Pathogen-Host Omics Data Figure 2. Unstructured Keyword Query. A) The keyword ‘‘bacillus anthracis’’ hits results for project related proteins, SOPs, literature and technologies. The query can then be refined further by using specific fields to form a structured query. Here the search is restricted to return only proteins with interaction data. B) Multiple gene and protein IDs provided by the PRCs are merged into one representation of the protein. C) All data types and experimental datasets from different centers are listed together. D) Matched fields are displayed to aid users in formulating queries. To reproduce these queries use this URL: http://pir.georgetown.edu/cgi-bin/textsearch_cat.pl?search = 1&field0 = all&query0 = bacillus+anthracis&an- dor1 = and&field1 = DATATYPE&query1 = interaction . doi:10.1371/journal.pone.0007162.g002 Web-based Protein Search – Searching Pathogen-Host Omics Data Simple Keyword Search. Due to the popularity of internet searches, support of unstructured keyword queries, even for structured data, has become critical for any web site. To support this feature, the default protein-centric search returns results for all project deliverables, data, reagents, protocols, technologies and publications. An example is shown in Figure 2 where a single keyword search ‘‘bacillus anthracis’’ finds 10,988 pathogen and host proteins with Mass spec, microarray or protein interaction data and also 13,251 reagents in the Master Reagent Directory (mostly ORF and Y2H clones and mutant bacterial strains of Bacillus anthracis), 2 SOPs, 16 project publications and 2 technologies. The matched fields column allows users to refine their queries and construct simple Boolean searches. Biological Use Case Examples – Analyzing Pathogen-Host Omics Data Example I: Integrative Analysis. Structured fields allow Boolean queries across organisms, data types and laboratories. Figure 3 shows a query where we make use of the controlled vocabulary in the ‘‘expression condition’’ field and searched for common host proteins detected in studies of Bacillus anthracis and Salmonella typhimurium infection in mouse macrophage cell lines. Currently 222 proteins meet these criteria, mostly from mass spectrometry studies by PNNL and the University of Michigan; however, if we further restrict the search to include only those also detected in microarray experiments, we find 16 proteins with mass spec data from S. typhimurium infections at one research center, and mass spec and microarray studies done using B. anthracis at another research center. From the customizable results display shown in Figure 3 we can view summary information on the proteins detected. Full details on the protein and individual experimental results are available via links [5]. Some benefits of the protein-centric mapping approach are visible in the default display. 1) Minimizing redundancy, the column PRC ID shows the different identifiers from different databases used by the research centers. In the case of one protein Q9WUA3/K6PP_MOUSE 6-phosphofructokinase type C (EC 2.7.1.11), a total of 9 identifiers from 4 different databases PLoS ONE | www.plosone.org 5 September 2009 | Volume 4 | Issue 9 | e7162