Getting started with scholidonline

scholidonline provides online utilities for working with scholarly identifiers. It builds on scholid for structural detection and normalization, and adds registry-backed functionality such as:

Existence checks
Identifier conversion across systems
Metadata retrieval
Retrieval of directly linked identifiers

This vignette introduces the interface and typical workflows when working with registry-connected identifier data.

Installation

install.packages("scholidonline")

Interface

scholidonline exposes a small set of user-facing functions:

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)

type	operation	target	providers	default_provider
arxiv	exists	NA	auto, arxiv	arxiv
arxiv	links	NA	auto, arxiv	arxiv
arxiv	meta	NA	auto, arxiv	arxiv
assembly	exists	NA	auto, ncbi	ncbi
assembly	meta	NA	auto, ncbi	ncbi
bioproject	exists	NA	auto, ncbi	ncbi
bioproject	meta	NA	auto, ncbi	ncbi
doi	exists	NA	auto, doi.org, crossref	doi.org
doi	links	NA	auto, crossref	crossref
doi	meta	NA	auto, crossref, doi.org	crossref
doi	convert	pmid	auto, ncbi, epmc	ncbi
doi	convert	pmcid	auto, ncbi, epmc	ncbi
geo	exists	NA	auto, ncbi	ncbi
geo	meta	NA	auto, ncbi	ncbi
openalex	exists	NA	auto, openalex	openalex
openalex	links	NA	auto, openalex	openalex
openalex	meta	NA	auto, openalex	openalex
openalex	convert	doi	auto, openalex	openalex
openalex	convert	pmid	auto, openalex	openalex
orcid	exists	NA	auto, orcid	orcid
orcid	links	NA	auto, orcid	orcid
orcid	meta	NA	auto, orcid	orcid
pmcid	exists	NA	auto, ncbi, epmc	ncbi
pmcid	links	NA	auto, ncbi, epmc	ncbi
pmcid	meta	NA	auto, ncbi, epmc	ncbi
pmcid	convert	pmid	auto, ncbi, epmc	ncbi
pmcid	convert	doi	auto, ncbi, epmc	ncbi
pmid	exists	NA	auto, ncbi, epmc	ncbi
pmid	links	NA	auto, ncbi, epmc	ncbi
pmid	meta	NA	auto, ncbi, epmc	ncbi
pmid	convert	doi	auto, ncbi, epmc	ncbi
pmid	convert	pmcid	auto, ncbi, epmc	ncbi
refseq	exists	NA	auto, ncbi	ncbi
refseq	meta	NA	auto, ncbi	ncbi
ror	exists	NA	auto, ror	ror
ror	meta	NA	auto, ror	ror
sra	exists	NA	auto, ncbi	ncbi
sra	meta	NA	auto, ncbi	ncbi
uniprot	exists	NA	auto, uniprot	uniprot
uniprot	meta	NA	auto, uniprot	uniprot

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"))

	type	operation	target	providers	default_provider
15	openalex	exists	NA	auto, openalex	openalex
16	openalex	links	NA	auto, openalex	openalex
17	openalex	meta	NA	auto, openalex	openalex
18	openalex	convert	doi	auto, openalex	openalex
19	openalex	convert	pmid	auto, openalex	openalex

Existence checks: `id_exists()`

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

scholidonline::id_exists(
  x    = "10.1000/182",
  type = "doi"
)
#> [1] TRUE

If type = NULL, the type is inferred automatically:

scholidonline::id_exists(
  x = c(
    "10.1000/182",
    "12345678"
  )
)
#> [1] TRUE TRUE

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"
)
#> [1] "10.1234/2013/999990"

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

scholidonline::id_convert(
  x = c("12345678", "PMC1234567"),
  to = "doi"
)
#> [1] "10.1234/2013/999990"              "10.1097/00000658-199503000-00007"

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)

input	type	provider	title	year	container	doi	pmid	pmcid	url
10.1038/nature12373	doi	crossref	Nanometre-scale thermometry in a living cell	2013	Nature	10.1038/nature12373	NA	NA	https://doi.org/10.1038/nature12373

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)

title	year	doi
Nanometre-scale thermometry in a living cell	2013	10.1038/nature12373

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)

	query	query_type	linked_type	linked_id	provider
1	PMC1234567	pmcid	pmid	7717779	ncbi
3	PMC1234567	pmcid	doi	10.1097/00000658-199503000-00007	ncbi

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:

Detect identifier types (via scholid)
Normalize identifiers
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
#> [1] "doi"   "pmcid" NA
x_norm
#> [1] "10.1000/182" "PMC1234567"  NA

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)
#> [1] TRUE TRUE   NA

Provider selection

Most functions accept a provider argument.

scholidonline::id_exists(
  x        = "10.1000/182",
  type     = "doi",
  provider = "crossref"
)
#> [1] FALSE

scholidonline::id_exists(
  x        = "10.1000/182",
  type     = "doi",
  provider = "doi.org"
)
#> [1] TRUE

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.