scholidonline

scholidonline provides lightweight online utilities for working with scholarly identifiers in R. It builds on scholid for identifier detection and normalization, and adds minimal-dependency functions to query external registries.

See the full documentation at the scholidonline website.

Installation

Install the released version from CRAN:

install.packages("scholidonline")

Scope

The package provides registry-backed online operations where supported for these identifier groups:

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

Operations include existence checks, metadata retrieval, linked-identifier discovery, and cross-system conversion. Not every type supports every operation; use scholidonline_capabilities() to inspect what is available for a given type.

Interface

User-available functions:

Function	Purpose
`scholidonline_types()`	Supported scholidonline identifier types
`scholidonline_capabilities()`	Supported scholidonline capabilities
`id_exists()`	Check whether identifiers exist in their registries
`id_convert()`	Convert identifiers across systems (e.g., PMID → DOI)
`id_metadata()`	Retrieve basic structured metadata
`id_links()`	Discover identifiers linked to the same scholarly record when exposed by the provider

Examples

# List supported scholidonline identifier types
scholidonline::scholidonline_types()

##  [1] "arxiv"      "assembly"   "bioproject" "doi"        "geo"       
##  [6] "openalex"   "orcid"      "pmcid"      "pmid"       "refseq"    
## [11] "ror"        "sra"        "uniprot"

# List scholidonline capabilities
scholidonline::scholidonline_capabilities()

##          type operation target               providers default_provider
## 1       arxiv    exists   <NA>             auto, arxiv            arxiv
## 2       arxiv     links   <NA>             auto, arxiv            arxiv
## 3       arxiv      meta   <NA>             auto, arxiv            arxiv
## 4    assembly    exists   <NA>              auto, ncbi             ncbi
## 5    assembly      meta   <NA>              auto, ncbi             ncbi
## 6  bioproject    exists   <NA>              auto, ncbi             ncbi
## 7  bioproject      meta   <NA>              auto, ncbi             ncbi
## 8         doi    exists   <NA> auto, doi.org, crossref          doi.org
## 9         doi     links   <NA>          auto, crossref         crossref
## 10        doi      meta   <NA> auto, crossref, doi.org         crossref
## 11        doi   convert   pmid        auto, ncbi, epmc             ncbi
## 12        doi   convert  pmcid        auto, ncbi, epmc             ncbi
## 13        geo    exists   <NA>              auto, ncbi             ncbi
## 14        geo      meta   <NA>              auto, ncbi             ncbi
## 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
## 20      orcid    exists   <NA>             auto, orcid            orcid
## 21      orcid     links   <NA>             auto, orcid            orcid
## 22      orcid      meta   <NA>             auto, orcid            orcid
## 23      pmcid    exists   <NA>        auto, ncbi, epmc             ncbi
## 24      pmcid     links   <NA>        auto, ncbi, epmc             ncbi
## 25      pmcid      meta   <NA>        auto, ncbi, epmc             ncbi
## 26      pmcid   convert   pmid        auto, ncbi, epmc             ncbi
## 27      pmcid   convert    doi        auto, ncbi, epmc             ncbi
## 28       pmid    exists   <NA>        auto, ncbi, epmc             ncbi
## 29       pmid     links   <NA>        auto, ncbi, epmc             ncbi
## 30       pmid      meta   <NA>        auto, ncbi, epmc             ncbi
## 31       pmid   convert    doi        auto, ncbi, epmc             ncbi
## 32       pmid   convert  pmcid        auto, ncbi, epmc             ncbi
## 33     refseq    exists   <NA>              auto, ncbi             ncbi
## 34     refseq      meta   <NA>              auto, ncbi             ncbi
## 35        ror    exists   <NA>               auto, ror              ror
## 36        ror      meta   <NA>               auto, ror              ror
## 37        sra    exists   <NA>              auto, ncbi             ncbi
## 38        sra      meta   <NA>              auto, ncbi             ncbi
## 39    uniprot    exists   <NA>           auto, uniprot          uniprot
## 40    uniprot      meta   <NA>           auto, uniprot          uniprot

# Check if an ID exists online
scholidonline::id_exists(
  "10.1000/182",
  type = "doi"
  )

## [1] TRUE

# Convert identifiers across systems
scholidonline::id_convert(
  "12345678",
  to = "doi",
  from = "pmid"
  )

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

# Retrieve scholarly metadata
out <- scholidonline::id_metadata(
  "10.1038/nature12373",
  type = "doi"
  )

# Show key fields
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

# Return identifiers linked to the same scholarly record when the provider
# exposes them. Returns an empty table when no linked identifiers are found.
out <- scholidonline::id_links(
  "31452104",
  provider = "epmc"
  )

knitr::kable(out)

	query	query_type	linked_type	linked_id	provider
2	31452104	pmid	doi	10.1007/978-1-4939-9752-7_10	epmc

Relationship to scholid

scholid provides dependency-free utilities for detecting, normalizing, classifying, and extracting scholarly identifiers (including types without online support here, such as ISBN, ISSN, and bibcode).

scholidonline builds on that foundation and adds online registry queries for a subset of those types.

License

MIT