| Type: | Package |
| Title: | Parse Full Text XML Documents from PubMed Central |
| Version: | 2.0 |
| Description: | Parse XML documents from the Open Access subset of Europe PubMed Central https://europepmc.org including section paragraphs, tables, captions and references. |
| URL: | https://github.com/ropensci/tidypmc |
| BugReports: | https://github.com/ropensci/tidypmc/issues |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| Imports: | xml2, tokenizers, stringr, tibble, dplyr, readr |
| Suggests: | europepmc, tidytext, rmarkdown, knitr, testthat, covr |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2024-08-26 21:22:09 UTC; chrisstubben |
| Author: | Chris Stubben [aut, cre] |
| Maintainer: | Chris Stubben <chris.stubben@hci.utah.edu> |
| Repository: | CRAN |
| Date/Publication: | 2024-08-27 04:10:03 UTC |
tidypmc package
Description
Parse full text XML documents from PubMed Central
Details
See the Github page for details at https://github.com/ropensci/tidypmc
Author(s)
Maintainer: Chris Stubben chris.stubben@hci.utah.edu
See Also
Useful links:
Collapse a list of PubMed Central tables
Description
Collapse rows into a semi-colon delimited list with column names and cell values
Usage
collapse_rows(pmc, na.string)
Arguments
pmc |
a list of tables, usually from |
na.string |
additional cell values to skip, default is NA and "" |
Value
A tibble with table and row number and collapsed text
Author(s)
Chris Stubben
Examples
x <- data.frame(
genes = c("aroB", "glnP", "ndhA", "pyrF"),
fold_change = c(2.5, 1.7, -3.1, -2.6)
)
collapse_rows(list(`Table 1` = x))
Find acronyms in parentheses
Description
This function searches for words preceding the acronym that start with the same initial letter and will likely fail in many situations.
Usage
extract_acronyms(txt)
Arguments
txt |
A tibble from pmc_text or character vector |
Value
A tibble with acronyms
Author(s)
Chris Stubben
Examples
txt <- c(
"An acronym like multinucleated giant cell (MGC)",
"is later mentioned as MGC in the paper.")
extract_acronyms(txt)
Print a hierarchical path string
Description
Print a hierarchical path string from a vector of names and levels
Usage
path_string(x, n)
Arguments
x |
a vector of names |
n |
a vector of numbers with indentation level |
Value
a character vector
Note
Used by pmc_text to print full path to subsection title
Author(s)
Chris Stubben
Examples
x <- c("carnivores", "bears", "polar", "grizzly", "cats", "tiger", "rodents")
n <- c(1, 2, 3, 3, 2, 3, 1)
path_string(x, n)
Split captions into sentences
Description
Split figure, table and supplementary material captions into sentences
Usage
pmc_caption(doc)
Arguments
doc |
|
Value
a tibble with tag, label, sentence number and text
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364") # OR
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"
))
x <- pmc_caption(doc)
x
dplyr::filter(x, sentence == 1)
Get article metadata
Description
Get a list of journal and article metadata in /front tag
Usage
pmc_metadata(doc)
Arguments
doc |
|
Value
a list
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364") # OR
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"
))
pmc_metadata(doc)
Format references cited
Description
Format references cited
Usage
pmc_reference(doc)
Arguments
doc |
|
Value
a tibble with id, pmid, authors, year, title, journal, volume, pages, and doi.
Note
Mixed citations without any child tags are added to the author column.
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364")
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"
))
x <- pmc_reference(doc)
x
Convert table nodes to tibbles
Description
Convert PubMed Central table nodes into a list of tibbles
Usage
pmc_table(doc)
Arguments
doc |
|
Value
a list of tibbles
Note
Saves the caption and footnotes as attributes and collapses multiline headers, expands all rowspan and colspan attributes and adds subheadings to column one.
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364")
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"
))
x <- pmc_table(doc)
sapply(x, dim)
x
attributes(x[[1]])
Split section paragraphs into sentences
Description
Split section paragraph tags into a table with subsection titles and
sentences using tokenize_sentences
Usage
pmc_text(doc, sentence = TRUE)
Arguments
doc |
|
sentence |
split paragraphs into sentences, default TRUE |
Value
a tibble with section, paragraph and sentence number and text
Note
Subsections may be nested to arbitrary depths and this function will return the entire path to the subsection title as a delimited string like "Results; Predicted functions; Pathogenicity". Tables, figures and formulas that are nested in section paragraphs are removed, superscripted references are replaced with brackets, and any other superscripts or subscripts are separared with ^ and _.
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364")
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"
))
txt <- pmc_text(doc)
txt
dplyr::count(txt, section, sort = TRUE)
Download XML from PubMed Central
Description
Download XML from PubMed Central
Usage
pmc_xml(id)
Arguments
id |
a PMC id starting with 'PMC' |
Value
xml_document
Source
https://europepmc.org/RestfulWebService
Examples
## Not run:
doc <- pmc_xml("PMC2231364")
## End(Not run)
Repeat table subheadings
Description
Repeat table subheadings in a new column
Usage
repeat_sub(x, column = "subheading", first = TRUE)
Arguments
x |
a tibble with subheadings |
column |
new column name, default subheading |
first |
add subheader as first column, default TRUE |
Details
Identifies subheadings in a data frame by checking for rows with a non-empty first column and all other columns are empty. Removes subheader rows and repeats values down a new column.
Value
a tibble
Author(s)
Chris Stubben
Examples
x <- data.frame(
genes = c("Up", "aroB", "glnP", "Down", "ndhA", "pyrF"),
fold_change = c(NA, 2.5, 1.7, NA, -3.1, -2.6)
)
x
repeat_sub(x)
repeat_sub(x, "regulated", first = FALSE)
Separate references cited into multiple rows
Description
Separates references cited in brackets or parentheses into multiple rows and splits the comma-delimited numeric strings and expands ranges like 7-9 into new rows
Usage
separate_refs(txt, column = "text")
Arguments
txt |
a table |
column |
column name, default "text" |
Value
a tibble
Author(s)
Chris Stubben
Examples
x <- data.frame(row = 1, text = "some important studies [7-9,15]")
separate_refs(x)
Separate locus tag into multiple rows
Description
Separates locus tags mentioned in full text and expands ranges like YPO1970-74 into new rows
Usage
separate_tags(txt, pattern, column = "text")
Arguments
txt |
a table |
pattern |
regular expression to match locus tags like YPO[0-9-]+ or the locus tag prefix like YPO. |
column |
column name to search, default "text" |
Value
a tibble with locus tag, matching text and rows.
Author(s)
Chris Stubben
Examples
x <- data.frame(row = 1, text = "some genes like YPO1002 and YPO1970-74")
separate_tags(x, "YPO")
Separate all matching text into multiple rows
Description
Separate all matching text into multiple rows
Usage
separate_text(txt, pattern, column = "text")
Arguments
txt |
a tibble, usually results from |
pattern |
either a regular expression or a vector of words to find in text |
column |
column name, default "text" |
Value
a tibble
Note
passed to grepl and str_extract_all
Author(s)
Chris Stubben
Examples
# doc <- pmc_xml("PMC2231364")
doc <- xml2::read_xml(system.file("extdata/PMC2231364.xml",
package = "tidypmc"))
txt <- pmc_text(doc)
separate_text(txt, "[ATCGN]{5,}")
separate_text(txt, "\\([A-Z]{3,6}s?\\)")
# pattern can be a vector of words
separate_text(txt, c("hmu", "ybt", "yfe", "yfu"))
# wrappers for separate_text with extra step to expand matched ranges
separate_refs(txt)
separate_tags(txt, "YPO")