---
pretty_name: PubMed Metadata V2
license: other
language:
- multilingual
task_categories:
- text-retrieval
size_categories:
- 10M<n<100M
tags:
- pubmed
- pubmed-central
- biomedical
- scholarly-metadata
- open-access
dataset_info:
  features:
  - name: pmid
    dtype: uint32
  - name: pmcid
    dtype: large_string
  - name: doi
    dtype: large_string
  - name: title
    dtype: large_string
  - name: abstract
    dtype: large_string
  - name: journal
    dtype: large_string
  - name: year
    dtype: uint16
  - name: publication_month
    dtype: uint8
  - name: publication_day
    dtype: uint8
  - name: issn
    dtype: large_string
  - name: eissn
    dtype: large_string
  - name: is_oa
    dtype: bool
  - name: issn_linking
    dtype: large_string
  - name: journal_abbrev
    dtype: large_string
  - name: nlm_unique_id
    dtype: large_string
  - name: country
    dtype: large_string
  - name: volume
    dtype: large_string
  - name: issue
    dtype: large_string
  - name: pages
    dtype: large_string
  - name: date_completed
    dtype: date32
  - name: date_revised
    dtype: date32
  - name: citation_status
    dtype: string
  - name: publication_status
    dtype: string
  - name: pub_model
    dtype: string
  - name: vernacular_title
    dtype: large_string
  - name: authors
    large_list:
    - name: display_name
      dtype: large_string
    - name: last_name
      dtype: large_string
    - name: fore_name
      dtype: large_string
    - name: initials
      dtype: large_string
    - name: suffix
      dtype: large_string
    - name: collective_name
      dtype: large_string
    - name: orcid
      dtype: large_string
    - name: affiliations
      large_list: large_string
    - name: valid
      dtype: bool
    - name: equal_contrib
      dtype: bool
  - name: publication_types
    large_list: large_string
  - name: languages
    large_list: large_string
  - name: mesh_terms
    large_list: large_string
  - name: mesh_major_topics
    large_list: large_string
  - name: keywords
    large_list: large_string
  - name: article_ids
    large_list: large_string
  splits:
  - name: train
    num_examples: 41860640
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
---

# 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](https://pubmed.ncbi.nlm.nih.gov/download/).
- PMC metadata: [PubMed Central Open Access bulk data](https://pmc.ncbi.nlm.nih.gov/tools/ftp/).
- OA journal metadata: [DOAJ Journal CSV](https://doaj.org/docs/journal-csv).
- DOAJ metadata terms: [DOAJ terms and conditions](https://doaj.org/terms/).
- Additional exact-identifier gap filling used NCBI ESummary, Europe PMC, OpenAlex,
  and Crossref metadata.