1. Basic Usage

We can retrieve any database entity, either by BiGG ID (str) or internal ID (int). For example, information on the E. coli model iML1515 can be obtained using the following command:

from biggr import objects as bo

model = bo.get("model", "iML1515")
print(model.organism)

Escherichia coli str. K-12 substr. MG1655

From this object, we can directly observe which properties and relations can be accessed.

print("\n".join(x for x in dir(model) if not x.startswith("_")))

base_filename
bigg_id
collection
collection_id
date_modified
escher_maps
from_dict
genome
genome_id
id
memote_results
model_compartmentalized_components
model_count
model_genes
model_reactions
organism
publication_models
published_filename
taxon
taxon_id

If we would like to obtain taxonomic information associated with the model, we could use the taxon_id property to obtain a new object:

taxon = bo.get("taxon", model.taxon_id)
print(taxon.name)

Escherichia coli str. K-12 substr. MG1655

However, the taxon relation can also be directly accessed from the model object. Accessing the taxon attribute causes a new API call to be made to obtain the associated entity. This manner of lazy-loading enables easy navigation of the database, without users having to bother with the API too much.

print(model.taxon.name)

Escherichia coli str. K-12 substr. MG1655

This enables more complex relations to be navigated seamlessly.

node = model.taxon
while node.rank.name.lower() != "family":
    if node.id == node.parent.id:
        node = None
        break
    node = node.parent
print(f"{node.name} ({node.rank.name})")

Enterobacteriaceae (family)