LPSN¶

The LPSN API provides nomenclature and taxonomy records for prokaryotic names.

LPSN requires a free API account. biodbs uses the LPSN web API directly with requests; it does not depend on the official lpsn Python package or python-keycloak.

Credentials¶

Use either a bearer token:

export BIODBS_LPSN_TOKEN="..."

Or username and password:

export BIODBS_LPSN_USERNAME="you@example.org"
export BIODBS_LPSN_PASSWORD="..."

Fetch Records¶

from biodbs.fetch.LPSN import LPSN_Fetcher

fetcher = LPSN_Fetcher()
data = fetcher.fetch([520424, 4948, 17724])

for entry in data:
    print(entry.id, entry.full_name, entry.category)

The LPSN /fetch endpoint accepts up to 100 IDs at a time. biodbs chunks longer ID lists automatically.

Advanced Search¶

hits = fetcher.advanced_search(category="species", riskgroup="1")
print(hits.ids())

Pythonic keyword names are converted to API parameter names:

hits = fetcher.advanced_search(
    taxon_name="Bacillus",
    validly_published="yes",
    correct_name="yes",
)

Flexible Search¶

hits = fetcher.flexible_search({"category": "species"})

To get full records after search:

records = fetcher.search_and_fetch(category="species", riskgroup="1")

Convenience Functions¶

from biodbs.fetch import lpsn_fetch, lpsn_advanced_search

records = lpsn_fetch([520424, 4948])
hits = lpsn_advanced_search(category="species")

Notes¶

LPSN data is subject to LPSN copyright and usage terms. Some taxonomy fields reflect current LPSN opinions and may change over time.