Reading bibliometric data into bibnets

In bibnets: Importing, Constructing, and Exporting Bibliometric Networks

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(bibnets)

1. Introduction and the standard schema

bibnets reads bibliographic data from two kinds of source. The first is the standard database exports — Scopus, Web of Science, OpenAlex, Lens.org, Dimensions, Crossref, BibTeX, and RIS — which it recognises and parses automatically; give it a single file, several files, or a whole folder and it works out each format on its own. The second is any custom table of your own: a CSV or data frame that is not a known export, where you simply name the columns that hold the authors, references, or keywords and bibnets reads it into the same structure. Either way you get the same structure — the bibnets format — that every network builder (author_network(), keyword_network(), reference_network(), document_network(), source_network(), country_network(), institution_network(), conetwork()) works from. The bibnets format is a data frame with one row per paper: most columns hold a single value (title, year, journal), while the fields that can have many values per paper — authors, references, keywords — hold a list in each row.

In full, the bibnets format has these columns:

| Column | Type | Meaning | |---|---|---| | id | chr | Document identifier (EID, OpenAlex W-ID, DOI, etc.) | | title | chr | Document title | | year | int | Publication year | | journal | chr | Source / journal / venue name | | doi | chr | DOI without the https://doi.org/ prefix | | cited_by_count | int | Citations received (as reported by source) | | abstract | chr | Abstract text; NA for sources that do not expose it | | type | chr | Document type (article, review, book-chapter, ...) | | authors | list | Character vector of author names per row | | references | list | Character vector of cited references per row | | keywords | list | Character vector of keywords per row |

Some sources add extra columns (such as index_keywords, keywords_plus, affiliations, or countries); these are kept after the standard ones.

This vignette documents the read_biblio() entry point and each reader, the generic-CSV path, network construction directly from custom columns and separators, the split_field() helper, and the manual construction of a compatible data frame.

2. Custom data and separators

Custom CSV — map columns by name

For CSV files that do not match any of the recognised signatures (in-house exports, custom dumps, public datasets), map each source column onto a standard field by name. The identifier column is named via id; each multi-valued field is named via its own argument — authors, keywords, references, countries, affiliations — and journal for the scalar source/venue. sep is the delimiter applied inside those cells. Naming any of these columns implies format = "generic", so you do not need to pass format yourself.

Hypothetical call:

data <- read_biblio(
  "my_data.csv",
  id       = "doc_id",
  authors  = "Authors",
  keywords = "Keywords",
  sep      = ";"
)

Demonstrated on the bundled OpenAlex CSV (which uses | as the delimiter). The source columns have long dotted names; mapping them by argument yields the standard authors and keywords list-columns:

f <- system.file("extdata", "openalex_works.csv", package = "bibnets")
generic <- read_biblio(
  f,
  id       = "id",
  authors  = "authorships.author.display_name",
  keywords = "primary_topic.display_name",
  sep      = "|"
)
generic$authors[[1]]
generic$keywords[[1]]

Each mapped column is split on sep and stored under its standard name as a list-column; the original source column is left in place. For any further columns that have no dedicated argument, list_cols splits them in place (keeping their original names).

Custom columns and separators (no reader needed)

Often a dataset is already a plain data frame or CSV with its own column names and its own delimiter — you do not need to coerce it into the standard schema first. Every network builder accepts a column argument named after the entity it builds (authors, keywords, references, journal, countries, affiliations) plus a sep for splitting a delimited character column. The builder splits, normalises, and builds in one call.

papers <- data.frame(
  id            = 1:4,
  `Author Names`= c("Smith J, Doe A, Lee K", "Smith J, Lee K",
                    "Doe A, Lee K", "Smith J, Doe A"),
  Tags          = c("ml, ai", "ml, nlp", "ai, nlp", "ml, ai"),
  check.names   = FALSE,
  stringsAsFactors = FALSE
)

# Point the builder at the column and give it the delimiter — no renaming.
author_network(papers, authors = "Author Names", sep = ",")
keyword_network(papers, keywords = "Tags", sep = ",")

The document identifier

The works dimension (the rows of the works x entities matrix) is the id column. You do not have to supply one: id = NULL (the default) uses an existing id column when present and otherwise numbers the rows, treating each row as one document. The example above has no id column and still works for that reason. To use a differently-named identifier column, name it with the id argument:

papers2 <- data.frame(
  paper_id = c("P1", "P2", "P3"),
  authors  = c("Alice, Bob", "Alice, Carol", "Bob, Carol"),
  stringsAsFactors = FALSE
)
author_network(papers2, authors = "authors", sep = ",", id = "paper_id")

Two entities are linked when they share the same id, so the identifier controls what counts as "the same document" during projection.

sep is any literal delimiter, so BibTeX-style " and " or pipe-delimited exports work too:

bib <- data.frame(
  id      = 1:3,
  creators = c("Alice and Bob", "Alice and Carol", "Bob and Carol"),
  stringsAsFactors = FALSE
)
author_network(bib, authors = "creators", sep = " and ")

A separate separator for references

In a coupling network the entity column and the references column can use different delimiters. Reference strings frequently contain internal commas ("Smith J, 2020, Journal"), so references is split on ";" by default, independent of sep. Override it with references_sep when your references use another delimiter:

d <- data.frame(
  id         = c("P1", "P2", "P3"),
  auth       = c("Alice, Bob", "Alice, Carol", "Bob, Carol"),
  references = c("R1, R2", "R1, R3", "R2, R3"),
  stringsAsFactors = FALSE
)
author_network(d, "coupling", authors = "auth", sep = ",",
               references_sep = ",")

Quoted values

Values exported with surrounding quotes ("Alice", or the CSV doubled form ""Alice"") are cleaned automatically — strip_quotes = TRUE is the default, so a quoted label and its bare form collapse to the same node. Internal apostrophes (e.g. O'Brien) are left untouched. Set strip_quotes = FALSE to keep the quotes as part of the label.

q <- data.frame(
  id      = 1:3,
  authors = c('"Alice"; "Bob"', '"Alice"; "Carol"', '"Bob"; "Carol"'),
  stringsAsFactors = FALSE
)
author_network(q)                       # quotes stripped -> ALICE, BOB, CAROL

A safety net for the wrong delimiter

If you pass a sep that does not actually split the column — for example the data is pipe-delimited but you left sep = ";" — and the values contain a structural delimiter (";", "|", or a tab), the builder warns you instead of silently treating each whole cell as one entity:

bad <- data.frame(
  id      = 1:3,
  authors = c("Smith J| Doe A", "Smith J| Lee K", "Doe A| Lee K"),
  stringsAsFactors = FALSE
)
invisible(author_network(bad))          # warns: values contain "|"

The check is deliberately quiet for commas and " and ", which appear inside perfectly valid single labels ("Last, First" names, one-reference-per-row citation strings, organisations like "Smith and Sons").

3. read_biblio()

read_biblio() accepts a single file, a vector of file paths, or a directory. When format = "auto" (the default) it detects the format from the contents of the file:

data <- read_biblio("export.csv")          # auto-detect format
data <- read_biblio("scopus_dir/")         # entire directory, rbind'd
data <- read_biblio(c("a.csv", "b.csv"))   # multiple files, rbind'd
data <- read_biblio("file.csv", format = "scopus")   # force a format

When given a directory, read_biblio() collects every .csv, .txt, .bib, .ris, .xls, and .xlsx file in it, reads each one, and combines the results with rbind(). For more than one file a summary message is emitted:

Read 3 files: 1247 rows total

Format detection is performed on the first non-empty line of the file:

• BibTeX: line 1 begins with @
• RIS: line 1 begins with TY -
• Web of Science plaintext: line 1 begins with FN or PT
• CSV-based: detection inspects the header row. When the first line matches the Dimensions preamble ("About the data: ..."), line 2 is used instead. Header tokens determine the format: eid for Scopus, lens id for Lens.org, publication id or dimensions url for Dimensions, authorships.author.display_name for the OpenAlex flat CSV.

If detection fails, read_biblio() raises an error that lists the supported formats and indicates how to pass format explicitly or name the entity columns (authors, keywords, ...), which reads the file as a generic CSV.

Two readers are not dispatched by read_biblio():

• read_openalex() accepts an in-memory tibble from openalexR::oa_fetch(), not a file path.
• read_crossref() accepts the data element of rcrossref::cr_works().

Both take R objects rather than files and are called directly.

4. Scopus

sc <- read_scopus("scopus.csv")

read_scopus() ingests the standard Scopus CSV export (File -> Export -> CSV from the Scopus search UI). Mappings from Scopus columns to the bibnets schema:

| Scopus column | Standard column | |---|---| | EID (or Article No.) | id | | Title | title | | Year | year | | Source title | journal | | DOI | doi (prefix stripped) | | Cited by | cited_by_count | | Abstract | abstract | | Document Type | type | | Authors (;-delimited) | authors (list) | | References (;-delimited) | references (list) | | Author Keywords (;-delimited) | keywords (list) | | Index Keywords (;-delimited) | index_keywords (list, extra) | | Affiliations (;-delimited) | affiliations (list, extra) | | Language of Original Document | language (extra) |

Scopus stores each cited reference as one semicolon-delimited string in a single cell. read_scopus() splits on ; and applies standardize_refs() to each entry: uppercasing, whitespace normalisation, and removal of a trailing DOI where present. References differing only in case or trailing DOI then resolve to the same node in co-citation and reference networks.

5. Web of Science

WoS exports come in two shapes:

wos1 <- read_wos("savedrecs.txt")                       # plaintext (default)
wos2 <- read_wos("savedrecs.tsv", format = "tab")       # tab-delimited

The plaintext format is a tagged record syntax. Each record begins with a PT (publication type) tag and ends with ER (end record). Within the record, every field is introduced by a 2-letter tag at the start of a line, with continuation lines indented:

| Tag | Field | |---|---| | AU | Authors (one per line) | | TI | Title | | SO | Source / journal | | PY | Year | | DI | DOI | | TC | Times cited | | AB | Abstract | | DT | Document type | | DE | Author keywords | | ID | Keywords plus (extra: keywords_plus) | | CR | Cited references (one per line) |

read_wos() walks the file, splitting on ER boundaries, and emits one row per record. The tab-delimited variant carries the same fields in a flat CSV-like grid. Either way the output schema is identical.

6. Dimensions

dm <- read_dimensions("dimensions_export.csv")

The Dimensions CSV begins with a metadata row of the form

"About the data: This export was generated on YYYY-MM-DD ..."

before the column header. read_dimensions() detects this preamble and skips it. If the line has been removed (for example, by manual editing of the file), the reader continues to function because it identifies the column row by the Dimensions header tokens Publication ID and Dimensions URL.

Extras returned: affiliations and countries as list-columns, analogous to the OpenAlex schema.

7. Lens.org

ln <- read_lens("lens_export.csv")

Key Lens columns and how they map:

| Lens column | Standard column | |---|---| | Lens ID | id | | Title | title | | Publication Year | year | | Source Title | journal | | DOI | doi | | Cited by Count | cited_by_count | | Abstract | abstract | | Publication Type | type | | Author/s | authors (list) | | Reference Identifiers | references (list) | | Keywords | keywords (list) |

8. BibTeX & RIS

bt <- read_bibtex("library.bib")
ri <- read_ris("savedrecs.ris")

read_bibtex() parses @type{key, field = {value}, ...} blocks. read_ris() parses tagged TY - ... ER - blocks; the structure is equivalent to WoS plaintext, but with a different tag dictionary.

Standard BibTeX and RIS do not contain cited-reference data, so the references column in the resulting data frame is empty on every row. These formats are sufficient for co-authorship and keyword co-occurrence networks. For co-citation, coupling, or direct citation networks, the appropriate sources are Scopus, Web of Science, OpenAlex (via oa_fetch()), Dimensions, Lens, or Crossref.

9. Crossref via rcrossref

library(rcrossref)
raw  <- cr_works(query = "graph neural networks", limit = 100)
data <- read_crossref(raw$data)

read_crossref() accepts the data element of the cr_works() result (a data frame, not the wrapping list). The function handles the two field-naming variants Crossref returns (container.title vs container-title; is.referenced.by.count vs is-referenced-by-count) and maps both to the standard schema.

10. OpenAlex — two paths

OpenAlex ships data through two routes that bibnets supports separately.

Path A: flat CSV

The package includes a 30-row OpenAlex flat CSV at inst/extdata/openalex_works.csv, corresponding to the export produced by downloading "Works" results from the OpenAlex web interface. Multi-valued fields use | as the delimiter.

f <- system.file("extdata", "openalex_works.csv", package = "bibnets")
oa <- read_openalex_csv(f)
str(oa, max.level = 1)
head(oa[, c("id", "title", "year", "journal", "type")], 5)

The list-columns:

oa$authors[[1]]
oa$affiliations[[1]]
oa$countries[[1]]

References and abstracts are absent from the OpenAlex flat export: references is empty and abstract is NA because the web download does not include those fields. Use OpenAlex via openalexR::oa_fetch() and read_openalex() when you need cited references or abstracts.

The remaining fields support several network constructions that do not require references — co-authorship, country, institution, keyword, source, and document networks:

co <- country_network(oa, counting = "fractional")
head(co, 5)

Path B: in-memory tibble from openalexR

This path is used when references and abstracts are required. openalexR::oa_fetch() returns a nested tibble with author, referenced_works, concepts, and keywords list-columns; read_openalex() converts it to the standard schema:

library(openalexR)
raw  <- oa_fetch(entity = "works", search = "learning analytics", per_page = 200)
data <- read_openalex(raw)

References are returned as OpenAlex Work IDs (e.g. W2769342982) rather than formatted citation strings. The IDs are stable identifiers suitable for co-citation and direct-citation networks; visualisations that need human-readable labels can join the IDs back to titles in a separate step.

11. Building data manually

When data does not come from any of the supported sources, a bibnets-compatible data frame can be constructed directly. The requirement is: standard scalar columns are character or integer; multi-valued fields are list-columns whose elements are character vectors.

df <- data.frame(
  id    = c("p1", "p2", "p3"),
  title = c("Paper A", "Paper B", "Paper C"),
  year  = c(2020L, 2021L, 2022L),
  stringsAsFactors = FALSE
)
df$authors <- list(
  c("ALICE", "BOB"),
  c("BOB", "CAROL"),
  c("ALICE", "CAROL", "DAVE")
)
df$references <- list(
  c("R1", "R2"),
  c("R1", "R3"),
  c("R2", "R3", "R4")
)
df$keywords <- list(
  c("graph", "network"),
  c("network", "embedding"),
  c("graph", "embedding", "neural")
)

author_network(df, "collaboration")
keyword_network(df)
reference_network(df)

build_bipartite() applies toupper(trimws(...)) to every entity label before constructing the sparse matrix, so "graph", "Graph", and "GRAPH" are mapped to the same node "GRAPH". Tests or comparisons that reference node names should use uppercase strings.

12. The split_field() helper

split_field() converts a character column with semicolon-delimited (or otherwise delimited) values into a list-column without going through read_biblio(format = "generic"):

split_field(c("Alice; Bob; Carol", "Dave; Eve"))
split_field(c("a|b|c", "d|e"), sep = "|")

This is the same operation that read_scopus() and the other readers apply internally to multi-valued columns; it is exported for use in custom pipelines.

13. Combining data from multiple sources

Different readers expose different extras: WoS provides keywords_plus, Scopus provides index_keywords, OpenAlex provides countries. To combine sources, restrict each frame to the standard columns and bind:

common <- c("id", "title", "year", "journal", "doi", "cited_by_count",
            "abstract", "type", "authors", "references", "keywords")

data(biblio_data)
b1 <- biblio_data
b2 <- biblio_data
b2$id <- paste0(b2$id, "_dup")

cols <- intersect(common, names(b1))
combined <- rbind(b1[, cols], b2[, cols])
nrow(combined)

Two practical notes:

1. When document IDs overlap across sources (which occurs when Scopus and WoS both index the same article), prefixing the IDs as shown prevents duplicate documents from inflating co-occurrence counts.
2. Source-specific extras (e.g. WoS keywords_plus) should be retained on the per-source frame and merged selectively rather than coerced into the combined frame.

14. Inspecting and sanity-checking

After reading, basic checks on the list-column sizes and the scalar columns help detect silent corruption. Empty list-columns and out-of-range years are common indicators that an export is incomplete.

data(scopus_quantum_cloud)
sc <- scopus_quantum_cloud

range(lengths(sc$authors))
range(lengths(sc$references))
range(lengths(sc$keywords))

head(sort(table(sc$journal), decreasing = TRUE), 5)
range(sc$year, na.rm = TRUE)
table(sc$type)

Indicators to check:

• A lengths() of 0 on every row of references for a Scopus or WoS file indicates that the export did not include the references column. Re-export from the source with the references field selected.
• A year of 0 or NA indicates an empty source field.
• A single dominant document type (e.g. only "article") is expected for filtered searches; broader mixes are expected for thematic searches.

15. Troubleshooting

| Symptom | Cause | Fix | |---|---|---| | Could not detect file format | First line doesn't match any signature | Pass format = "scopus" (etc.) explicitly, or name the entity columns (authors, keywords, ...) to read it as a generic CSV | | Empty references list on every row | BibTeX/RIS or OpenAlex flat CSV — these don't carry citations | Use Scopus/WoS, OpenAlex via oa_fetch(), Dimensions, Lens, or Crossref | | Invalid multibyte string on read | Wrong encoding | Most readers accept encoding = "latin1"; pass it through read_biblio(..., encoding = "latin1") | | Author names look like LASTNAME, F.J. not FJ LASTNAME | Default is flip_names = FALSE | The reader returns names as-is from the source. Cluster them by string match downstream, or pass flip_names = TRUE if all names follow Last, First | | Dimensions file silently fails | "About the data" preamble removed and column header edited | read_dimensions() detects the standard preamble and falls back to header-token detection; the failure mode requires the column header itself to have been edited | | Co-authorship network contains duplicate nodes (e.g. "Alice" and "ALICE") | Mixed casing in the source | The standard readers and build_bipartite() apply toupper(trimws(...)) to entity labels. Manually constructed frames should apply the same normalisation |

Further reading

• The companion vignette, vignette("bibnets"), covers network construction on the in-package datasets.
• vignette("parsing-author-names") covers parse_names() for normalising author labels before a network is built.
• All network builders (author_network(), keyword_network(), reference_network(), document_network(), source_network(), country_network(), institution_network(), conetwork()) accept the same core arguments (type, counting, similarity, threshold, top_n, format) plus the custom-column arguments shown above (id, the entity column, sep, references_sep, strip_quotes), so switching between network types on data already in the standard schema requires only a function-name change.

bibnets documentation built on June 19, 2026, 1:06 a.m.