Getting started with scholidonline

Installation

install.packages("scholidonline")

Interface

scholidonline exposes a small set of user-facing functions:

• scholidonline_types()
• scholidonline_capabilities()
• id_exists()
• id_convert()
• id_metadata()
• id_links()

Supported identifier types

You can inspect which identifier types are supported:

scholidonline::scholidonline_types()
#>  [1] "arxiv"      "assembly"   "bioproject" "doi"        "geo"       
#>  [6] "openalex"   "orcid"      "pmcid"      "pmid"       "refseq"    
#> [11] "ror"        "sra"        "uniprot"

Inspecting capabilities

scholidonline is registry-driven. You can inspect all supported operations, conversions, and providers:

out <- scholidonline::scholidonline_capabilities()
knitr::kable(out)

Not every supported type offers every operation. For example, ROR and UniProt support existence checks and metadata, while DOI and PMID also support linked identifiers and conversion. To inspect one type:

out <- scholidonline::scholidonline_capabilities()
knitr::kable(subset(out, type == "openalex"))

Existence checks: id_exists()

id_exists() verifies whether identifiers exist in their respective registries.

scholidonline::id_exists(
  x    = "10.1000/182",
  type = "doi"
)

If type = NULL, the type is inferred automatically:

scholidonline::id_exists(
  x = c(
    "10.1000/182",
    "12345678"
  )
)

Return values:

• TRUE → confirmed by registry
• FALSE → confirmed not found
• NA → cannot be classified or normalized

Conversion: id_convert()

Many scholarly identifiers are cross-linked across systems.

Common examples:

• PMID → DOI
• PMCID → PMID
• DOI → PMCID

scholidonline::id_convert(
  x    = "12345678",
  from = "pmid",
  to   = "doi"
)

If from = NULL, the source type is inferred per element:

scholidonline::id_convert(
  x = c("12345678", "PMC1234567"),
  to = "doi"
)

Unresolvable mappings return NA_character_.

Metadata retrieval: id_metadata()

id_metadata() retrieves harmonized metadata from external registries.

out <- scholidonline::id_metadata(
  x    = "10.1038/nature12373",
  type = "doi"
)
knitr::kable(out)

Metadata completeness depends on the registry. For NCBI accession types such as BioProject, title is the short registry title from Entrez ESummary, not the full project description on the NCBI website; use url for the complete record.

You can restrict returned fields:

out <- scholidonline::id_metadata(
  x = "10.1038/nature12373",
  type = "doi",
  fields = c("title", "year", "doi")
)
knitr::kable(out)

Linked identifiers: id_links()

id_links() returns related identifiers discovered via registry queries. Returns an empty table when the provider exposes no linked identifiers for that record.

out <- scholidonline::id_links(
  x    = "PMC1234567",
  type = "pmcid"
)
knitr::kable(out)

The result is a long data.frame with one row per link. When no links are found, the same columns are returned with zero rows.

Working with mixed data

A common workflow for messy identifier columns:

1. Detect identifier types (via scholid)
2. Normalize identifiers
3. Check registry existence

Example:

x <- c(
  "https://doi.org/10.1000/182",
  "PMCID: PMC1234567",
  "not an id"
)

types <- scholid::detect_scholid_type(x)

x_norm <- rep(NA_character_, length(x))

for (i in seq_along(x)) {
  if (is.na(types[i])) {
    next
  }

  x_norm[i] <- scholid::normalize_scholid(
    x = x[i],
    type = types[i]
  )
}

types
x_norm

id_exists(x) below uses the default type = "auto", so each element is classified and normalized automatically. You do not need to pass a vector type argument.

scholidonline::id_exists(x)

Provider selection

Most functions accept a provider argument.

scholidonline::id_exists(
  x        = "10.1000/182",
  type     = "doi",
  provider = "crossref"
)

scholidonline::id_exists(
  x        = "10.1000/182",
  type     = "doi",
  provider = "doi.org"
)

If provider = "auto" (default), a sensible registry is chosen automatically, potentially with fallback behavior.

Available providers depend on the identifier type and operation. Use scholidonline_capabilities() to inspect them.

The chosen provider affects:

• Response speed
• Metadata richness
• Crosswalk coverage

Scope of scholidonline

scholidonline focuses on identifier types with stable public registries and accessible APIs. The package supports online operations for:

• Bibliographic core: DOI, PMID, PMCID, arXiv
• Graph and people: OpenAlex, ORCID
• Organizations: ROR
• Life science: UniProt; NCBI accessions (GEO, BioProject, RefSeq, SRA, genome assembly)

Not every type supports every operation. For example, ROR and UniProt support existence checks and metadata, while DOI and PMID additionally support linked identifiers and conversion. Use scholidonline_capabilities() as the authoritative summary.

Many other identifier types (e.g., ISBN, ISSN, bibcode, RRID) are structurally supported by scholid, but are not covered by scholidonline because they lack a stable, open registry API fit for this package.