This document is a work in progress. See https://github.com/IDR/SubmissionWorkflow/pull/38 instead
|File||Tag||Possible Values||Ontology Accession||Notes|
|Study||Study Type||high content screen||EFO_0007550|
|high content analysis of cells||EFO_0005397|
(if HCA of cells in plates but no library of reagents)
|protein localization using 3D-SIM|
|protein localization using dSTORM|
|4D timelapse of in vivo cells|
|3D-tracking of tagged chromatin loci|
|in situ hybridization||OBI_0001686|
|Study||Screen Technology Type||gene deletion screen||EFO_0007552|
|ORF overexpression screen|
|Study||Screen Type||primary screen||EFO_0007556|
|Study||Library Type||siRNA library||EFO_0007564|
|diploid homozygous deletion library||EFO_0007562|
|haploid deletion library||EFO_0007561|
|tag protein fusion library||EFO_0007565|
|GFP protein fusion library||EFO_0007566|
|YFP protein fusion library||EFO_0007567|
|HA-Flag protein fusion library||EFO_0007568|
|Study||Cell Line or Strain||Values from EFO|
|Study||Library Experimental Conditions|
Values from EFO e.g. compound, environmental stress, media
|Study||Protocol Type||growth protocol||EFO_0003789|
|HCS library protocol||EFO_0007571|
|HCS image acquistion and feature extraction protocol||EFO_0007572|
|HCS data analysis protocol||EFO_0007573|
|image acquisition and feature extraction protocol||(not HCS)|
|data analysis protocol||(not HCS)|
|Study||Phenotype Score Type||automated|
|automated then manual||e.g. first automated to identify nuclear foci, then manual to identify subcompartment|
|Study||Processed Data Column Type||location||e.g. plate name, well name|
The siRNA, ORF, compound etc used to perturb the cells
The target gene for siRNAs, the gene which has been knocked out or mutated, or the gene targeted for creating a tagged protein.
The symbol of the targeted gene. Can have the name of the genome build in parentheses e.g Gene Symbol (Ensembl 81)
More information about the target gene.
The column containing information about any experimental variables e.g. media, environmental stress
e.g. median GPF intensity for a GFP-tagged protein
E.g. "Replicate Number", or "Has Phenotype", or "Phenotype Annotation Level"
Processed Data Column Annotation Level
For results/phenotypes at the well level.
|(for "data" or "phenotype" columns)||single replicate of reagent|
A result/phenotype determined at the level of a single replicate of a reagent (siRNA, gene knock out, tagged protein, test chemical etc).
|multiple replicates of reagent|
A result/phenotype determined at the level of multiple replicates of the same reagent (siRNA, gene knock out, tagged protein, compound etc).
A result/phenotype determined at the gene level (e.g. after taking into account the results from several siRNAs targetting the same genes)
A result determined by grouping together results based on one or more experimental condition values.
|experimental condition and gene||A result/phenotype determined from a combination of the gene and experimental condition|
|experimental condition and reagent||A result/phenotype determined from a combination of the reagent and experimental condition|
A result determined from the analysis of the phenotypes e.g. grouping of phenotypes into groups like 'shape hits'
A result determined by grouping together of the results of multiple reagents e.g. classification of clusters of phenotypes
Annotation is linked to an individual 5D image
A result/phenotype determined at the protein level (e.g. after taking into account the results from images of the same protein)
|Library||Control Type||empty well|
e.g. transfection control, or gene knock down that gives a known phenotype
e.g. scrambled siRNA, DMSO, cells but no treatment. Expected to have no effect on cells
|Phenotype||use CMPO terms where possible|