Reference for terms and their definition.
Glossary and Acronyms
- Morphological profiling (aka image-based profiling): Method to study cell phenotypes by quantifying their shape, size and intensity features.
- Phenotypic activity: Metric that indicates how well can we distinguish a perturbation from its negative controls ref.
- Phenotypic consistency: Metric that indicates how well does a perturbation match an annotated resource (e.g., gene-target known interactions).
- Phenotypic distinctiveness: Metric showing how distinctive a perturbation is relative to the other perturbations in a given experiment.
- Cosine similarity: Metric correlated to how close two vectors are. It assumes all the elements in them (usually features) have the same weight.
- Retrievability: Umbrella term for the methods that assess the quality of a set of samples in a profiling experiment: phenotypic activity, consistency and distinctiveness.
- Consensus profile: Aggregated profiles across all biological replicates (e.g., across all wells) of a given perturbation, generally it is the median of every feature.
Acronyms
- JUMP: Joint Undertaking for Morphological Profiling
- mAP: mean Average Precision
- CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats. This method was used to produce the CRISPR datasets, whence genes were knocked-out.
- ORF: Open Reading Frame. The ORF dataframe is comprised of overexpressed genes.
Other definitions
These definitions are related to cytomining libraries and may not be relevant to the more recent tools. They are kept here in case you encounter them in papers/metadata.
- poscon_diverse: Other positive controls, this is experiment-specific.
- poscon_cp: Standard positive control used for compound studies(cp stands for compound probes).
- q-value: Expected False Discovery Rate (FDR): the proportion of false positives among all positive results.