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haydn-jones/PubMed-Metadata

PubMed Metadata V2 Snapshot of PubMed citation metadata, augmented with PMC records that were not safely represented in PubMed's current PMID-to-PMCID mapping. The PubMed portion was built from the NLM PubMed 2026 annual baseline and daily update XML files through pubmed26n1592.xml.gz. Updates are applied in numeric order, revised records replace earlier versions, and citations whose latest event is a deletion are omitted. The dataset was built on 2026-08-16. The single train… See the full description on the dataset page: https://huggingface.co/datasets/haydn-jones/PubMed-Metadata.

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Dataset Card

PubMed Metadata V2

Snapshot of PubMed citation metadata, augmented with PMC records that were not safely represented in PubMed's current PMID-to-PMCID mapping.

The PubMed portion was built from the NLM PubMed 2026 annual baseline and daily update XML files through pubmed26n1592.xml.gz. Updates are applied in numeric order, revised records replace earlier versions, and citations whose latest event is a deletion are omitted. The dataset was built on 2026-08-16.

The single train split contains 41,860,640 records:

—40,990,549 records have a unique, non-null PMID;
—870,091 PMC-only records have a null PMID and are keyed by PMCID;
—879,135 validated PMC records were added to the current PubMed snapshot; and
—2,553 existing PMID rows were safely updated with their missing PMCID and available metadata.

Open-access flag

is_oa is a non-null operational full-text accessibility flag:

text

pmcid is present
OR
(issn, eissn, or issn_linking matches a current DOAJ journal
 AND publication year >= that journal's all-content open-license start year)

—12,906,383 rows are marked is_oa=true.
—12,338,603 rows have a PMCID; every one is marked is_oa=true.
—567,780 rows are marked open through the date-aware DOAJ rule without a PMCID.

This flag indicates practical full-text accessibility. It does not assert that an article has a permissive reuse license: PMC content has article-specific rights, and users must check the applicable license before reuse.

Columns

Column	Type	Description
`pmid`	`uint32`	PubMed identifier; unique when present. Null for PMC-only records without a safely resolved PMID.
`pmcid`	string	PubMed Central identifier, when available.
`doi`	string	Digital Object Identifier, normalized to its identifier value.
`title`	string	Article or book-document title as plain text.
`abstract`	string	Abstract sections joined with newlines; section labels are retained.
`journal`	string	Full journal title.
`year`	`uint16`	Best available publication year.
`publication_month`	`uint8`	Explicit publication month, when available.
`publication_day`	`uint8`	Explicit publication day, when available.
`issn`	string	Print ISSN.
`eissn`	string	Electronic ISSN.
`is_oa`	boolean	PMCID-or-date-aware-DOAJ accessibility flag described above.
`issn_linking`	string	NLM linking ISSN used to associate journal formats and title histories.
`journal_abbrev`	string	NLM/ISO journal abbreviation.
`nlm_unique_id`	string	NLM Catalog identifier for the journal.
`country`	string	Journal publication country recorded by NLM.
`volume`	string	Journal volume; kept as text because values are not always numeric.
`issue`	string	Journal issue; kept as text because values are not always numeric.
`pages`	string	Pagination or electronic location text.
`date_completed`	date	Date NLM completed processing the citation.
`date_revised`	date	Most recent explicit revision date in the record.
`citation_status`	string	PubMed/Medline citation status.
`publication_status`	string	PubMed publication status such as `ppublish` or `epublish`.
`pub_model`	string	Print/electronic publication model.
`vernacular_title`	string	Title in the original language, when supplied separately.
`authors`	list of structs	Ordered authors, including names, ORCID, affiliations, validity, and equal-contribution metadata.
`publication_types`	list of strings	NLM publication-type labels.
`languages`	list of strings	PubMed language codes.
`mesh_terms`	list of strings	MeSH descriptor headings assigned to the citation.
`mesh_major_topics`	list of strings	MeSH descriptors or descriptor/qualifier combinations marked as major topics.
`keywords`	list of strings	Author, publisher, or indexing keywords.
`article_ids`	list of strings	Identifier values carried in the source record.

Each element of authors has this structure:

text

display_name: string
last_name: string
fore_name: string
initials: string
suffix: string
collective_name: string
orcid: string
affiliations: list[string]
valid: bool
equal_contrib: bool

Sources and terms

—Citation metadata: NLM PubMed baseline and daily update files.
—PMC metadata: PubMed Central Open Access bulk data.
—OA journal metadata: DOAJ Journal CSV.
—DOAJ metadata terms: DOAJ terms and conditions.
—Additional exact-identifier gap filling used NCBI ESummary, Europe PMC, OpenAlex, and Crossref metadata.