) using tBLASTn against the NCBI nr database. Using NCBI’s nr which is produced independently of similar, but not identical, sources as iProClass also helps assure no sequences were missing from our warehouse. This additional analysis resulted in a total of 10 Bacillus anthracis specific proteins proposed as high-quality targets for development of diagnostic probes. We then supplemented this information with data from the PRC projects and Master Protein Directory to create a matrix of information (Figure 6). Six of the ten targets have data from the University of Michigan PRC showing that they were differentially expressed in published microarray experiments. Nine of the ten are available as clones produced by the Harvard Institute of Proteomics. A search of all the microarray data from the University of Michigan (using http://proteinbank.vbi.vt.edu/ ProteinBank/p/search/searchproteins.dll) showed that the four proteins not differentially expressed (listed as clones only in Figure 6) were still constitutively expressed well above background Pathogen-Host Omics Data in all studies (not shown). Either the proteins or the DNA coding for these proteins can be used to develop and test pathogen detection systems. All the ‘‘core unique’’ proteins detected in this study lacked meaningful functional annotation (i.e., were annotated simply as ‘‘uncharacterized protein’’), which is not surprising as such unique proteins are not easy to characterize. One protein identified as a target is a remnant of a prophage protein. Such proteins are well known to be related to virulence [56]. Another protein is from the pXO2 plasmid. A similar approach was taken for Salmonella species using CUPID and public PRC data and several candidate diagnostic proteins are currently being validated in the laboratory (data not shown). Discussion A systems approach to biology or medicine requires the sharing, integration and navigation of large and diverse experimental data sets to develop the models and hypotheses required to make new discoveries and to develop new treatments. To date this has most often been done with selected research data or within an institution or program where common instrumentation and methods make standardization of experimental practices and data management easier to achieve [57,58,59]. Alternative approaches require a reanalysis of all the data by a common methodology as has been done in some data repositories [60,61] or assigning some common statistical metric to all data of a certain type to allow functional coupling [62]. These approaches are all potentially useful, but practically difficult to achieve on a large scale with heterogeneous data. The protein-centric approach we employed is a relatively simple, yet powerful and practical, approach to integrate and Figure 6. Ten potential diagnostic markers for pathogenic strains of Bacillus anthracis. The prioritized protein list was obtained by computationally screening potential targets using CUPID [54], PRC data and other computational means described in the text. doi:10.1371/journal.pone.0007162.g006 PLoS ONE | www.plosone.org 9 September 2009 | Volume 4 | Issue 9 | e7162