bacdive 0.3

BacDive-API - Programmatic Access to the BacDive Database

BacDive API

Using the BacDive API requires registration. Registration is free but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See About BacDive for details.

Please register here.

The Python package can be initialized using your login credentials:

import bacdive

client = bacdive.BacdiveClient('[e-mail]', 'password')

# the search method fetches all BacDive-IDs matching your query
# and returns the number of IDs found
count = client.search(taxonomy='Bacillus subtilis subtilis')
print(count, 'strains found.')

# the retrieve method lets you iterate over all strains
# and returns the full entry as dict
# Entries can be further filtered using a list of keys (e.g. ['keywords'])
for strain in client.retrieve():
    print(strain)

Example queries:

# Search by BacDive-IDs (either semicolon separated or as list):
query = {"id": 24493}
query = {"id": "24493;12;132485"}
query = {"id": [24493, 12, 132485]}

# Search by culture collection number
query = {"culturecolno": "DSM 26640"}

# Search by taxonomy (either as full name or as list):
# With genus name, species epithet (optional), and subspecies (optional).
query = {"taxonomy": "Bacillus subtilis subsp. subtilis"}
query = {"taxonomy": ("Escherichia", "coli")}

# Search by sequence accession numbers:
query = {"16s": "AF000162"} # 16S sequence
query = {"genome": "GCA_006094295"} # genome sequence

# run query
client.search(**query)

Filtering

Results from the retrieve Method of both clients can be further filtered. The result contains a list of matched keyword dicts:

filter=['keywords', 'culture collection no.']
result = client.retrieve(filter)
print({k:v for x in result for k,v in x.items()})

The printed result will look like this:

{'1161': [{'keywords': ['human pathogen', 'Bacteria']},
          {'culture collection no.': 'DSM 4393, pC194, SB202'}],
 '1162': [{'keywords': ['human pathogen', 'Bacteria']},
          {'culture collection no.': 'DSM 4514, ATCC 37015, BD170, NCIB 11624, '
                                     'pUB110'}],
 '1163': [{'keywords': ['human pathogen', 'Bacteria']},
          {'culture collection no.': 'DSM 4554, ATCC 37128, BGSC 1E18, pE194'}],
 '1164': [{'keywords': 'Bacteria'},
          {'culture collection no.': 'DSM 4750, 1E7, BGSC 1E7, pE194-cop6'}],
...

New in v0.3

We added AI-based predictions to the BacDive database. Predicted traits are excluded by default. To include them, you have to call the method includePredictions():

client.includePredictions()

You can exclude predictions again by calling:

client.excludePredictions()