data-raw/pmc-reference.md

In jaytimm/PubmedMTK: PubMed Mining Toolkit

PMC as reference

Build abstract corpus

Open Access Common Use PMID list available here.

setwd(ld)
pmc <- read.csv('oa_comm_use_file_list.csv')
pmc0 <- subset(pmc, !is.na(PMID))

corpus <-  PubmedMTK::pmtk_get_records2(pmids = pmc0$PMID, 
                                        cores = 10, 
                                        ncbi_key = key) 

corpus0 <- data.table::rbindlist(corpus)

MeSH annotation frequency

m0 <- PubmedMTK::pmtk_gather_mesh(x = corpus0)

pmtk_tbl_pmc_ref <- m0[ , list(doc_count = length(unique(pmid))),
           by = list(type, term)]
total_pmid <- length(unique(m0$pmid))
pmtk_tbl_pmc_ref[, doc_prop := doc_count/total_pmid]

##                  type                             term doc_count     doc_prop
##       1: meshHeadings                       algorithms     35621 1.963793e-02
##       2: meshHeadings           crystallography,_x-ray      6384 3.519512e-03
##       3: meshHeadings data_interpretation,_statistical      3216 1.772987e-03
##       4: meshHeadings                 fourier_analysis       472 2.602145e-04
##       5: meshHeadings              molecular_structure      8696 4.794122e-03
##      ---                                                                     
## 1304693: meshHeadings         tricuspid_valve_stenosis         1 5.513020e-07
## 1304694: meshHeadings                    ethylestrenol         1 5.513020e-07
## 1304695:    chemNames         monoethylglycinexylidide         1 5.513020e-07
## 1304696:    chemNames                           savlon         1 5.513020e-07
## 1304697:    chemNames            7-propyl_spirolactone         1 5.513020e-07

jaytimm/PubmedMTK documentation built on Sept. 25, 2022, 10:49 p.m.