#### "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:

| --- | --- |
| "GeneticP | Models genetic perturbations such as CRISPR. |
| erturbati |
| on"(*args, |
| **kwargs) |
| --- | --- |
| "Biologic | Proteins, peptides, antibodies, enzymes, growth factors, etc. |
| "() |
| --- | --- |
| "Compound | Models a (chemical) compound such as a drug. |
| "() |
| --- | --- |
| "Compound | Models compound perturbations such as drugs. |
| Perturbat |
| ion"(*arg |
| s, |
| **kwargs) |
| --- | --- |
| "Environm | Models environmental perturbations such as heat, acid, or smoke perturbations. |
| entalPert |
| urbation" |
| (*args, |
| **kwargs) |
| --- | --- |
| "Combinat | Combination of several perturbations. |
| ionPertur |
| bation"(* |
| args, |
| **kwargs) |
| --- | --- |

* pertdb.GeneticPerturbation

  * "GeneticPerturbation"

 * "GeneticPerturbation.name"

 * "GeneticPerturbation.type"

 * "GeneticPerturbation.sequence"

 * "GeneticPerturbation.on_target_score"

 * "GeneticPerturbation.off_target_score"

 * "GeneticPerturbation.targets"

 * "GeneticPerturbation.artifacts"

* pertdb.Biologic

  * "Biologic"

 * "Biologic.name"

 * "Biologic.type"

 * "Biologic.proteins"

 * "Biologic.targets"

 * "Biologic.artifacts"

* pertdb.Compound

  * "Compound"

 * "Compound.type"

 * "Compound.chembl_id"

 * "Compound.smiles"

 * "Compound.canonical_smiles"

 * "Compound.inchikey"

 * "Compound.molweight"

 * "Compound.molformula"

 * "Compound.moa"

 * "Compound.targets"

 * "Compound.artifacts"

 * "Compound.save()"

 * "Compound.update_smiles()"

* pertdb.CompoundPerturbation

  * "CompoundPerturbation"

 * "CompoundPerturbation.name"

 * "CompoundPerturbation.concentration"

 * "CompoundPerturbation.concentration_unit"

 * "CompoundPerturbation.duration"

 * "CompoundPerturbation.compound"

 * "CompoundPerturbation.artifacts"

* pertdb.EnvironmentalPerturbation

  * "EnvironmentalPerturbation"

 * "EnvironmentalPerturbation.name"

 * "EnvironmentalPerturbation.ontology_id"

 * "EnvironmentalPerturbation.value"

 * "EnvironmentalPerturbation.unit"

 * "EnvironmentalPerturbation.duration"

 * "EnvironmentalPerturbation.targets"

 * "EnvironmentalPerturbation.artifacts"

* pertdb.CombinationPerturbation

  * "CombinationPerturbation"

 * "CombinationPerturbation.members"

 * "CombinationPerturbation.name"

 * "CombinationPerturbation.genetic_perturbations"

 * "CombinationPerturbation.compound_perturbations"

 * "CombinationPerturbation.environmental_perturbations"

 * "CombinationPerturbation.artifacts"

Auxiliary registries:

| --- | --- |
| "Perturba | Models perturbation targets such as "Gene", "Pathway", and "Protein". |
| tionTarge |
| t"(*args, |
| **kwargs) |
| --- | --- |

* pertdb.PerturbationTarget

  * "PerturbationTarget"

 * "PerturbationTarget.name"

 * "PerturbationTarget.genes"

 * "PerturbationTarget.pathways"

 * "PerturbationTarget.proteins"

 * "PerturbationTarget.artifacts"

Helper types:

| --- | --- |
| "GeneticP | alias of "Literal"['control', 'CRISPR-Cas9', 'CRISPR-Cas13', 'CRISPRi', 'CRISPRa', |
| erturbati | 'overexpression', 'mutant overexpression', 'shRNA', 'siRNA', 'transgene', 'transient- |
| onSystem" | transfection'] |
| --- | --- |
| "Biologic | alias of "Literal"['control', 'protein', 'peptide', 'antibody', 'enzyme', 'growth-factor', |
| Type" | 'cytokine', 'hormone', 'vaccine', 'oligonucleotide', 'co-culture', 'ligand'] |
| --- | --- |

* pertdb.GeneticPerturbationSystem

  * "GeneticPerturbationSystem"

* pertdb.BiologicType

  * "BiologicType"