scholid

scholid provides lightweight, dependency-free utilities for working with scholarly identifiers in R. The package is designed as a small, well-tested foundation that can be safely reused by other packages and data workflows. For the supported identifier types, see Scope and scholid_types().

See the full documentation at the scholid website.

For online lookup, conversion, metadata retrieval, and linked identifier discovery, see scholidonline.

Installation

Install the released version from CRAN:

install.packages("scholid")

Scope

The package focuses on common identifier systems used in scholarly communication:

• DOI
• arXiv
• ADS bibcode
• OpenAlex
• Software Heritage (SWHID)
• ARK
• ISNI
• ORCID iD
• ROR
• RRID
• UniProt
• RefSeq
• SRA
• GEO
• BioProject
• Genome assembly (GCA/GCF)
• ISBN
• ISSN
• PubMed Central (PMCID)
• PubMed (PMID)

Interface

User-available functions:

Function	Purpose
scholid_types()	List supported scholarly identifier types
is_scholid(x, type)	Test whether values conform to a given identifier type
normalize_scholid(x, type)	Normalize identifiers to canonical form
scholid_key(x, type)	Give keys for comparing and deduplicating identifiers
format_scholid(x, type, as)	Write identifiers as resolver URLs, CURIEs, or arXiv DOIs
extract_scholid(text, type)	Extract identifiers of a given type from free text
locate_scholid(text, types)	Find identifiers of several types in free text, with their positions
classify_scholid(x)	Guess the identifier type of each input value
detect_scholid_type(x)	Detect identifier types from canonical or wrapped input values

Examples

# list supported scholarly identifier types
scholid::scholid_types()

##  [1] "doi"        "arxiv"      "bibcode"    "openalex"   "swhid"     
##  [6] "ark"        "isni"       "orcid"      "ror"        "rrid"      
## [11] "uniprot"    "refseq"     "sra"        "geo"        "bioproject"
## [16] "assembly"   "isbn"       "issn"       "pmcid"      "pmid"

# test whether values match a given identifier type
scholid::is_scholid(
  x    = "10.1000/182",
  type = "doi"
)

## [1] TRUE

# normalize identifiers to canonical form
scholid::normalize_scholid(
  x    = "https://doi.org/10.1000/182",
  type = "doi"
)

## [1] "10.1000/182"

# give keys that match an ISBN-10 and its ISBN-13
scholid::scholid_key(
  x    = c("0306406152", "978-0-306-40615-7"),
  type = "isbn"
)

## [1] "9780306406157" "9780306406157"

# write identifiers as resolver URLs or CURIEs
scholid::format_scholid(
  x    = "PMID: 12345678",
  type = "pmid"
)

## [1] "https://pubmed.ncbi.nlm.nih.gov/12345678/"

scholid::format_scholid(
  x    = "0000-0002-1825-0097",
  type = "orcid",
  as   = "curie"
)

## [1] "orcid:0000-0002-1825-0097"

# extract identifiers of a given type from free text
scholid::extract_scholid(
  text = "See https://doi.org/10.1000/182 for details.",
  type = "doi"
)

## [[1]]
## [1] "10.1000/182"

# locate identifiers of all types in free text, with their positions
scholid::locate_scholid(
  text = "See doi:10.1000/182 and ISBN 978-0-306-40615-7."
)

##   element type                id             match start end
## 1       1  doi       10.1000/182       10.1000/182     9  19
## 2       1 isbn 978-0-306-40615-7 978-0-306-40615-7    30  46

# classify the identifier type of each input value
scholid::classify_scholid(
  x = c(
    "10.1000/182",
    "0000-0002-1825-0097",
    "not an id"
  )
)

## [1] "doi"   "orcid" NA

# detect identifier types from canonical or wrapped input values
scholid::detect_scholid_type(
  x = c(
    "https://doi.org/10.1000/182",
    "ORCID: 0000-0002-1825-0097",
    "arXiv:2101.00001",
    "not an id"
  )
)

## [1] "doi"   "orcid" "arxiv" NA

For more detailed usage patterns check out the Get started vignette.

License

MIT