I want to find articles from a subset of functions (EC codes) that possibly are related to a disease (inflammatory bowel disease). Which is the best way to search/filter the bibliography to those on bacteria?
Cross-posted in Bioconductor, but I used the BrendaDB to extract references for some enzymatic functions detected in a microbial analysis.
EC refID title pubmed
EC:2.5.1.3 1 Camiener, G.W.; Brown, G.M.: The biosynthesis of thiamine. 2. Fractionation of enzyme system and identification of thiazole monophosphate and thiamine monophosphate as intermediates. J. Biol. Chem. (1960) 235, 2411-2417. 13807175
EC:1.1.1.305 1 Gatzeva-Topalova, P.Z.; May, A.P.; Sousa, M.C.: Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry (2005) 43, 13370-13379. 15491143
EC:2.1.2.13 1 Gatzeva-Topalova, P.Z.; May, A.P.; Sousa, M.C.: Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry (2005) 44, 5328-5338. 15807526
BrendaDb returns the reference and PubMed id of some publications associated with the enzyme process (EC or KO code), I have filtered functions to "just" 200 via differential analysis but still I want to know which of those are the most relevant. For each function, like EC:3.4.11.18, there are up to 200 references, and it could be very long and fruitless to manually look up all the ~14000 references I have in total. Some of these references are from other organisms, like studies in tomatoes or about humans.
Using the original citation, I could search in literature databases (via {fulltext}, {tidypmc} or {europepmc}) and try to find which of them are from microorganisms (scanning for organisms names retrieved via {taxadb}). But I would want to avoid developing my own method if this already exists somewhere.
Is there a method/function, within brendaDb or outside, to filter these publications by organism and exclude those not about bacteria?
