# Preclinical Database — v1.0

Released 2026-07-23. 134,565 publications, 186,628 extracted rows.

## Release notes

Initial public release of the Preclinical Database, comprising 134,565 PubMed Central full-text articles and covering 2,602 diseases, 11,753 drug compounds, and 100 animal species. AI-powered curation combined high-confidence screening for in vivo preclinical studies with LLM-based extraction and ontology-guided standardization of disease, drug, and animal entities using MeSH, Disease Ontology, PubChem, DrugBank, and UMLS.

## Files in this bundle

- `pcdb_complete.tsv` — one row per extracted (publication × entity-group) tuple. This is the primary source; every downstream artifact derives from it.
- `pcdb.tsv` — condensed variant with a subset of columns.
- `disease_entities.tsv` — disease catalog (2,602 rows). PCDB IDs, MeSH IDs, Disease Ontology IDs, synonyms, MeSH tree positions.
- `drug_entities.tsv` — drug catalog (11,753 rows). PCDB IDs, DrugBank IDs, MeSH IDs, UMLS IDs, synonyms.
- `animal_entities.tsv` — animal-species catalog (100 rows). PCDB IDs, MeSH IDs, synonyms.
- `unmapped_entity_extractions.tsv` — extractions the LLM produced that couldn't be resolved to a MeSH/DO/DrugBank/PubChem/UMLS entry. Useful for downstream mapping work.
- `preclinical_database.xlsx` — spreadsheet view for non-programmatic browsing.
- `CHANGELOG.md` — release notes
- `README.md` — this file

## Loading examples (pcdb_complete.tsv)

### Python (pandas)

```python
import pandas as pd
df = pd.read_csv("pcdb_complete.tsv", sep="\t")
```

### Python (polars)

```python
import polars as pl
df = pl.read_csv("pcdb_complete.tsv", separator="\t")
```

### DuckDB

```sql
SELECT * FROM read_csv_auto('pcdb_complete.tsv', delim='\t', header=true);
```

### R

```r
df <- read.delim("pcdb_complete.tsv", sep="\t", stringsAsFactors=FALSE)
```

## Citation

If this dataset supports your work, please cite the Preclinical Database.
A formal citation will appear here once our paper is published.

## License

Provided for academic research use. See https://preclinicaldb.org for terms.
