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Scriptorium Scriptorium

CSL and bibliographic standards

Last updated: 2026-10-20

Synthesis

Section titled “Synthesis”

Scriptorium does not generate bibliographies; it operates on bibliographies the author has already curated. This design choice rests on hallucination evidence (see hallucination-in-llm-citations) and on the practical observation that the scholarly identifier ecosystem already does this work well. The relevant standards split into three layers: a style layer (how citations are rendered) — Citation Style Language (CSL); a storage layer (how references are stored) — BibTeX/BibLaTeX, CSL-JSON, RIS; and an identifier layer (how works, authors, organizations, and funders are pinpointed) — DOI / CrossRef / DataCite, ORCID, ROR, the Open Funder Registry (now transitioning into ROR), and CURIE prefixes coordinated by the Bioregistry.

Each layer is independently mature. CSL governs nearly every modern reference manager (Zotero, Mendeley, Paperpile, and most academic word-processor integrations). Persistent identifier coverage is now high enough that “the bibliography exists in machine-readable form with stable identifiers” is a reasonable assumption for any contemporary manuscript. Manubot’s reliance on Bioregistry CURIE prefixes — the Bioregistry held 1,504 records when it was described in 2022, and switching to it added 365 prefixes to the ~700 manubot had supported through Identifiers.org — illustrates the practical reach of this infrastructure beyond pure DOI/ORCID lookups.

Scriptorium’s job is to read whatever bibliography the manuscript ships with, treat it as authoritative, and never silently introduce references that are not in it. That posture only works because the existing standards are good enough to make “the author’s bibliography” a stable artifact to anchor against.

Evidence

Section titled “Evidence”

Citation Style Language (CSL). Created by Bruce D’Arcus and shaped by early contributions from Simon Kornblith of Zotero; Zotero was the first program to adopt CSL, and CSL is an XML-based specification. Mendeley followed and (with Columbia University Libraries) obtained an Alfred P. Sloan Foundation grant to build the CSL style editor. Mendeley and Elsevier have donated to the CSL project since 2014.1

The current specification (CSL 1.0.2) defines:

  • A style language (XML) describing how to render citations and bibliographies for a given journal or discipline.
  • A data interchange format (CSL-JSON) for individual references.
  • A locale mechanism for language- and region-specific conventions.

The CSL Style Repository hosts thousands of journal- and discipline-specific styles, maintained by community contributions. Zotero, Mendeley, Paperpile, Pandoc (via citeproc), and several journal submission systems consume CSL natively. This makes CSL the de facto interoperability standard for “what should this citation look like in this venue.”

BibTeX / BibLaTeX. The older LaTeX-native ecosystem remains dominant in physics, mathematics, computer science, and statistics. BibTeX’s @article{...} syntax is well-understood and stable. BibLaTeX is the modern successor with richer entry types and Unicode support. Most reference managers can export to BibTeX, and most manuscript workflows in LaTeX-heavy fields use BibTeX as the canonical bibliography format. Scriptorium should accept BibTeX/ BibLaTeX as a first-class input.

DOIs and CrossRef. The Digital Object Identifier system, operated for scholarly content primarily by CrossRef and DataCite, is the most widely deployed persistent identifier for academic works. CrossRef’s 2025 public data file contained metadata for over 165 million research outputs (https://www.crossref.org/blog/2025-public-data-file-now-available/), and its 2026 public data file, released 17 March 2026, contains nearly 180 million records, 12.7 million of them new since the previous year (https://www.crossref.org/blog/2026-public-data-file-now-available/). CrossRef exposes structured metadata via a public REST API. CrossRef’s metadata records increasingly carry references to other works, ORCID author identifiers, and ROR institutional identifiers — turning the citation graph itself into queryable infrastructure. The 2026 data file reports ORCID identifiers for authors up 20% and ROR identifiers for organisations up 250% year on year.2

DataCite. Mirrors CrossRef for datasets, software, and other research outputs. Particularly important in data-citation contexts; DataCite’s metadata schema is closely aligned with CrossRef’s to support interoperability.

ORCID. Persistent identifier for individual researchers. ORCID records can be tied to publications, peer reviews, grants, and affiliations. The ORCID/CrossRef auto-update system propagates publication records to ORCID profiles automatically when an article is registered with CrossRef. This makes ORCID a reasonable disambiguator for “who is the author” in contexts where lastname-only attribution is ambiguous.3

ROR. The Research Organization Registry, launched in 2019, is operated by California Digital Library, CrossRef, and DataCite. ROR provides CC0-licensed open identifiers for research organizations, replacing the historically fragmented landscape of institutional identifiers. ROR is now the de facto standard for affiliation identification in CrossRef metadata.4

Open Funder Registry (FundRef) → ROR. CrossRef’s funder identifier service is being folded into ROR. CrossRef announced the plan to transition the Open Funder Registry into ROR in 2023; since 5 March 2025 members can deposit ROR IDs anywhere they previously deposited Funder IDs, while Funder IDs remain supported “until the community is ready to transition.”5 On 15 September 2026 CrossRef began matching funder names deposited without an identifier to ROR IDs (reported 99% precision); existing Open Funder Registry IDs are not replaced and previously deposited records are unchanged.6 For MANUSCRIPT_STATE.yaml, this means a funder may legitimately be identified by either a Funder ID (which CrossRef represents as a DOI) or a ROR ID; consistency within one manuscript matters more than which scheme is used.

Bioregistry and CURIE prefixes. The Bioregistry is a meta-registry that catalogs identifier prefixes across biology, biomedicine, and adjacent fields. CURIEs (Compact URIs) take the form prefix:identifier (e.g., doi:10.1136/bmj.b2680, clinicaltrials:NCT04280705, pmid:19622839). When it was described in Scientific Data (version 0.5.132, October 2022), the Bioregistry integrated 23 external registries and contained 1,504 records; it has grown since, and the live count is published at https://bioregistry.io. Manubot — the open scholarly-publishing tool — initially used Identifiers.org for ~700 prefixes, then migrated to Bioregistry, which added support for 365 more, for both broader coverage and more rigorous validation (open contribution model; better regex patterns; resolution of namespace inconsistencies).78

This matters for scriptorium because it means a manuscript’s “citations” need not all be DOI-based. A reference to clinicaltrials:NCT04280705 or arXiv:2401.01234 is a fully machine-resolvable citation under existing standards, and scriptorium should treat such references as first-class.

How this informs scriptorium

Section titled “How this informs scriptorium”

Bibliography is input, not output. Scriptorium reads BibTeX, CSL-JSON, or in-manuscript citation keys (Pandoc-style [@doi:10.1136/bmj.b2680] or \cite{...}) and treats the resulting reference set as the canonical “what citations exist in this manuscript.” Any skill operating on the manuscript can ask: is this in-text citation present in the bibliography? That is a syntactic check, not a generative act.

Citation audit operates on the citation set, not on free-text references. Because CSL/BibTeX entries carry stable identifiers, citation-audit does not have to parse rendered prose to figure out which paper a citation refers to. It can ask the structured question: “in-text citation [Smith 2019] resolves to bibliography entry smith2019, which has DOI 10.1234/abcd. Does the manuscript’s claim accompanying this citation match what we know about that DOI?”

No skill writes new bibliography entries. Even when reviewer-simulation recommends “consider adding a recent meta-analysis,” the recommendation does not propose specific bibtex keys, DOIs, or author strings. Adding bibliography entries is the author’s act, using their reference manager and the identifier-resolution services above.

MANUSCRIPT_STATE bibliography pointer. The state schema includes a bibliography field pointing to the canonical bibliography file (e.g., bibliography: refs.bib). Skills resolve in-text citations against this file. If the field is absent, citation-aware skills can still operate on in-text citation keys but should emit a warning that the bibliography link is missing.

Manubot pattern as design influence. Manubot’s three-stage pipeline (Pandoc parses citation keys → manubot-cite filter retrieves metadata via CrossRef / Bioregistry → citeproc renders styled output) is a clean separation of concerns that scriptorium should mirror in spirit: identifier resolution, metadata retrieval, and rendering are three different jobs, and conflating them is where errors enter.

Implementation priority for scriptorium

Section titled “Implementation priority for scriptorium”

Verdict: No (as a standalone skill).

Why this is useful context anyway: these standards define the input contract every citation-aware skill relies on — the bibliography pointer in MANUSCRIPT_STATE.yaml, citation-audit’s assumption of an identifier-resolved bibliography, and the project rule that no skill writes bibliography entries. A skill that validated CSL, formatted references, or resolved identifiers would duplicate mature infrastructure (reference managers, CrossRef, Bioregistry, manubot/quartobot); see the roadmap non-goal “No replacement for reference managers”. The 2026-10 refresh (CrossRef corpus size, the Funder Registry → ROR transition, the Bioregistry count) did not change this verdict.

Open questions / weak evidence

Section titled “Open questions / weak evidence”
  • Coverage of non-biomedical fields by Bioregistry is uneven; scriptorium should not assume every domain has a comparable identifier catalog.
  • Some venues still demand plain-text references with no identifiers (older journals, certain humanities outlets). Scriptorium degrades gracefully to “citation key only” in those cases but loses the ability to do identifier-level verification.
  • The interaction between CSL styles and journal-specific pre-submission validation is messier than the standards suggest; journals’ production pipelines often diverge from their published style guides.

References

Section titled “References”

Footnotes

Section titled “Footnotes”

  1. Citation Style Language. About. https://citationstyles.org/about/ ↩

  2. CrossRef. Public REST API and infrastructure documentation. https://crossref.org/ . 2025 public data file: https://www.crossref.org/blog/2025-public-data-file-now-available/ . Rittman M, del Ojo Elías C, Montilla L. 2026 public data file now available. CrossRef blog, 17 March 2026. https://www.crossref.org/blog/2026-public-data-file-now-available/ ; dataset doi:10.13003/nggf-vt1j. ↩

  3. ORCID. Public-facing documentation. https://orcid.org/ . CrossRef–ORCID auto-update: https://www.crossref.org/community/orcid/ ↩

  4. Research Organization Registry (ROR). About page. https://ror.org/about/ ↩

  5. Feeney P. Come ROR with us: Using ROR IDs in place of Funder IDs. CrossRef blog, 5 March 2025. https://www.crossref.org/blog/come-ror-with-us-using-ror-ids-in-place-of-funder-ids/ ↩

  6. Rittman M, Gaudioso Pedraza R, del Ojo Elias C, Portenoy J, Tkaczyk D. Improving how funding connects to research outputs. CrossRef blog, 15 September 2026. https://www.crossref.org/blog/improving-how-funding-connects-to-research-outputs/ ↩

  7. Hoyt CT, Balk M, Callahan TJ, et al. Unifying the identification of biomedical entities with the Bioregistry. Scientific Data. 2022;9:714. doi:10.1038/s41597-022-01807-3. PMID: 36402838. ↩

  8. Manubot. Usage documentation, citation prefix support. https://github.com/manubot/rootstock/blob/main/USAGE.md ↩