Pathogen-Host Omics Data Figure 1. General infrastructure and information flow of the Biodefense Resource Center. The Master Protein Directory provides protein- centric data integration, search and analysis capabilities. The Proteomics Catalog houses web pages with information on the PRCs, the NIAID Proteomics Program and project related publications. The Proteomics Data Center contains complete experimental data and protocols for each PRC data set in relational databases but is not integrated in the protein-centric manner. All databases are linked on the web. doi:10.1371/journal.pone.0007162.g001 attempting to combine data across research laboratories unless identical sequence databases, processes, platforms and organism names are used. Examples of database identifiers used include Genbank/EMBL/DDBJ accessions and locus tags, UniGene acces- sions, RefSeq accessions, IPI accessions, NCBI gi numbers and IDs unique to a sequencing center or organism-specific database. The first step was to map all experimental results to a common representation of a protein. This was achieved by mapping all protein and gene IDs and names to iProClass proteins. The majority of the mapping using IDs from public resources was done using mapping services and tables provide on the Protein Information Resource (PIR) web site (http:// proteininformationresource.org/pirwww/search/idmapping.shtml) and FTP site (ftp://ftp.pir.georgetown.edu/databases/iproclass/). However, some mapping problems needed to be addressed either by auto- mated rules, direct sequence comparisons or manual analysis and annotation. Problems and Solutions Mapping difficulties fell into 4 categories: 1) One-to-many mappings: a common problem, especially when eukaryotic host proteins derived from alternate splicing or viral polyproteins are involved. UniProtKB usually merges information on alternate splice forms or polyproteins, which helped minimize this problem for our purposes, but in cases where multiple mappings exist, we selected as most informative the entry in the manually reviewed UniProtKB/ SwissProt section; if no SwissProt entry was found, the longer sequence in UniProtKB/TrEMBL section was selected. Users could always find the alternate mappings via the iProClass related sequences link on the MPD entry page to precompiled BLAST results on all iProClass sequences. 2) Retired sequences: genomic sequences from databases such as RefSeq, IPI, or UniGene are not static and, as information changes, some gene predictions and translations are retired with each new build. Retired sequences often required manual mapping by a curator to match original gene or peptide results to current protein sequences. Primarily UniParc (UniProt sequence archive) [15] was used for this purpose. 3) Protein sequences not available in iProClass or any public repository: this occurred most often with Toxoplasma gondii whose genome sequencing was still in progress and stable builds were not yet available. However, the problem also occurred PLoS ONE | www.plosone.org 3 September 2009 | Volume 4 | Issue 9 | e7162