Where are the x_concepts?

[giuliogcantone]

I noticed that fetching for authors or sources does not parse anymore x_concepts.
I know that is deprecated, yet that information is kept in the API, can be restored in the parsed tibble?

[yjunechoe]

We'd prefer to encourage users to not use deprecated information anymore moving forward (in accordance with OpenAlex's plan), so I doubt we'd bring it back for the default behavior of oa_fetch().

But the option remains available to power users (just at your own risk) via a manual extraction of the x_concepts field from output = "list" and a separate call to concepts2df():

library(openalexR)

authors <- oa_fetch("authors", options = list(sample = 1), output = "list")

library(dplyr)

df <- authors2df(authors) |>
  mutate(x_concepts = lapply(authors, \(x) concepts2df(x$x_concepts)))

colnames(df)
#>  [1] "id"                        "display_name"              "display_name_alternatives"
#>  [4] "relevance_score"           "ids"                       "orcid"                    
#>  [7] "works_count"               "cited_by_count"            "counts_by_year"           
#> [10] "2yr_mean_citedness"        "h_index"                   "i10_index"                
#> [13] "last_known_institutions"   "topics"                    "works_api_url"            
#> [16] "x_concepts"
  
df$x_concepts
#> [[1]]
#> # A tibble: 3 × 4
#>   id                             display_name     wikidata                 level
#>   <chr>                          <chr>            <chr>                    <int>
#> 1 https://openalex.org/C15744967 Psychology       https://www.wikidata.or…     0
#> 2 https://openalex.org/C41008148 Computer science https://www.wikidata.or…     0
#> 3 https://openalex.org/C71924100 Medicine         https://www.wikidata.or…     0

[giuliogcantone]

I noticed that while authors2df parses x_concepts, sources2d doesn't. Even processing a source entity by authors2df does not parse x_concepts.

[yjunechoe]

I noticed that while authors2df parses x_concepts, sources2d doesn't. Even processing a source entity by authors2df does not parse x_concepts.

I'm not sure that I follow (a reprex would help here). I'll just note that I see a couple Source objects are returning empty x_concepts fields, presumably because OpenAlex is starting to roll out the field's removal as part of its deprecation process.

# PubMed
s1 <- oa_fetch(identifier = "S4306525036", output = "list")
s1$x_concepts
#> list()

# DOAJ
s2 <- oa_fetch(identifier = "S4306401280", output = "list")
s2$x_concepts
#> list()

IMO {openalexR} can't do much here for a deprecated feature that's unstable and unmaintained from the API's end like this.