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|---|
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End of preview. Expand in Data Studio
PDB DataCite records
This dataset has one DataCite Metadata Schema 4.7 record for each entry in the PDB archive, current and obsolete. The identifier of each record is the PDB entry DOI, 10.2210/pdbxxxx/pdb.
| Item | Value |
|---|---|
| Records | 267,244 |
| Incomplete records | 16, in incomplete/. These obsolete entries have no title. |
| Current entries | 262,513 |
| Obsolete entries | 4,747 |
| Snapshot | 2026-10-30 (the most recent last-modified time in the wwPDB holdings files) |
| Schema | DataCite Metadata Schema 4.7. All XML records are valid for the 4.7 XSD. |
Files
| Path | Content |
|---|---|
json/part-NNNNN.jsonl.gz |
DataCite REST API payloads, {"data": {"type": "dois", "attributes": {...}}}, one record on each line. |
xml/part-NNNNN.jsonl.gz |
DataCite XML records, one {"doi", "xml"} object on each line. |
incomplete/json/, incomplete/xml/ |
The records of the entries that have no value for a mandatory property, in the same formats. These records are not ready for DataCite. |
incomplete/reasons.jsonl |
One line for each incomplete record, with pdb_id, doi and missing. missing gives the mandatory properties that have no value. |
MANIFEST.json |
The record counts, the list of files, and the SHA-256 of the files that made the records. |
The JSON files and the XML files have the same records in the same order. Each file has 10,000 records. The last file has 7,244 records.
Use
from datasets import load_dataset
records = load_dataset("adambuttrick/pdb-datacite", "json", split="train")
xml = load_dataset("adambuttrick/pdb-datacite", "xml", split="train")
Source
The records use data from the wwPDB mmCIF entry files at files.wwpdb.org only. Three lookups add identifiers to PDB values:
| Lookup | Input | Output |
|---|---|---|
| Funder table | _pdbx_audit_support.funding_organization |
ROR ID (ROR v2.15, reviewed table) |
| Resolver patterns | PDB, EMDB, BMRB, SASBDB or UniProt accession, EC number | DOI or URL |
| NCBI Taxonomy URI | NCBI taxonomy ID | Taxonomy browser URI |
The code that makes the records is at adambuttrick/pdb-to-datacite. CROSSWALK.md in that repository gives the full mapping.
License
PDB data is available under CC0 1.0. The ROR data in the funder table is also CC0 1.0. These records are available under CC0 1.0.
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