Package {scholidonline}

Type:	Package
Title:	Resolution, Conversion, Linking and Metadata for Scholarly Identifiers
Version:	0.2.0
Language:	en-US
Description:	Enables querying of scholarly identifier services to verify identifier existence, convert identifiers across systems, retrieve bibliographic metadata, and discover linked identifiers. Supports identifier types including DOI, PMID, PMCID, arXiv, ORCID, OpenAlex, ROR, UniProt, and selected NCBI accessions (GEO, BioProject, RefSeq, SRA, and genome assembly).
License:	MIT + file LICENSE
URL:	https://thomas-rauter.github.io/scholidonline/
BugReports:	https://github.com/Thomas-Rauter/scholidonline/issues
Depends:	R (≥ 4.0.0)
Imports:	scholid (≥ 0.2.0), httr2, rlang
Suggests:	testthat (≥ 3.0.0), knitr (≥ 1.30), rmarkdown
Encoding:	UTF-8
RoxygenNote:	7.3.3
Config/testthat/edition:	3
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2026-06-14 17:10:33 UTC; thomasrauter
Author:	Thomas Rauter [aut, cre, fnd]
Maintainer:	Thomas Rauter <rauterthomas0@gmail.com>
Repository:	CRAN
Date/Publication:	2026-06-14 17:50:02 UTC

Convert scholarly identifiers across systems

Description

Convert scholarly identifiers across registries, for example from PMID to DOI.

Usage

id_convert(
  x,
  to = scholidonline_types(),
  from = NULL,
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

Details

Only some source/target type pairs are supported. Use scholidonline_capabilities() with operation = "convert" (or filter the returned table) to see which conversions are available and which providers implement them.

Value

A character vector of converted identifiers. Elements that cannot be identified, normalized, or converted return NA_character_.

Examples

  id_convert("12345678", to = "doi", from = "pmid")
  id_convert("10.1038/nature12373", to = "pmid", from = "doi")

Check whether scholarly identifiers exist

Description

Check whether scholarly identifiers are found in their respective registries.

Usage

id_exists(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

Details

Existence checking is not available for every identifier type supported by scholid. Use scholidonline_capabilities() to see which types support the exists operation and which providers implement it.

type must be a single value or "auto". For mixed identifier columns, omit type or use type = "auto" so each element is classified separately.

Value

A logical vector. TRUE indicates that the identifier was found, FALSE indicates that it was not found, and NA indicates that the input could not be identified, normalized, or checked reliably.

Examples

  id_exists("10.1038/nature12373", type = "doi")
  id_exists(c("31452104", "PMC6784763"))

Return identifiers linked to the same scholarly record

Description

Return identifiers that external registries link to the same scholarly record or to a closely corresponding version of it.

Usage

id_links(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  ...,
  quiet = FALSE
)

Arguments

Details

id_links() is vectorized over x and returns a long data.frame with one row per discovered identifier link.

Typical links include DOI <-> PMID, DOI <-> PMCID, PMID <-> PMCID, arXiv ID <-> DOI, ORCID -> DOI for works recorded in ORCID, and OpenAlex work -> DOI, PMID, or PMCID where present in the OpenAlex record.

Link discovery is not available for every supported identifier type; use scholidonline_capabilities() to check whether links is supported.

Only identifier links explicitly exposed by the queried provider are returned. id_links() does not retrieve general metadata or broader related records unless the provider represents them as direct identifier links.

Trivial self-links are excluded from the result.

type must be a single value or "auto". For mixed identifier columns, omit type or use type = "auto" so each element is classified separately.

Value

A data.frame with columns query, query_type, linked_type, linked_id, and provider. If no links are found, a zero-row data.frame with these columns is returned.

Examples

  out <- id_links("31452104", provider = "epmc")
  knitr::kable(out)

Retrieve scholarly metadata

Description

Retrieve structured metadata for scholarly identifiers from external registries.

Usage

id_metadata(
  x,
  type = c("auto", scholidonline_types()),
  provider = c("auto", .scholidonline_providers()),
  fields = NULL,
  ...,
  quiet = FALSE
)

Arguments

Details

id_metadata() is vectorized over x and returns a data.frame with one row per input identifier.

For providers that support batch lookup, such as arXiv, multiple identifiers may be resolved using a single provider request. This does not change the public return shape: the output still contains one row per input identifier.

The function returns a harmonized cross-provider data.frame with columns title, year, container, doi, pmid, pmcid, and url. For bibliographic identifiers, container is typically a journal or source title and linked DOI/PMID/PMCID fields may be populated. For other types, the same columns are reused with type-appropriate meaning (for example, protein name and organism for UniProt, organization name and country for ROR, or accession title and organism for NCBI accessions). Bibliographic link columns are NA when not applicable.

For NCBI accession types such as BioProject, title is the registry's short project or record title from Entrez ESummary, not the full description shown on the NCBI website. Use url for the complete record.

type must be a single value or "auto". For mixed identifier columns, omit type or use type = "auto" so each element is classified separately.

Value

A data.frame with one row per input identifier. By default, the returned columns are input, type, provider, title, year, container, doi, pmid, pmcid, and url. Inputs that cannot be identified, normalized, or resolved are returned as rows with missing metadata fields.

Examples

  out <- id_metadata("10.1038/nature12373", type = "doi")
  knitr::kable(out)
  out <- id_metadata(c("31452104", "PMC6821181"))
  knitr::kable(out)
  out <- id_metadata(
    "10.1038/nature12373",
     fields = c("title", "year", "doi")
     )
  knitr::kable(out)

Supported scholidonline capabilities

Description

Return a summary of the capabilities supported by the scholidonline package.

The returned table describes, for each supported identifier type:

• which single-identifier operations are available (exists, links, meta),

• which identifier conversions are available,

• which providers support each capability, and

• which provider is used by default when provider = "auto".

This function is useful for discovering what scholidonline can do for a given identifier type or conversion pair.

Usage

scholidonline_capabilities()

Value

A data.frame with one row per supported capability and the following columns:

• type: source identifier type

• operation: operation name (exists, links, meta, or convert)

• target: target identifier type for conversion operations, otherwise NA

• providers: comma-separated names of providers supporting the capability

• default_provider: default provider used when provider = "auto"

Examples

caps <- scholidonline_capabilities()

subset(caps, type == "pmid" & operation == "convert")

subset(caps, type == "doi" & target == "pmcid")

Supported scholidonline identifier types

Description

Return the set of identifier types supported by the scholidonline package.

This is the set of identifier types for which scholidonline provides registry-backed functionality. Available operations vary by type; use scholidonline_capabilities() to see which of existence checks, metadata retrieval, link discovery, and identifier conversion are supported for each type.

Usage

scholidonline_types()

Value

A character vector of supported identifier type strings.

Examples

scholidonline_types()
"doi" %in% scholidonline_types()