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How Scholarly Identifiers Are Defined

Source: vignettes/scholid_definitions.Rmd
scholid_definitions.Rmd

Introduction

This vignette explains how common scholarly identifiers are formally defined, what their structural components are, and what it means for them to be valid in a programmatic context.

When working with identifiers in R, it is essential to distinguish between:

  • Structural validity (does it match the formal grammar?)
  • Checksum validity (does the control digit verify?)
  • Registry validity (does the identifier actually exist?)

The functions in scholid validate identifiers at the structural level and verify checksums where defined (ORCID, ROR, ISNI, ISBN, ISSN). They do not check registry or online existence. The regexes in each section describe the canonical form that is_scholid() expects; wrapped URLs and labels should be normalized with normalize_scholid() first. Checksum rules are documented separately where they apply.

Classification order

classify_scholid() and detect_scholid_type() walk types in the order returned by scholid_types() (most specific first). The first matching type wins. This matters when patterns overlap: for example, OpenAlex is checked before PMID, and six-character UniProt accessions such as P12345 are not treated as OpenAlex keys.

PMID is a fallback type (detect_last in the registry): bare digit strings are only classified or detected as PMID when no more specific type matches. During extraction, PMID candidates use 4–9 digits and do not match digits immediately following PMC.

For the authoritative type list and order, call scholid_types() in R.

Supported types (overview)

Type Example Checksum Notes
doi 10.1000/182 No Prefix 10.; opaque suffix
arxiv 2101.00001v2 No Modern or legacy archive form
bibcode 1992ApJ...400L...1W No Fixed 19 characters
openalex W2741809807 No Not UniProt-shaped 6-char accessions
swhid swh:1:cnt:94a9ed02… No Requires swh: prefix; optional qualifiers
ark ark:/12148/btv1b8449691v No Requires ark: label; 5-digit NAAN
isni 000000012146438X Yes Compact 16 characters
orcid 0000-0002-1825-0097 Yes Hyphenated canonical form
ror 01an7q238 Yes Lowercase Crockford base32
rrid RRID:AB_262044 No RRID: prefix; authority allowlist
uniprot P12345 No Uppercase; no version suffix
refseq NM_001744.6 No Prefix allowlist; version required
sra SRR1553610 No INSDC S/E/D + R + entity letter
geo GSE2553 No GSE, GSM, GPL, or GDS
bioproject PRJNA257197 No INSDC PRJ* prefixes
assembly GCF_000001405.40 No GCA_ or GCF_; nine digits + version
isbn 9780306406157 Yes ISBN-10 or ISBN-13
issn 2434-561X Yes Hyphenated canonical display
pmcid PMC1234567 No Literal PMC prefix
pmid 12345678 No Fallback; excludes valid ISBNs

The sections below follow a consistent layout: Structure, Validation in scholid, Checksum (if applicable), and Structural regex.

DOI (Digital Object Identifier)

Governing body: International DOI Foundation
Standard: ISO 26324

Structure

A DOI has two parts:

prefix/suffix

Prefix

  • Always begins with 10.
  • Followed by a registrant code (4–9 digits)

Example:

10.1000
10.1038

Suffix

  • Assigned by the registrant
  • May contain almost any printable character
  • Has no globally fixed grammar
  • Case-sensitive in theory

Example:

10.1000/182
10.1038/s41586-020-2649-2

Validation in scholid

DOI validation is structural only. There is no checksum. Registry existence is not checked. Wrapped forms (https://doi.org/…, doi: labels) should be normalized before classification.

Structural Regex

Canonical form (as enforced by is_scholid()):

^10\.\d{4,9}/\S+$

This checks: - Prefix starts with 10. - 4–9 digits - A slash - Non-whitespace suffix

ISNI (International Standard Name Identifier)

Governing body: ISNI International Agency
Standard: ISO 27729
Documentation: ISNI

Structure

An ISNI uniquely identifies public identities of contributors to media content. The identifier is 16 characters: 15 decimal digits plus a check character.

Compact canonical form:

000000012146438X

Human-readable presentation uses an ISNI prefix and spaces in blocks of four:

ISNI 0000 0001 2146 438X

Preferred resolver URLs include:

https://isni.org/isni/000000012146438X

ORCID iDs use the same ISO/IEC 7064 MOD 11-2 checksum on 16 characters but are canonicalized in scholid with hyphens. Compact checksum-valid 16-character strings are treated as ISNI; hyphenated strings are treated as ORCID.

Validation in scholid

ISNI validation requires a checksum-valid compact 16-character string. Hyphenated ORCID-shaped input is not accepted as ISNI; normalize or classify as ORCID instead. Registry existence is not checked.

Checksum

Uses ISO/IEC 7064 MOD 11-2, identical to ORCID. The check character may be 0–9 or X.

Structural Regex

Compact canonical form:

^\d{15}[\dX]$

ORCID

Governing body: ORCID, Inc.
Standard basis: ISO 7064 (checksum algorithm)

Structure

An ORCID iD consists of 16 characters:

0000-0002-1825-0097

Components

  • 16 digits total
  • Grouped as 4-4-4-4
  • Final character is a checksum digit
  • Check digit may be X

Internally (without hyphens):

0000000218250097

Checksum

Uses ISO 7064 Mod 11-2 algorithm.
A structurally correct ORCID may still be invalid if the checksum does not match.

Validation in scholid

ORCID validation requires a checksum-valid hyphenated iD. Unhyphenated 16-character strings are not accepted as ORCID by is_scholid(); if they match the ISNI compact pattern and checksum, they classify as isni instead. Wrapped https://orcid.org/ URLs should be normalized first.

Structural Regex

Hyphenated canonical form (used by is_scholid()):

^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$

Unhyphenated internal form:

^\d{15}[\dX]$

ROR (Research Organization Registry)

Governing body: ROR Community
Documentation: ROR identifier pattern

Structure

A ROR iD is a 9-character lowercase string:

0abcdef94

Preferred external form is the full URL:

https://ror.org/01an7q238

Checksum

The last two characters are a checksum derived from the preceding seven characters using Crockford base32 encoding and ISO/IEC 7064 MOD 97-10 rules, matching ROR’s identifier generation implementation.

Validation in scholid

ROR validation requires a checksum-valid lowercase compact iD. https://ror.org/ URLs should be normalized before classification. Registry existence is not checked.

Structural Regex

Canonical compact form:

^0[a-hjkmnp-tv-z0-9]{6}[0-9]{2}$

RRID (Research Resource Identifier)

Governing body: Resource Identification Initiative (SciCrunch)
Documentation: RRID Initiative

Structure

A RRID cites a research resource such as an antibody, cell line, model organism, software tool, or plasmid. The canonical form includes the literal RRID: prefix followed by an authority-specific accession:

RRID:AB_262044
RRID:CVCL_2260
RRID:SCR_007358
RRID:IMSR_JAX:000664
RRID:MGI:3840442
RRID:Addgene_80088

Preferred resolver URLs include:

https://scicrunch.org/resolver/RRID:AB_262044

Validation in scholid

RRID validation is structural only. There is no checksum algorithm, and registry existence is not checked.

To limit false positives, scholid accepts only canonical RRID:-prefixed forms and validates the accession body against a conservative allowlist of known RRID authority prefixes (for example AB, CVCL, SCR, IMSR, MGI, Addgene). Bare local IDs such as AB_262044 without the RRID: prefix are rejected.

Structural Regex

Canonical prefix (body matched against an authority allowlist, not .+):

^RRID:(?:AB_\d+|CVCL_[0-9A-Z]+|SCR_\d+|…)$

The full allowlist is defined in the package registry; see the RRID implementation for the current authority patterns.

UniProt (UniProtKB accession)

Governing body: UniProt Consortium
Documentation: UniProt accession numbers

Structure

A UniProtKB accession uniquely identifies a protein record. Accessions are 6 or 10 uppercase alphanumeric characters following UniProt-defined patterns.

Examples:

P12345
Q9H0H5
A0A022YWF9

Preferred resolver URLs include:

https://www.uniprot.org/uniprot/P12345
https://identifiers.org/uniprot/P12345

Validation in scholid

UniProt validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession without version suffixes or entry name qualifiers. Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

Six-character accessions such as P12345 are not accepted as OpenAlex keys (OpenAlex is checked earlier in classification order, but is_openalex() explicitly rejects UniProt-shaped strings).

Structural Regex 

^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$

RefSeq (NCBI Reference Sequence accession)

Governing body: NCBI RefSeq
Documentation: RefSeq accession prefixes

Structure

A RefSeq accession uniquely identifies a curated sequence record. The format is a two-letter molecule-type prefix, an underscore, an alphanumeric accession body, a period, and a version number.

Examples:

NM_001744.6
NP_001735.1
NC_003619.1
NZ_CASIGT010000001.1

Preferred resolver URLs include:

https://www.ncbi.nlm.nih.gov/nuccore/NM_001744.6
https://www.ncbi.nlm.nih.gov/protein/NP_001735.1
https://identifiers.org/refseq/NM_001744.6

Validation in scholid

RefSeq validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession with version suffix. Known RefSeq prefixes are allowlisted. Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

GCA_ / GCF_ genome assembly accessions are a separate type (assembly) and are not matched as RefSeq.

Structural Regex 

^(?:AC|AP|NC|NG|NM|NP|NR|NT|NW|NZ|XM|XP|XR|YP|WP)_[A-Z0-9]+\.[0-9]+$

SRA (Sequence Read Archive accession)

Governing body: INSDC Sequence Read Archive (NCBI, EBI, DDBJ)
Documentation: Search in SRA Entrez

Structure

An SRA accession identifies a study, sample, experiment, or run in the INSDC archives. The format is a three-letter prefix (source database plus entity type) followed by digits.

Examples:

SRP006081
SRS123456
SRX1234567
SRR1553610
ERR1234567
DRR1234567

Preferred resolver URLs include:

https://www.ncbi.nlm.nih.gov/sra/SRR1553610
https://identifiers.org/sra/SRR1553610

Validation in scholid

SRA validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession without version suffix. The first letter denotes the source archive (S NCBI, E EBI, D DDBJ); the third letter denotes entity type (P study, S sample, X experiment, R run). Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

Structural Regex 

^[SED]R[RXSP][0-9]{5,}$

GEO (Gene Expression Omnibus accession)

Governing body: NCBI GEO
Documentation: GEO programmatic access

Structure

A GEO accession identifies a curated dataset, series, sample, or platform record. The format is a three-letter entity prefix followed by digits.

Examples:

GSE2553
GSM313800
GPL96
GDS505

Preferred resolver URLs include:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2553
https://identifiers.org/geo/GSE2553

Validation in scholid

GEO validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession. Supported entity prefixes are GSE (series), GSM (sample), GPL (platform), and GDS (dataset). Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

Structural Regex 

^(?:GSE|GSM|GPL|GDS)[0-9]{2,}$

BioProject (INSDC BioProject accession)

Governing body: INSDC BioProject (NCBI, EBI, DDBJ)
Documentation: BioProject handbook

Structure

A BioProject accession identifies a research project that groups related sequence and sample records. The format is a five-letter INSDC prefix followed by digits.

Examples:

PRJNA257197
PRJEB12345
PRJDB303

Preferred resolver URLs include:

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197
https://identifiers.org/bioproject/PRJNA257197

Validation in scholid

BioProject validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession. Known prefixes (PRJNA, PRJEB, PRJDB, PRJDA, PRJEA) are allowlisted. Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

Structural Regex 

^(?:PRJNA|PRJEB|PRJDB|PRJDA|PRJEA)[0-9]{2,}$

Genome assembly (INSDC GCA/GCF accession)

Governing body: INSDC / NCBI Assembly
Documentation: Genome assembly accessions

Structure

A genome assembly accession identifies a collection of sequences comprising an assembled genome. GenBank assemblies use the GCA_ prefix; NCBI RefSeq assembly counterparts use GCF_. The accession body is nine digits followed by a version number.

Examples:

GCF_000001405.40
GCA_000001405.29
GCA_009914755.4

Preferred resolver URLs include:

https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40
https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/
https://identifiers.org/insdc.gcf:GCF_000001405.40

Validation in scholid

Assembly validation is structural only. Registry existence is not checked.

Canonical form is the uppercase accession with version suffix. Only GCA_ and GCF_ prefixes are accepted, with exactly nine digits in the accession body. Wrapped URLs and lowercase accessions should be normalized with normalize_scholid() before classification.

RefSeq gene and protein accessions (NM_, NP_, …) are validated separately and are not accepted as assembly.

Structural Regex 

^GC[AF]_[0-9]{9}\.[0-9]+$

ISBN (International Standard Book Number)

Governing body: International ISBN Agency
Standard: ISO 2108

Two Forms

ISBN-10

  • 9 digits + checksum digit
  • Check digit may be X

Example:

0306406152
030640615X

ISBN-13

  • 13 digits
  • Usually begins with 978 or 979
  • EAN-13 checksum algorithm

Example:

9780306406157

Validation in scholid

ISBN validation requires a checksum-valid ISBN-10 or ISBN-13 in compact form (no hyphens or spaces in canonical output). Labeled or spaced input should be normalized first. Registry existence is not checked.

Structural Regex

ISBN-10 (canonical compact):

^\d{9}[\dX]$

ISBN-13:

^\d{13}$

ISSN (International Standard Serial Number)

Governing body: ISSN International Centre
Standard: ISO 3297

Structure

An ISSN has 8 characters:

1234-567X

Components

  • 7 digits
  • 1 checksum digit (0–9 or X)
  • Canonical display includes a hyphen after 4 digits

Internal numeric form:

1234567X

Validation in scholid

ISSN validation requires a checksum-valid ISSN. Canonical form uses a hyphen after the fourth digit (1234-567X). Extraction targets hyphenated tokens; normalize for compact checks. Registry existence is not checked.

Structural Regex

Hyphenated (common in extraction):

^\d{4}-\d{3}[\dX]$

Compact form:

^\d{7}[\dX]$

arXiv Identifier

Authority: arXiv (Cornell University)

Two Formats

Modern (post-2007) 

YYMM.NNNN
YYMM.NNNNN

Optional version suffix:

YYMM.NNNN(v2)

Components: - 4-digit year/month - Dot - 4–5 digit submission number - Optional version vN

Structural regex:

^\d{4}\.\d{4,5}(v\d+)?$

Legacy (pre-2007) 

archive/YYMMNNN

Example:

hep-th/9901001

Structural regex:

^[a-z\-]+/\d{7}(v\d+)?$

Validation in scholid

arXiv validation is structural only. Both modern (YYMM.NNNNN) and legacy (archive/YYMMNNN) forms are accepted. Optional version suffix vN is allowed. Wrapped arXiv: labels and https://arxiv.org/ URLs should be normalized before classification. No checksum; registry existence is not checked.

ADS Bibcode

Authority: SAO/NASA Astrophysics Data System (ADS)
Documentation: ADS bibliographic codes

Structure

An ADS bibcode is a fixed 19-character identifier for bibliographic records in astronomy and related fields. The format follows SIMBAD/NED conventions:

YYYYJJJJJVVVVM PPPPA

Where:

  • YYYY — publication year (four digits)
  • JJJJJ — journal abbreviation, left-justified, padded with .
  • VVVV — volume, right-justified, padded with .
  • M — qualifier (e.g. L for letters)
  • PPPP — page, right-justified, padded with .
  • A — first letter of the first author’s surname

Example:

1992ApJ...400L...1W

Preferred resolver URLs include:

https://ui.adsabs.harvard.edu/abs/1992ApJ...400L...1W

Validation in scholid

Bibcode validation is structural only. There is no checksum algorithm, and ADS existence is not checked.

To limit false positives, scholid requires exactly 19 characters, a letter in the journal field, and a letter as the final author-initial character. Case is preserved in canonical form.

Structural Regex 

^\d{4}[A-Za-z0-9.]{14}[A-Za-z]$

OpenAlex ID

Governing body: OurResearch (OpenAlex)
Documentation: OpenAlex key concepts

Structure

Every OpenAlex entity has a persistent ID. The official form is a URL:

https://openalex.org/W2741809807

The short key (W2741809807) is commonly used in API calls and tabular data. Keys are case-insensitive; scholid canonicalizes them to uppercase.

A key consists of:

  • a single letter prefix indicating entity type (W, A, S, I, T, K, P, F, or G)
  • a numeric tail (at least five digits)

Examples:

W2741809807
A5023888391
I97018004

Validation in scholid

OpenAlex validation is structural only. There is no checksum algorithm, and registry existence is not checked.

Deprecated concept IDs (C prefix) are not accepted. Bare keys are accepted only when they match the structural pattern; wrapped URLs should be normalized with normalize_scholid() before classification.

Six-character keys that match the UniProt accession pattern (for example P12345) are rejected by is_openalex() to avoid overlap with UniProt.

Works, authors, and institutions in OpenAlex often also have DOI, ORCID, or ROR identifiers respectively; those types are checked earlier during classification.

Structural Regex

Canonical uppercase key:

^[WASTIKPFG][0-9]{5,}$

ARK (Archival Resource Key)

Governing body: ARK Alliance
Documentation: ARK specification

Structure

An ARK is a persistent identifier for digital, physical, or abstract objects. The core identifier has the form:

ark:/NAAN/Name[Qualifier]

Where:

  • NAAN — Name Assigning Authority Number (in scholid, five digits)
  • Name — opaque name assigned by the authority
  • Qualifier — optional hierarchical (/) or variant (.) suffix

Examples:

ark:/12148/btv1b8449691v/f29
ark:/13030/654xz321

Resolver URLs often embed the ARK after the host, for example:

https://n2t.net/ark:/12148/btv1b8449691v

The labels ark: and ark:/ are equivalent; scholid canonicalizes to ark:/.

Validation in scholid

ARK validation is structural only. Resolver existence is not checked.

To limit false positives, scholid requires an explicit ark: label, a five-digit NAAN, and a non-empty name body. Bare paths without the ark: prefix are rejected.

Structural Regex

Canonical form:

^ark:/[0-9]{5}/[0-9A-Za-z][0-9A-Za-z._/=-]*$

SWHID (SoftWare Hash IDentifier)

Governing body: Software Heritage
Standard: ISO/IEC 18670
Documentation: SWHID specification

Structure

A SWHID identifies a software artifact archived by Software Heritage. The core identifier has four colon-separated fields:

swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2

Where:

  • swh is the scheme prefix
  • 1 is the scheme version
  • cnt is the object type (cnt, dir, rev, rel, or snp)
  • the final field is a 40-character lowercase hex SHA-1 intrinsic identifier

Optional qualifiers may follow, separated by semicolons:

swh:1:cnt:4d99d2d18326621ccdd70f5ea66c2e2ac236ad8b;origin=https://example.org/repo.git;path=/src/main.c;lines=9-15

Resolver URLs include:

https://archive.softwareheritage.org/swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2

Validation in scholid

SWHID validation is structural only. The embedded hash is an intrinsic content identifier, but verifying that it matches the referenced artifact requires access to the artifact itself and is not performed by scholid.

To limit false positives, scholid requires the explicit swh: prefix and rejects bare 40-character hex strings (for example Git commit hashes). Known qualifier keys (origin, visit, anchor, path, lines) are validated conservatively when present.

Structural Regex

Core form:

^swh:1:(cnt|dir|rev|rel|snp):[0-9a-f]{40}$

PMID (PubMed Identifier)

Authority: U.S. National Library of Medicine

Structure

A PMID is a decimal integer assigned by PubMed. There is no checksum.

Example:

12345678

Validation in scholid

PMID validation is intentionally permissive at the character level: canonical form is digits only (^\d+$), but is_scholid() also rejects values that are valid ISBNs to reduce cross-type false positives.

Because bare digit strings are ambiguous, PMID is registered as a fallback type (detect_last): classify_scholid() and the primary pass of detect_scholid_type() try other types first. Use PMID only when nothing more specific matches.

For extraction, candidates are 4–9 digits and must not immediately follow the literal PMC (so PMC12345 does not yield a PMID 12345).

Wrapped forms such as PMID: 12345678 should be detected via detect_scholid_type() and normalized before strict validation.

Structural Regex

Canonical form accepted by is_scholid() (after ISBN exclusion):

^\d+$

Extraction pattern (digit run length and PMC boundary):

(?<![[:alnum:]_./-]|PMC)\d{4,9}(?![[:alnum:]_]|[-/.][[:alnum:]_])

PMCID (PubMed Central Identifier)

Authority: PubMed Central

Structure 

PMC1234567

Components:

  • Literal prefix PMC
  • One or more digits

Validation in scholid

PMCID validation is structural only: canonical form is PMC followed by digits. There is no checksum. Registry existence is not checked.

PMCIDs are checked before PMID in classification order, so PMC1234567 is never classified as a bare PMID. Extraction uses a dedicated PMC prefix pattern.

Structural Regex

Canonical form:

^PMC\d+$