Database

PlasmidNet uses a local SQLite database built from PLSDB and NCBI data.

Data Sources

Source	Plasmids	Description
PLSDB 2025	72,556	Curated plasmid database (version 2024_05_31_v2)
NCBI Nucleotide	109,806	Additional complete plasmids not in PLSDB
Total	182,362

Tables

Table	Rows	Description
`nuccore`	72,556	Plasmid metadata (accession, length, GC, topology, dates)
`taxonomy`	7,439	Host taxonomy (kingdom to strain)
`typing`	72,556	MOB typing (Inc groups, mobility, relaxase, MPF, pMLST)
`amr`	600,896	AMR gene annotations from PLSDB + NCBI (gene, drug class, positions)
`plasmidfinder`	60,619	PlasmidFinder typing results
`typing_markers`	333,648	MOB suite detailed markers
`pgap_features`	613,902	PGAP annotations (TA, phage, transposase)
`biosample_location`	23,522	Geographic locations with host category
`ncbi_extra`	109,806	NCBI plasmids not in PLSDB

Building the Database

# 1. Download PLSDB CSVs from Figshare
mkdir -p data/raw
# Files are downloaded automatically by build_db.py

# 2. Build SQLite database
python build_db.py

# 3. (Optional) Harvest additional plasmids from NCBI
python ncbi_harvest.py

# 4. Rebuild with NCBI data
python build_db.py

Figshare Files Used

Downloaded from doi:10.6084/m9.figshare.27252609.v2:

File	Size	Content
nuccore.csv	16 MB	Plasmid metadata
typing.csv	22 MB	MOB typing results
amr.tsv	36 MB	AMR annotations
taxonomy.csv	2.3 MB	Host taxonomy
biosample.csv	11 MB	Sample metadata + locations
plasmidfinder.csv	15 MB	PlasmidFinder results
typing_markers.csv	75 MB	MOB detail markers
proteins.csv	637 MB	PGAP annotations (filtered to 60 MB for TA/phage/transposase)

Updating

To update when PLSDB releases a new version:

Download new CSVs from Figshare
Place in data/raw/
Run python build_db.py
Run python ncbi_harvest.py to catch new NCBI plasmids
Delete data/correlations_cache.json to rebuild correlations

Database Size

SQLite file: ~200 MB
Startup memory: ~107 MB (correlations cached to JSON)
Heroku compatible: Built during deploy via bin/post_compile