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.
#> ! schema module 'bionty' is not installed → no access to its labels & registries (resolve via `pip install bionty`)
#> ! schema module 'wetlab' is not installed → no access to its labels & registries (resolve via `pip install wetlab`)
#> ! schema module 'ourprojects' is not installed → no access to its labels & registries (resolve via `pip install ourprojects`)
#> → connected lamindb: laminlabs/lamindataWell
Base classes: ?Registry
Donor
Base classes: ?Registry
Simple fields
-
id(integer) -
age(IntegerField) -
bmi(FloatField) -
uid(character) -
name(character) -
batch(character) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character)
Relational fields
-
run(Run) -
sex(bionty$Phenotype) -
diseases(bionty$Disease) -
organism(bionty$Organism) -
artifacts(Artifact) -
ethnicity(bionty$Ethnicity) -
created_by(User)
Biologic
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
abbr(character) -
name(character) -
type(character) -
synonyms(character) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character)
Relational fields
-
run(Run) -
targets(wetlab$PerturbationTarget) -
proteins(bionty$Protein) -
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$Compound) -
artifacts(Artifact) -
created_by(User) -
compoundperturbation(wetlab$CompoundPerturbation)
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
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$Biosample) -
created_by(User)
PerturbationTarget
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
name(character) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character)
Relational fields
-
run(Run) -
genes(bionty$Gene) -
pathways(bionty$Pathway) -
proteins(bionty$Protein) -
artifacts(Artifact) -
created_by(User) -
genetic_targets(wetlab$GeneticPerturbation) -
biologic_targets(wetlab$Biologic) -
compound_targets(wetlab$CompoundPerturbation) -
environmental_targets(wetlab$EnvironmentalPerturbation)
GeneticPerturbation
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
name(character) -
system(character) -
sequence(character) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character) -
on_target_score(FloatField) -
off_target_score(FloatField)
Relational fields
-
run(Run) -
targets(wetlab$PerturbationTarget) -
artifacts(Artifact) -
created_by(User) -
combination_perturbations(wetlab$CombinationPerturbation)
CompoundPerturbation
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
name(character) -
duration(DurationField) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character) -
concentration(FloatField) -
concentration_unit(character)
Relational fields
-
run(Run) -
targets(wetlab$PerturbationTarget) -
compound(wetlab$Compound) -
artifacts(Artifact) -
created_by(User) -
combination_perturbations(wetlab$CombinationPerturbation)
CombinationPerturbation
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
name(character) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character) -
ontology_id(character)
Relational fields
-
run(Run) -
artifacts(Artifact) -
created_by(User) -
genetic_perturbations(wetlab$GeneticPerturbation) -
compound_perturbations(wetlab$CompoundPerturbation) -
environmental_perturbations(wetlab$EnvironmentalPerturbation)
EnvironmentalPerturbation
Base classes: ?Registry
Simple fields
-
id(integer) -
uid(character) -
name(character) -
unit(character) -
value(FloatField) -
duration(DurationField) -
created_at(POSIXct) -
updated_at(POSIXct) -
description(character) -
ontology_id(character)
Relational fields
-
run(Run) -
targets(wetlab$PerturbationTarget) -
artifacts(Artifact) -
created_by(User) -
combination_perturbations(wetlab$CombinationPerturbation)