Find publications

Searching for a single locus tag in a full-text database like PMC is straightforward, for example, enter "BPSS1492" in the search box and this returns 13 articles. To find all full-text articles with any locus tag, we use the tag prefix and first digit from the GFF3 file to build a wildcard search, in this case "(BPSL0* OR BPSL1* OR BPSL2* OR BPSL3* OR BPSS0* OR BPSS1* OR BPSS2*)" since there are two chromosomes. We restrict the number of spurious matches by limiting the results to articles with the genus name in the title or abstract. We also find matches to articles in the OA subset since these are available for text-mining as XML. This query returns 70 publications on Sep 4, 2014.

tags <- "(BPSL0* OR BPSL1* OR BPSL2* OR BPSL3* OR BPSS0* OR BPSS1* OR BPSS2*)"
bp <- ncbiPMC(paste(tags, "AND (Burkholderia[TITLE] OR Burkholderia[ABSTRACT]) AND open access[FILTER]")) 
bp[1:10,]
          pmc                                   authors year                                                                                                                                     title                                          journal volume   pages   epubdate     pmid
1  PMC3623717         Hara Y, Chin CY, Mohamed R, et al 2013                                    Multiple-antigen ELISA for melioidosis - a novel approach to the improved serodiagnosis of melioidosis                          BMC Infectious Diseases     13     165 2013/04/04 23556548
2  PMC3607239           Puah SM, Puthucheary S, Chua KH 2013 Potential Immunogenic Polypeptides of Burkholderia pseudomallei Identified by Shotgun Expression Library and Evaluation of Their Efficacy        International Journal of Medical Sciences     10 539-547 2013/03/13 23532805
3  PMC3579680 Janse I, Hamidjaja RA, Hendriks AC, et al 2013                            Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei                          BMC Infectious Diseases     13      86 2013/02/14 23409683
4  PMC3564208      Choh LC, Ong GH, Vellasamy KM, et al 2013                                                                                             Burkholderia vaccines: are we moving forward? Frontiers in Cellular and Infection Microbiology      3       5 2013/02/05 23386999
5  PMC3540353                                Dowling AJ 2013                                       Novel gain of function approaches for vaccine candidate identification in Burkholderia pseudomallei Frontiers in Cellular and Infection Microbiology      2     139 2013/01/09 23316481
6  PMC3527420     Chen R, Barphagha IK, Karki HS, et al 2012               Dissection of Quorum-Sensing Genes in Burkholderia glumae Reveals Non-Canonical Regulation and the New Regulatory Gene tofM                                         PLoS ONE      7  e52150 2012/12/20 23284909
7  PMC3521395        Khoo JS, Chai SF, Mohamed R, et al 2012                  Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs                                     BMC Genomics     13     S13 2012/12/07 23282220
8  PMC3443583         Ong HS, Mohamed R, Firdaus-Raih M 2012  Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp              Comparative and Functional Genomics   2012  752867 2012/09/06 22991502
9  PMC3419357   Burtnick MN, Heiss C, Roberts RA, et al 2012                            Development of capsular polysaccharide-based glycoconjugates for immunization against melioidosis and glanders Frontiers in Cellular and Infection Microbiology      2     108 2012/08/15 22912938
10 PMC3418162             Chieng S, Carreto L, Nathan S 2012                                                                       Burkholderia pseudomallei transcriptional adaptation in macrophages                                     BMC Genomics     13     328 2012/07/23 22823543