pertdb

Registries for perturbations and their targets [source].

Install and mount pertdb in a new instance:

pip install pertdb
lamin init --storage ./test-pertdb --modules bionty,pertdb

Import the package and create an object:

import pertdb
biologic = pertdb.Biologic(name="IFNG").save()

Main registries:

GeneticPerturbation(*args, **kwargs)	Models genetic perturbations such as CRISPR.
Biologic()	Proteins, peptides, antibodies, enzymes, growth factors, etc.
Compound()	Models a (chemical) compound such as a drug.
CompoundPerturbation(*args, **kwargs)	Models compound perturbations such as drugs.
EnvironmentalPerturbation(*args, **kwargs)	Models environmental perturbations such as heat, acid, or smoke perturbations.
CombinationPerturbation(*args, **kwargs)	Combination of several perturbations.

Auxiliary registries:

PerturbationTarget(*args, **kwargs)

Models perturbation targets such as Gene, Pathway, and Protein.

Helper types:

GeneticPerturbationSystem	alias of Literal['control', 'CRISPR-Cas9', 'CRISPR-Cas13', 'CRISPRi', 'CRISPRa', 'overexpression', 'mutant overexpression', 'shRNA', 'siRNA', 'transgene', 'transient-transfection']
BiologicType	alias of Literal['control', 'protein', 'peptide', 'antibody', 'enzyme', 'growth-factor', 'cytokine', 'hormone', 'vaccine', 'oligonucleotide', 'co-culture', 'ligand']