Typical PubMed search using “Brucella suis (strain 2 OR S2)” had 63 hits
Typical PubMed search using “Brucella suis (strain 2 OR S2)” had 63 hits as of April 20, 2011, while a corresponding VO (VO_0000722; B. suis strain 2) was identified in only 18 out of 14,947 Brucella related papers. Manual review of the results revealed that the PubMed search had only 12 true positives out of 63 hits, while VO-SciMiner indexing had 17 true positives out of 18 hits. This result demonstrates a significantly improved precision can be obtained using VO-based SciMiner indexing.Identification of Brucella vaccine-associated genesFrom 14,947 Brucella-related papers, 1,009 distinct interactions between 51 Brucella vaccine VO terms and 140 Brucella genes were identified. Grouped based on their functional annotations, the details of these 140 Brucella genes and their various annotations are listed in Table 3. Based on sub-cellular localization annotation, these 140 Brucella proteins are located in different subcellular areas, including outer membrane (10 proteins), cytoplasm (75 proteins), periplasm (10 proteins), cytoplasmic membrane (25 proteins), extracellular matrix (2 proteins) and unknown location (18 proteins). Based on their roles in host-pathogen interactions, the 140 identified Brucella genes associated with Brucella vaccines can be classified into three groups: (1) protective antigens, (2) virulence factors, and (3) unknown. Protective antigens elicit a protective immune response,and are frequently used for PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25636517 vaccine development. VOSciMiner identified all 14 known protective Brucella antigens [12]. Virulence factors are expressed and secreted by pathogens and often responsible for causing diseases in the host. Out of the 140 Brucella genes associated with Brucella vaccines, 46 are known Brucella virulence factors based on the updated curation information from the Brucella Bioinformatics Portal (BBP; http://www.phidias.us/bbp) [10,22] (Table 3). In total, 81 Brucella genes are neither known protective antigens nor virulence factors. Since these genes have been studied in the context of Brucella vaccines, it seems possible that some of them are potential virulence factors and/or protective antigens. For example, RopB has not been implicated in inducing immune protection. However, our recent reverse vaccinology analysis using Vaxign [16] found that Brucella abortus RopB is a potential Brucella adhesin with a probability of 0.815 [12]. This could make RopB a promising target for future vaccine development as a potential protective antigen. A functional analysis of the 140 genes and their subgroups is critical to illustrate their association with Brucella vaccine research. Brucella genes have been well categorized with the COG system [18]. We performed a functional enrichment analysis identifying significantly over-represented COG categories within PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25962748 all 140 genes or 46 virulence factors. These include: “carbohydrate transport and metabolism”, “cell wall, membrane, and envelope biogenesis”, “intracellular trafficking, secretion, and vesicular transport”, and “posttranslational modification, protein Dactinomycin chemical information turnover, chaperones” (Table 4). Interestingly, the COG category “replication, recombination and repair” is significantly over-represented in the 140 genes (p-value = 0.001); however, this category is not enriched in the virulence factor group (p-value = 0.428). In total, 14 out of 140 Brucella genes belong toTable 2 VO-based indexing results using VO-SciMiner and PubMed (as of April 20, 2011)VO-SciMiner without child VOs PubMed Sear.
