Wetlab Module

This vignette introduces the wetlab module in LaminDB, designed specifically for managing metadata associated with wetlab experiments. This module provides a structured and standardized way to represent various aspects of your experimental workflows, ensuring data consistency and facilitating reproducibility.

For reference, here is the documentation on the wetlab module for the LaminDB Python package.

What is wetlab?

The wetlab module extends LaminDB with specialized registries for capturing essential information about your wetlab experiments. These registries include:

• Experiments: Represent overall experiments with details like objectives, design, and timelines.
• Biosamples: Capture information about biological specimens used in experiments (e.g., tissue, cells, blood).
• Techsamples: Represent processed or derived samples created from raw biological materials.
• Treatments: Model various types of treatments applied to samples, including compound treatments, environmental perturbations, and genetic modifications.
• Treatment Targets: Specify the targets of treatments, such as genes, proteins, or pathways.
• Wells: Represent individual wells in microplates or other experimental setups.

Well

Base classes: ?Registry

Simple fields

• id (integer)
• row (character)
• uid (character)
• name (character)
• column (IntegerField)
• created_at (POSIXct)
• updated_at (POSIXct)

Relational fields

• run (Run)
• artifacts (Artifact)
• created_by (User)

Compound

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• abbr (character)
• name (character)
• synonyms (character)
• chembl_id (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)
• ontology_id (character)

Relational fields

• run (Run)
• source (bionty$Source)
• parents (wetlab$Compound)
• children (wetlab$Compound)
• artifacts (Artifact)
• compounds (wetlab$CompoundTreatment)
• created_by (User)

Biosample

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• batch (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)

Relational fields

• run (Run)
• tissues (bionty$Tissue)
• diseases (bionty$Disease)
• organism (bionty$Organism)
• artifacts (Artifact)
• cell_lines (bionty$CellLine)
• cell_types (bionty$CellType)
• created_by (User)
• techsamples (wetlab$Techsample)

Experiment

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• date (DateField)
• name (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)

Relational fields

• run (Run)
• artifacts (Artifact)
• created_by (User)

Techsample

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• batch (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)

Relational fields

• run (Run)
• artifacts (Artifact)
• biosamples (wetlab$Biosample)
• created_by (User)

TreatmentTarget

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)

Relational fields

• run (Run)
• genes (bionty$Gene)
• pathways (bionty$Pathway)
• proteins (bionty$Protein)
• artifacts (Artifact)
• created_by (User)
• genetic_targets (wetlab$GeneticTreatment)
• compound_targets (wetlab$CompoundTreatment)
• environmental_targets (wetlab$EnvironmentalTreatment)

GeneticTreatment

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• system (character)
• sequence (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• on_target_score (FloatField)
• off_target_score (FloatField)

Relational fields

• run (Run)
• targets (wetlab$TreatmentTarget)
• artifacts (Artifact)
• created_by (User)
• genetic_treatments (wetlab$CombinationTreatment)

CompoundTreatment

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• duration (DurationField)
• created_at (POSIXct)
• updated_at (POSIXct)
• concentration (FloatField)
• concentration_unit (character)

Relational fields

• run (Run)
• targets (wetlab$TreatmentTarget)
• artifacts (Artifact)
• compounds (wetlab$Compound)
• created_by (User)
• compound_treatments (wetlab$CombinationTreatment)

CombinationTreatment

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• created_at (POSIXct)
• updated_at (POSIXct)
• description (character)
• ontology_id (character)

Relational fields

• run (Run)
• genetics (wetlab$GeneticTreatment)
• artifacts (Artifact)
• compounds (wetlab$CompoundTreatment)
• created_by (User)
• environmentals (wetlab$EnvironmentalTreatment)

EnvironmentalTreatment

Base classes: ?Registry

Simple fields

• id (integer)
• uid (character)
• name (character)
• unit (character)
• value (FloatField)
• duration (DurationField)
• created_at (POSIXct)
• updated_at (POSIXct)
• ontology_id (character)

Relational fields

• run (Run)
• targets (wetlab$TreatmentTarget)
• artifacts (Artifact)
• created_by (User)
• environmental_treatments (wetlab$CombinationTreatment)