Scratchpad

This is where we fiddle around with our data and code.

1 Load packages

2 Working with open scholarly metadata

# Get list of refs from the OpenCitations API.
# Get list of refs from the OpenCitations API
response <- GET("https://opencitations.net/index/api/v2/references/doi:10.1007/s10814-021-09163-3")
content <- content(response, "text")
parsed_data <- fromJSON(content)
seed_refs <- sub('.*doi:', '', parsed_data$cited)
seed_refs <- gsub( " .*$", "", seed_refs)
seed_refs <- data.frame(seed_refs)
colnames(seed_refs)[1] <- "doi"

# Retrieve bibliographic metadata for each referenced work from Crossref.
seed_refs_cr <- cr_works(seed_refs$doi)
seed_refs_cr <- seed_refs_cr$data
seed_refs$title <- seed_refs_cr$title[match(seed_refs$doi, seed_refs_cr$doi)]
seed_refs$container_title <- seed_refs_cr$container.title[match(seed_refs$doi, seed_refs_cr$doi)]
seed_refs$type <- seed_refs_cr$type[match(seed_refs$doi, seed_refs_cr$doi)]
seed_refs$date <- seed_refs_cr$created[match(seed_refs$doi, seed_refs_cr$doi)]
seed_refs$year <- substr(seed_refs$date, 1, 4)

It’s not necessary to retrieve abstracts via API. They are too messy and inconsistent, and it’s a pain to deal with html tags.

# Generate lists of authors, indexed by DOIs.
# TBD

I’m missing a step here, from my previous work several months ago. Need to find the code that generated seed_refs_bib.

# Filter bib file for items with a DOI.
seed_refs_bib <- bib2df::bib2df(paste("https://opencitations.net/index/api/v2/references/doi:",seed_refs_bib[!is.na(seed_refs_bib$DOI),]$DOI))

# Query CrossRef for metadata pertaining to references with a DOI.
f1_cr <- cr_works(seed_refs_bib[!is.na(seed_refs_bib$DOI),]$DOI)
f1_cr <- f1_cr$data

# Query OpenCitations for references pertaining to f1.
f1_oc <- oc_coci_meta(seed_refs_bib[!is.na(seed_refs_bib$DOI),]$DOI)
response <- GET("seed_refs_bib[!is.na(seed_refs_bib$DOI),]$DOI")
content <- content(response, "text")
parsed_data <- fromJSON(content)
f1_oc <- sub('.*doi:', '', parsed_data$cited)
f1_oc <- gsub( " .*$", "", f1_oc)
f1_oc <- data.frame(f1_oc)
colnames(f1_oc)[1] <- "doi"

# For data cleaning purposes.
# Modify the variables to find articles without DOI, non-articles with DOI, etc.
seed_refs_bib %>%
  filter(CATEGORY != "ARTICLE",
    !is.na(DOI)
  )

seed_refs_bib %>%
  filter(CATEGORY == "BOOK"
  )

Scratchpad

1 Load packages

2 Working with open scholarly metadata

3 Cleaning and integrating the annotations spreadsheet

4 Basic descriptive statistics

5 Citation networks

6 Citation contexts

7 Citation clusters