openalexR

Getting bibliographic records from OpenAlex

https://github.com/ropensci/openalexr

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 5 DOI reference(s) in README
  • Academic publication links
  • Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (20.7%) to scientific vocabulary

Keywords

bibliographic-data bibliographic-database bibliometrics bibliometrix science-mapping
Last synced: 7 months ago · JSON representation

Repository

Getting bibliographic records from OpenAlex

Basic Info
Statistics
  • Stars: 121
  • Watchers: 7
  • Forks: 22
  • Open Issues: 31
  • Releases: 3
Topics
bibliographic-data bibliographic-database bibliometrics bibliometrix science-mapping
Created about 4 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  dpi = 150
)
```

# openalexR 



[![R-CMD-check](https://github.com/ropensci/openalexR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/openalexR/actions/workflows/R-CMD-check.yaml) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![CRAN status](https://www.r-pkg.org/badges/version/openalexR)](https://CRAN.R-project.org/package=openalexR) `r badger::badge_cran_download("openalexR", "grand-total")` [![Codecov test coverage](https://codecov.io/gh/ropensci/openalexR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/openalexR?branch=main) [![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/560_status.svg)](https://github.com/ropensci/software-review/issues/560)



**openalexR** helps you interface with the [OpenAlex](https://openalex.org) API to retrieve bibliographic information about publications, authors, institutions, sources, funders, publishers, topics and keywords with 5 main functions:

-   `oa_fetch`: composes three functions below so the user can execute everything in one step, *i.e.*, `oa_query |> oa_request |> oa2df`

-   `oa_query`: generates a valid query, written following the OpenAlex API syntax, from a set of arguments provided by the user.

-   `oa_request`: downloads a collection of entities matching the query created by `oa_query` or manually written by the user, and returns a JSON object in a list format.

-   `oa2df`: converts the JSON object in classical bibliographic tibble/data frame.

-   `oa_random`: get random entity, *e.g.*, `oa_random("works")` gives a different work each time you run it

## 📜 Citation

If you use openalexR in research, please cite:

  Aria, M., Le T., Cuccurullo, C., Belfiore, A. & Choe, J. (2024), *openalexR: An R-Tool for Collecting Bibliometric Data from OpenAlex*, **The R Journal**, 15(4), 167-180, DOI: https://doi.org/10.32614/RJ-2023-089.

## 🙌 Support OpenAlex

If OpenAlex has helped you, consider writing a [Testimonial](https://forms.monday.com/forms/4d5ad5a8e6a72ae31987a29118f1d437?r=use1) which will help support the OpenAlex team and show that their work is making a *real and necessary* impact.

## ⚙️ Setup

You can install the developer version of openalexR from [GitHub](https://github.com) with:

```{r eval=FALSE}
install.packages("remotes")
remotes::install_github("ropensci/openalexR")
```

You can install the released version of openalexR from [CRAN](https://CRAN.R-project.org) with:

```{r eval=FALSE}
install.packages("openalexR")
```

Before we go any further, we highly recommend you set `openalexR.mailto` option so that your requests go to [the polite pool](https://docs.openalex.org/how-to-use-the-api/rate-limits-and-authentication#the-polite-pool) for faster response times.
If you have OpenAlex Premium, you can add your API key to the `openalexR.apikey` option as well.
These lines best go into `.Rprofile` with `file.edit("~/.Rprofile")`.

```{r eval=FALSE}
options(openalexR.mailto = "example@email.com")
options(openalexR.apikey = "EXAMPLE_APIKEY")
```

Alternatively, you can open `.Renviron` with `file.edit("~/.Renviron")` and add:
```
openalexR.mailto = example@email.com
openalexR.apikey = EXAMPLE_APIKEY
```

```{r warning=FALSE, message=FALSE}
library(openalexR)
library(dplyr)
library(ggplot2)
```

```{r set-theme, include=FALSE}
theme_set(theme_classic())
theme_update(
  plot.background = element_rect(fill = "transparent", colour = NA),
  panel.background = element_rect(fill = "transparent", colour = NA)
)

knitr::opts_chunk$set(dev.args = list(bg = "transparent"))
```

## 🌿 Examples

There are different [filters](https://ropensci.github.io/openalexR/articles/Filters)/arguments you can use in `oa_fetch`, depending on which [entity](https://docs.openalex.org/#data) you're interested in: 
`r cat(setdiff(oa_entities(), "concepts"), sep = ", ")`.
We show a few examples below.

### 📚 Works

**Goal**: Download all information about a givens set of publications (known DOIs).

Use `doi` as a [works filter](https://ropensci.github.io/openalexR/articles/Filters.html#works):

```{r}
works_from_dois <- oa_fetch(
  entity = "works",
  doi = c("10.1016/j.joi.2017.08.007", "https://doi.org/10.1007/s11192-013-1221-3"),
  verbose = TRUE
)
```

We can view the output tibble/dataframe, `works_from_dois`, interactively in RStudio or inspect it with base functions like `str` or `head`. We also provide the experimental `show_works` function to simplify the result (e.g., remove some columns, keep first/last author) for easy viewing.

*Note*: the following table is wrapped in `knitr::kable()` to be displayed nicely in this README, but you will most likely not need this function.

```{r}
# str(works_from_dois, max.level = 2)
# head(works_from_dois)
# show_works(works_from_dois)

works_from_dois |>
  show_works() |>
  knitr::kable()
```

**Goal**: Download all works given their PMIDs.

Use `pmid` as a filter:

```{r}
works_from_pmids <- oa_fetch(
  entity = "works",
  pmid = c("14907713", 32572199),
  verbose = TRUE
)
works_from_pmids |>
  show_works() |>
  knitr::kable()
```


**Goal**: Download all works published by a set of authors (known ORCIDs).

Use `author.orcid` as a filter (either canonical form with  or without will work):

```{r}
works_from_orcids <- oa_fetch(
  entity = "works",
  author.orcid = c("0000-0001-6187-6610", "0000-0002-8517-9411"),
  verbose = TRUE
)
works_from_orcids |>
  show_works() |>
  knitr::kable()
```

**Goal**: Download all works that have been cited more than 50 times, published between 2020 and 2021, and include the strings "bibliometric analysis" or "science mapping" in the title. Maybe we also want the results to be sorted by total citations in a descending order.

```{r}
works_search <- oa_fetch(
  entity = "works",
  title.search = c("bibliometric analysis", "science mapping"),
  cited_by_count = ">50",
  from_publication_date = "2020-01-01",
  to_publication_date = "2021-12-31",
  options = list(sort = "cited_by_count:desc"),
  verbose = TRUE
)
works_search |>
  show_works() |>
  knitr::kable()
```

### 🧑 Authors

**Goal**: Download author information when we know their ORCID.

Here, instead of `author.orcid` like earlier, we have to use `orcid` as an argument. This may be a little confusing, but again, a different entity (**authors** instead of **works**) requires a [different set of filters](https://ropensci.github.io/openalexR/articles/Filters.html#authors).

```{r}
authors_from_orcids <- oa_fetch(
  entity = "authors",
  orcid = c("0000-0001-6187-6610", "0000-0002-8517-9411")
)
authors_from_orcids |>
  show_authors() |>
  knitr::kable()
```

**Goal**: Acquire information on the authors of this package.

We can use other filters such as `display_name` and `has_orcid`:

```{r}
authors_from_names <- oa_fetch(
  entity = "authors",
  display_name = c("Massimo Aria", "Jason Priem"),
  has_orcid = TRUE
)
authors_from_names |>
  show_authors() |>
  knitr::kable()
```

**Goal**: Download all authors' records of scholars who work at the [University of Naples Federico II](https://explore.openalex.org/institutions/I71267560) (OpenAlex ID: I71267560) and have published at least 500 publications.

Let's first check how many records match the query, then download the entire collection. We can do this by first defining a list of arguments, then adding `count_only` (default `FALSE`) to this list:

```{r}
my_arguments <- list(
  entity = "authors",
  last_known_institutions.id = "I71267560",
  works_count = ">499"
)
do.call(oa_fetch, c(my_arguments, list(count_only = TRUE)))

if (do.call(oa_fetch, c(my_arguments, list(count_only = TRUE)))[1]>0){
do.call(oa_fetch, my_arguments) |>
  show_authors() |>
  knitr::kable()
}
```

## 🍒 Example analyses

**Goal**: Rank institutions in Italy by total number of citations.

We want download all records regarding Italian institutions (country_code:it) that are classified as educational (type:education). Again, we check how many records match the query then download the collection:

```{r italy-insts, fig.height=3.5, fig.width=7}
italy_insts <- oa_fetch(
  entity = "institutions",
  country_code = "it",
  type = "education",
  verbose = TRUE
)
italy_insts |>
  slice_max(cited_by_count, n = 8) |>
  mutate(display_name = forcats::fct_reorder(display_name, cited_by_count)) |>
  ggplot() +
  aes(x = cited_by_count, y = display_name, fill = display_name) +
  geom_col() +
  scale_fill_viridis_d(option = "E") +
  guides(fill = "none") +
  labs(
    x = "Total citations", y = NULL,
    title = "Italian references"
  ) +
  coord_cartesian(expand = FALSE)
```

And what do they publish on?

```{r concept-cloud, fig.height=5, fig.width=7}
# The package wordcloud needs to be installed to run this chunk
# library(wordcloud)
concept_cloud <- italy_insts |>
  select(inst_id = id, topics) |>
  tidyr::unnest(topics) |>
  filter(type == "field") |>
  select(display_name, count) |>
  group_by(display_name) |>
  summarise(score = sqrt(sum(count)))
pal <- c("black", scales::brewer_pal(palette = "Set1")(5))
set.seed(1)
wordcloud::wordcloud(
  concept_cloud$display_name,
  concept_cloud$score,
  scale = c(2, .4),
  colors = pal
)
```

**Goal**: Visualize big journals' topics.

We first download all records regarding journals that have published more than 300,000 works, then visualize their scored topics:

```{r big-journals, message=FALSE, fig.height=8, fig.width=8}
# The package ggtext needs to be installed to run this chunk
# library(ggtext)
jours_all <- oa_fetch(
  entity = "sources",
  works_count = ">200000",
  verbose = TRUE
)

clean_journal_name <- function(x) {
  x |>
    gsub("\\(.*?\\)", "", x = _) |>
    gsub("Journal of the|Journal of", "J.", x = _) |>
    gsub("/.*", "", x = _)
}

jours <- jours_all |>
  filter(type == "journal") |>
  slice_max(cited_by_count, n = 9) |>
  distinct(display_name, .keep_all = TRUE) |>
  select(jour = display_name, topics) |>
  tidyr::unnest(topics) |>
  filter(type == "field") |>
  group_by(id, jour, display_name) |> 
  summarise(score = (sum(count))^(1/3), .groups = "drop") |> 
  left_join(concept_abbrev, by = join_by(id, display_name)) |>
  mutate(
    abbreviation = gsub(" ", "
", abbreviation), jour = clean_journal_name(jour), ) |> tidyr::complete(jour, abbreviation, fill = list(score = 0)) |> group_by(jour) |> mutate( color = if_else(score > 10, "#1A1A1A", "#D9D9D9"), # CCCCCC label = paste0("", abbreviation, "") ) |> ungroup() jours |> ggplot() + aes(fill = jour, y = score, x = abbreviation, group = jour) + facet_wrap(~jour) + geom_hline(yintercept = c(25, 50), colour = "grey90", linewidth = 0.2) + geom_segment( aes(x = abbreviation, xend = abbreviation, y = 0, yend = 55), color = "grey95" ) + geom_col(color = "grey20") + coord_polar(clip = "off") + theme_bw() + theme( plot.background = element_rect(fill = "transparent", colour = NA), panel.background = element_rect(fill = "transparent", colour = NA), panel.grid = element_blank(), panel.border = element_blank(), axis.text = element_blank(), axis.ticks.y = element_blank() ) + ggtext::geom_richtext( aes(y = 75, label = label), fill = NA, label.color = NA, size = 3 ) + scale_fill_brewer(palette = "Set1", guide = "none") + labs(y = NULL, x = NULL, title = "Journal clocks") ``` ## ❄️ Snowball search The user can also perform *snowballing* with `oa_snowball`. Snowballing is a literature search technique where the researcher starts with a set of articles and find articles that cite or were cited by the original set. `oa_snowball` returns a list of 2 elements: *nodes* and *edges*. Similar to `oa_fetch`, `oa_snowball` finds and returns information on a core set of articles satisfying certain criteria, but, unlike `oa_fetch`, it also returns information the articles that cite and are cited by this core set. ```{r snowballing} # The packages ggraph and tidygraph need to be installed to run this chunk library(ggraph) library(tidygraph) snowball_docs <- oa_snowball( identifier = c("W1964141474", "W1963991285"), verbose = TRUE ) ggraph(graph = as_tbl_graph(snowball_docs), layout = "stress") + geom_edge_link(aes(alpha = after_stat(index)), show.legend = FALSE) + geom_node_point(aes(fill = oa_input, size = cited_by_count), shape = 21, color = "white") + geom_node_label(aes(filter = oa_input, label = id), nudge_y = 0.2, size = 3) + scale_edge_width(range = c(0.1, 1.5), guide = "none") + scale_size(range = c(3, 10), guide = "none") + scale_fill_manual(values = c("#a3ad62", "#d46780"), na.value = "grey", name = "") + theme_graph() + theme( plot.background = element_rect(fill = "transparent", colour = NA), panel.background = element_rect(fill = "transparent", colour = NA), legend.position = "bottom" ) + guides(fill = "none") ``` ## 🌾 N-grams **Update 2024-09-15**: The n-gram API endpoint is [not currently in service](https://docs.openalex.org/api-entities/works/get-n-grams#api-endpoint). The following code chunk is not evaluated. OpenAlex offers (limited) support for [fulltext N-grams](https://docs.openalex.org/api-entities/works/get-n-grams#fulltext-coverage) of Work entities (these have IDs starting with `"W"`). Given a vector of work IDs, `oa_ngrams` returns a dataframe of N-gram data (in the `ngrams` list-column) for each work. ```{r ngrams, eval=FALSE, fig.height=3} ngrams_data <- oa_ngrams( works_identifier = c("W1964141474", "W1963991285"), verbose = TRUE ) ngrams_data lapply(ngrams_data$ngrams, head, 3) ngrams_data |> tidyr::unnest(ngrams) |> filter(ngram_tokens == 2) |> select(id, ngram, ngram_count) |> group_by(id) |> slice_max(ngram_count, n = 10, with_ties = FALSE) |> ggplot(aes(ngram_count, forcats::fct_reorder(ngram, ngram_count))) + geom_col(aes(fill = id), show.legend = FALSE) + facet_wrap(~id, scales = "free_y") + labs( title = "Top 10 fulltext bigrams", x = "Count", y = NULL ) ``` `oa_ngrams` can sometimes be slow because the N-grams data can get pretty big, but given that the N-grams are `"cached via CDN"`](), you may also consider parallelizing for this special case (`oa_ngrams` does this automatically if you have `{curl} >= v5.0.0`). ## 💫 About OpenAlex ![oar-img](man/figures/oar.png) ::: {style="text-align: right"} Schema credits: [\@dhimmel](https://github.com/dhimmel) ::: [OpenAlex](https://openalex.org) is a fully open catalog of the global research system. It's named after the ancient [Library of Alexandria](https://en.wikipedia.org/wiki/Library_of_Alexandria). The OpenAlex dataset describes scholarly entities and how those entities are connected to each other. There are five types of entities: - **Works** are papers, books, datasets, etc; they cite other works - **Authors** are people who create works - **Sources** are journals and repositories that host works - **Institutions** are universities and other orgs that are affiliated with works (via authors) - **Publishers** are companies that publish works - **Funders** are organizations that fund works - **Topics** are tags automatically given to works based on information about the work; grouped into subfields, which are grouped into fields, which are grouped into top-level domains - **Keywords** are terms associated with works derived from Topics (at most 5 per work) ## 🤝 Code of Conduct Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms. ## 👓 Acknowledgements Package hex was made with [Midjourney](https://www.midjourney.com/home/) and thus inherits a [CC BY-NC 4.0 license](https://creativecommons.org/licenses/by-nc/4.0/legalcode).

Owner

  • Name: rOpenSci
  • Login: ropensci
  • Kind: organization
  • Email: info@ropensci.org
  • Location: Berkeley, CA

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        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=jsonlite"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "progress",
      "name": "progress",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=progress"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 2.10"
    },
    "SystemRequirements": null
  },
  "fileSize": "3833.673KB",
  "releaseNotes": "https://github.com/ropensci/openalexR/blob/master/NEWS.md",
  "readme": "https://github.com/ropensci/openalexR/blob/main/README.md",
  "contIntegration": [
    "https://github.com/ropensci/openalexR/actions/workflows/R-CMD-check.yaml",
    "https://app.codecov.io/gh/ropensci/openalexR?branch=main"
  ],
  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental",
  "keywords": [
    "bibliographic-data",
    "bibliographic-database",
    "bibliometrics",
    "bibliometrix",
    "science-mapping"
  ]
}

GitHub Events

Total
  • Issues event: 57
  • Watch event: 19
  • Delete event: 8
  • Issue comment event: 124
  • Push event: 27
  • Pull request review event: 30
  • Pull request review comment event: 15
  • Pull request event: 35
  • Fork event: 1
  • Create event: 9
Last Year
  • Issues event: 57
  • Watch event: 19
  • Delete event: 8
  • Issue comment event: 124
  • Push event: 27
  • Pull request review event: 30
  • Pull request review comment event: 15
  • Pull request event: 35
  • Fork event: 1
  • Create event: 9

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 314
  • Total Committers: 8
  • Avg Commits per committer: 39.25
  • Development Distribution Score (DDS): 0.389
Past Year
  • Commits: 139
  • Committers: 7
  • Avg Commits per committer: 19.857
  • Development Distribution Score (DDS): 0.446
Top Committers
Name Email Commits
lelaboratoire g****r@g****m 192
massimoaria a****a@u****t 74
June Choe y****e@s****u 23
let20 t****e@b****m 15
Maëlle Salmon m****n@y****e 5
June Choe 5****e 3
Sebastian Karcher k****r@u****u 1
yhan818 y****8@g****m 1
Committer Domains (Top 20 + Academic)

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 192
  • Total pull requests: 144
  • Average time to close issues: 21 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 56
  • Total pull request authors: 9
  • Average comments per issue: 3.06
  • Average comments per pull request: 1.18
  • Merged pull requests: 127
  • Bot issues: 11
  • Bot pull requests: 0
Past Year
  • Issues: 42
  • Pull requests: 33
  • Average time to close issues: 16 days
  • Average time to close pull requests: 6 days
  • Issue authors: 18
  • Pull request authors: 5
  • Average comments per issue: 2.74
  • Average comments per pull request: 1.97
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • rkrug (33)
  • trangdata (26)
  • yhan818 (17)
  • massimoaria (15)
  • github-actions[bot] (11)
  • yjunechoe (8)
  • JeffreySmithA (6)
  • raffaem (5)
  • philiplindsay (4)
  • giuliogcantone (3)
  • krisgulati (3)
  • adrientaudiere (2)
  • zilch42 (2)
  • milliken (2)
  • rgoldsto (2)
Pull Request Authors
  • trangdata (95)
  • yjunechoe (47)
  • massimoaria (25)
  • raffaem (6)
  • maelle (2)
  • rkrug (2)
  • yhan818 (2)
  • cjbarrie (1)
  • adam3smith (1)
Top Labels
Issue Labels
enhancement (10) question (8) OpenAlex (8) vignette (3) bug (3) documentation (2) priority: high (1) duplicate (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 8,937 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: openalexR

Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL' API

  • Versions: 13
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 8,937 Last month
Rankings
Forks count: 5.2%
Stargazers count: 5.6%
Downloads: 13.1%
Average: 13.2%
Dependent packages count: 17.7%
Dependent repos count: 24.4%
Maintainers (1)
Last synced: 7 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • curl * imports
  • httr * imports
  • jsonlite * imports
  • progress * imports
  • tibble * imports
  • dplyr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/check-pkgdown.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-daily.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite