Validate References

Validate References

Check BibTeX bibliography entries for completeness, accuracy, and consistency. This skill covers verifying required fields per entry type, resolving DOIs via the CrossRef API, checking URL accessibility, detecting duplicate entries, and producing a structured validation report that flags issues by severity. It ensures that .bib files are publication-ready before rendering.

When to Use

• Preparing a manuscript bibliography for journal submission
• Auditing a shared .bib file for quality before a project milestone
• After merging bibliographies from multiple sources
• When citations render incorrectly and you need to diagnose .bib issues
• As a CI check on .bib files in version-controlled projects

Do NOT use for agent-memory or documentation cross-references — see repair-broken-references. This skill validates bibliographic entries and DOI resolution; the name collision with "references" in the link-checking sense is the only thing the two share. For the reachability and budget of a Claude Code memory directory, see verify-memory-integrity.

Inputs

• Required: Path to a .bib file
• Optional: Validation level (basic, standard, strict; default: standard)
• Optional: Whether to check DOI resolution online (default: TRUE)
• Optional: Whether to check URL accessibility (default: TRUE)
• Optional: Output report path (default: prints to console)
• Optional: CrossRef API email for polite pool (recommended for large files)

Procedure

Step 1: Install and Load Required Packages

required_packages <- c("RefManageR", "httr2", "curl")
missing <- required_packages[!vapply(required_packages, requireNamespace,
                                     logical(1), quietly = TRUE)]
if (length(missing) > 0) install.packages(missing)

library(RefManageR)

Expected: All packages load without errors.

On failure: If httr2 is unavailable, install it with install.packages("httr2"). For systems without curl headers: sudo apt install libcurl4-openssl-dev.

Step 2: Parse and Inventory the Bibliography

bib <- RefManageR::ReadBib("references.bib", check = FALSE)
message(sprintf("Loaded %d entries from references.bib", length(bib)))

# Inventory entry types
entry_types <- vapply(bib, function(x) tolower(attr(x, "bibtype")), character(1))
type_counts <- sort(table(entry_types), decreasing = TRUE)
message("Entry types:")
for (type in names(type_counts)) {
  message(sprintf("  %s: %d", type, type_counts[[type]]))
}

Expected: Summary of entry types (article, book, inproceedings, etc.) and total count matching the number of @type{ blocks in the file.

On failure: Parsing errors indicate malformed BibTeX. Check for unmatched braces, missing commas between fields, or invalid UTF-8 characters.

Step 3: Validate Required Fields per Entry Type

# BibTeX required fields by entry type
required_fields <- list(
  article       = c("author", "title", "journal", "year"),
  book          = c("author", "title", "publisher", "year"),
  inproceedings = c("author", "title", "booktitle", "year"),
  incollection  = c("author", "title", "booktitle", "publisher", "year"),
  phdthesis     = c("author", "title", "school", "year"),
  mastersthesis = c("author", "title", "school", "year"),
  techreport    = c("author", "title", "institution", "year"),
  misc          = c("author", "title", "year"),
  unpublished   = c("author", "title", "note")
)

validate_fields <- function(bib) {
  issues <- list()
  for (i in seq_along(bib)) {
    key <- names(bib)[i]
    entry_type <- tolower(attr(bib[[i]], "bibtype"))
    req <- required_fields[[entry_type]]
    if (is.null(req)) {
      issues[[length(issues) + 1]] <- list(
        key = key, severity = "warning",
        message = sprintf("Unknown entry type: %s", entry_type)
      )
      next
    }
    for (field in req) {
      value <- bib[[i]][[field]]
      if (is.null(value) || !nzchar(trimws(as.character(value)))) {
        issues[[length(issues) + 1]] <- list(
          key = key, severity = "error",
          message = sprintf("Missing required field: %s (type: %s)", field, entry_type)
        )
      }
    }
  }
  issues
}

field_issues <- validate_fields(bib)
message(sprintf("Field validation: %d issues found", length(field_issues)))

Expected: A list of issues where required fields are missing. Zero issues for a well-maintained bibliography.

On failure: This step runs locally and should not fail. If it does, check that the .bib file parsed correctly in Step 2.

Step 4: Resolve and Validate DOIs

validate_dois <- function(bib, email = NULL) {
  issues <- list()

  # Set polite API headers
  headers <- list(`User-Agent` = "R-bibliography-validator/1.0")
  if (!is.null(email)) {
    headers[["mailto"]] <- email
  }

  for (i in seq_along(bib)) {
    key <- names(bib)[i]
    doi <- bib[[i]]$doi
    if (is.null(doi) || !nzchar(doi)) {
      issues[[length(issues) + 1]] <- list(
        key = key, severity = "info",
        message = "No DOI present"
      )
      next
    }

    # Normalize DOI
    doi <- gsub("^https?://doi\\.org/", "", doi)
    doi <- gsub("^doi:", "", doi, ignore.case = TRUE)
    doi <- trimws(doi)

    # Resolve via CrossRef
    tryCatch({
      resp <- httr2::request(sprintf("https://api.crossref.org/works/%s", doi)) |>
        httr2::req_headers(!!!headers) |>
        httr2::req_timeout(10) |>
        httr2::req_perform()

      if (httr2::resp_status(resp) != 200) {
        issues[[length(issues) + 1]] <- list(
          key = key, severity = "error",
          message = sprintf("DOI does not resolve: %s (HTTP %d)", doi,
                            httr2::resp_status(resp))
        )
      }
    }, error = function(e) {
      issues[[length(issues) + 1]] <<- list(
        key = key, severity = "warning",
        message = sprintf("DOI check failed for %s: %s", doi, e$message)
      )
    })

    Sys.sleep(0.5)  # Rate limiting
  }
  issues
}

# Only run online checks if requested
doi_issues <- validate_dois(bib, email = "your.email@example.com")
message(sprintf("DOI validation: %d issues found", length(doi_issues)))

Expected: Each DOI resolves successfully (HTTP 200 from CrossRef). Entries without DOIs are flagged as informational.

On failure: Network errors or rate limiting produce warnings rather than hard failures. Set the email parameter for higher rate limits from CrossRef's polite pool.

Step 5: Check URL Accessibility

validate_urls <- function(bib) {
  issues <- list()

  for (i in seq_along(bib)) {
    key <- names(bib)[i]
    url <- bib[[i]]$url

    if (is.null(url) || !nzchar(url)) next

    tryCatch({
      resp <- httr2::request(url) |>
        httr2::req_method("HEAD") |>
        httr2::req_timeout(10) |>
        httr2::req_error(is_error = function(resp) FALSE) |>
        httr2::req_perform()

      status <- httr2::resp_status(resp)
      if (status >= 400) {
        issues[[length(issues) + 1]] <- list(
          key = key, severity = "warning",
          message = sprintf("URL returned HTTP %d: %s", status, url)
        )
      }
    }, error = function(e) {
      issues[[length(issues) + 1]] <<- list(
        key = key, severity = "warning",
        message = sprintf("URL unreachable: %s (%s)", url, e$message)
      )
    })

    Sys.sleep(0.3)
  }
  issues
}

url_issues <- validate_urls(bib)
message(sprintf("URL validation: %d issues found", length(url_issues)))

Expected: All URLs return HTTP 200 (or 301/302 redirects). Broken links flagged.

On failure: Some servers block HEAD requests. Retry with GET for failed HEAD checks. Timeout errors are common for slow academic servers.

Step 6: Detect Duplicate Entries

detect_duplicates <- function(bib) {
  issues <- list()

  # Check for duplicate DOIs
  dois <- vapply(bib, function(x) {
    d <- x$doi
    if (is.null(d)) NA_character_ else tolower(trimws(d))
  }, character(1))

  doi_table <- table(dois[!is.na(dois)])
  dup_dois <- names(doi_table[doi_table > 1])
  for (d in dup_dois) {
    keys <- names(bib)[which(dois == d)]
    issues[[length(issues) + 1]] <- list(
      key = paste(keys, collapse = ", "), severity = "error",
      message = sprintf("Duplicate DOI %s in entries: %s", d,
                        paste(keys, collapse = ", "))
    )
  }

  # Check for duplicate titles (fuzzy)
  titles <- vapply(bib, function(x) {
    t <- x$title
    if (is.null(t)) NA_character_ else tolower(gsub("[^a-z0-9 ]", "", tolower(t)))
  }, character(1))

  seen <- character(0)
  for (i in seq_along(titles)) {
    if (is.na(titles[i])) next
    for (j in seen) {
      if (identical(titles[i], titles[as.integer(j)])) {
        issues[[length(issues) + 1]] <- list(
          key = sprintf("%s, %s", names(bib)[as.integer(j)], names(bib)[i]),
          severity = "warning",
          message = sprintf("Possible duplicate titles: '%s'",
                            substr(bib[[i]]$title, 1, 60))
        )
      }
    }
    seen <- c(seen, as.character(i))
  }

  issues
}

dup_issues <- detect_duplicates(bib)
message(sprintf("Duplicate detection: %d issues found", length(dup_issues)))

Expected: Zero duplicates for a clean bibliography. Any detected duplicates are flagged with the specific entry keys involved.

Step 7: Generate Validation Report

generate_report <- function(all_issues, bib, output_file = NULL) {
  errors   <- Filter(function(x) x$severity == "error", all_issues)
  warnings <- Filter(function(x) x$severity == "warning", all_issues)
  infos    <- Filter(function(x) x$severity == "info", all_issues)

  lines <- c(
    "# Bibliography Validation Report",
    "",
    sprintf("**File**: references.bib"),
    sprintf("**Entries**: %d", length(bib)),
    sprintf("**Date**: %s", Sys.Date()),
    "",
    sprintf("## Summary: %d errors, %d warnings, %d info",
            length(errors), length(warnings), length(infos)),
    ""
  )

  if (length(errors) > 0) {
    lines <- c(lines, "## Errors", "")
    for (issue in errors) {
      lines <- c(lines, sprintf("- **[%s]** %s", issue$key, issue$message))
    }
    lines <- c(lines, "")
  }

  if (length(warnings) > 0) {
    lines <- c(lines, "## Warnings", "")
    for (issue in warnings) {
      lines <- c(lines, sprintf("- **[%s]** %s", issue$key, issue$message))
    }
    lines <- c(lines, "")
  }

  report_text <- paste(lines, collapse = "\n")

  if (!is.null(output_file)) {
    writeLines(report_text, output_file)
    message(sprintf("Report written to %s", output_file))
  }

  cat(report_text)
  invisible(all_issues)
}

all_issues <- c(field_issues, doi_issues, url_issues, dup_issues)
generate_report(all_issues, bib, output_file = "validation-report.md")

Expected: A structured markdown report listing all issues grouped by severity.

Validation

• All entries have required fields for their type (no errors in field check)
• All DOIs resolve to valid CrossRef records
• No duplicate DOIs exist in the bibliography
• All URLs are accessible (HTTP 200 or redirect)
• Validation report generated without R errors
• Zero errors in report for a publication-ready bibliography

Common Pitfalls

• DOI format inconsistency: DOIs may appear as 10.1234/..., https://doi.org/10.1234/..., or doi:10.1234/.... Normalize before comparing
• CrossRef rate limiting: Unauthenticated requests are limited to ~50/second. Always use the email parameter to join the polite pool for higher limits
• Transient URL failures: Academic servers occasionally timeout. Retry failed URLs once before flagging them as broken
• Entry type variations: BibLaTeX uses @online where BibTeX uses @misc. The validator should handle both
• False positive duplicates: Entries like "Introduction" or "Methods" as titles trigger fuzzy matching. Review flagged duplicates manually
• Missing DOIs for older works: Pre-2000 publications often lack DOIs. Flag as informational, not as errors
• Author names are separated by and, not commas: BibTeX splits an author or editor field on the word and surrounded by spaces and not enclosed in braces. A comma delimits parts inside a single name (von Last, First or von Last, Jr, First), so a comma-joined list collapses silently into one author rather than several, and a trailing comma makes BibTeX complain that a name ends with a comma
• Organizations as authors need an extra pair of braces: An institution left bare in an author field is dissected into First/von/Last like a personal name, and any internal and splits it into two people. Wrap it in its own braces: author = {{National Aeronautics and Space Administration}}
• One person under two spellings: Donald E. Knuth in one entry and D. E. Knuth in another alphabetize as two different authors. Settle on one form per person, or write D[onald] E. Knuth, which BibTeX alphabetizes as if the brackets were absent
• Journal name inconsistency: One entry writes Journal of the American Chemical Society, another writes J. Am. Chem. Soc., and nothing above notices, because Step 6 compares DOIs and article titles and never looks at the journal field. The CrossRef record fetched in Step 4 carries the journal's ISSN and container-title, and often its short-container-title (J. Am. Chem. Soc. for this journal), so group entries by ISSN and flag any group whose journal values disagree. Flag rather than normalize: ISO 4 governs title-word abbreviation through the LTWA maintained by the ISSN International Centre, but NLM/MEDLINE strips the punctuation from that assignment, so PubMed writes J Am Chem Soc for the same journal. Pick the form the target journal's style requires
• A resolving DOI is not a matching DOI: HTTP 200 confirms the DOI is registered, not that it points at the entry's work. A wrong but registered DOI resolves exactly like a correct one, so compare the CrossRef record Step 4 already fetched against the entry: title (an array), the family names in author, and issued.date-parts. Normalize both sides first, or LaTeX escapes and Unicode accents will manufacture mismatches
• False mismatches from CrossRef's own shape: a year off by one need not be an error, because published-online and published-print are separate fields that can fall in different years. 10.1093/bioinformatics/btz848 is online 2019 and print 2020, with issued following the online date. short-container-title is sometimes an empty array, so a missing journal abbreviation is not a mismatch, and a record paginated by article number can carry article-number with no page field at all

Related Skills

• manage-bibliography - fix issues found by this validator (dedup, add fields)
• format-citations - format validated entries into styled citations
• repair-broken-references - the correct destination for broken internal links, dead URLs, stale imports, and orphaned files in documentation or agent memory
• verify-memory-integrity - read-only reachability and budget check for a Claude Code memory directory; not a bibliography tool despite the shared word
• ../reporting/format-apa-report - APA reports require complete, validated references
• ../r-packages/write-vignette - vignettes with citations need valid .bib entries