The metadata schema is shown below.
erDiagram
WELL }|--|| PLATE : ""
WELL {
string Metadata_Source "Data-generating center ID"
string Metadata_Plate "Plate ID"
string Metadata_Well "Well position"
string Metadata_JCP2022 "JUMP Perturbation ID"
}
PLATE {
string Metadata_Source "Data-generating center ID"
string Metadata_Batch "Batch ID"
string Metadata_Plate "Plate ID"
string Metadata_PlateType "One of: TARGET1, TARGET2, POSCON8, DMSO, ORF, COMPOUND, COMPOUND_EMPTY"
}
WELL }o--o| COMPOUND : ""
COMPOUND {
string Metadata_JCP2022 PK "JUMP perturbation ID"
string Metadata_InChI "International Chemical ID"
string Metadata_InChIKey "Hashed InChI"
string Metadata_SMILES "SMILES"
}
COMPOUND ||--|| COMPOUND_SOURCE : ""
COMPOUND_SOURCE {
string Metadata_JCP2022 "JUMP perturbation ID"
string Metadata_Compound_Source "Compound-nominating centerID"
}
WELL }o--o| ORF : ""
ORF {
string Metadata_JCP2022 PK "JUMP perturbation ID"
string Metadata_broad_sample "Broad perturbation ID"
string Metadata_Name "Internal perturbation ID"
string Metadata_Vector "ORF expression vector"
float Metadata_Prot_Match "% match to protein sequence"
int Metadata_Insert_Length "ORF sequence length"
string Metadata_Taxon_ID "NCBI taxonomy ID"
string Metadata_Symbol "NCBI gene symbol"
string Metadata_NCBI_Gene_ID "NCBI gene ID"
string Metadata_Transcript "NCBI reference sequence"
string Metadata_Gene_Description "NCBI gene definition"
string Metadata_pert_type "One of: trt, poscon, negcon"
}
WELL }o--o| CRISPR : ""
CRISPR {
string Metadata_JCP2022 PK "JUMP perturbation ID"
string Metadata_Symbol "NCBI gene symbol"
string Metadata_NCBI_Gene_ID "NCBI gene ID"
}
PLATE }|--|| MICROSCOPE-CONFIG : ""
MICROSCOPE-CONFIG {
string Metadata_Source "Data-generating center ID"
string Metadata_Microscope_Name "Microscope model name"
string Metadata_Widefield_vs_Confocal "One of: Widefield, Confocal"
string Metadata_Excitation_Type "One of: Laser, LED"
float Metadata_Objective_NA "Objective numerical aperture"
int Metadata_N_Brightfield_Planes_Min "Min number of brightfield planes taken"
int Metadata_N_Brightfield_Planes_Max "Max number of brightfield planes taken"
int Metadata_Distance_Between_Z_Microns "Distance between Z planes in um (only if > 1um)"
int Metadata_Sites_Per_Well "Number of sites per well"
string Metadata_Filter_Configuration "Filter configuration ID"
}
MICROSCOPE-FILTER ||--|{ MICROSCOPE-CONFIG : ""
MICROSCOPE-FILTER {
string Metadata_Filter_Configuration "Filter configuration ID"
float Metadata_Excitation_Low_DNA "Excitation wavelength min, DNA channel"
float Metadata_Excitation_Low_ER "Excitation wavelength min, ER channel"
float Metadata_Excitation_Low_RNA "Excitation wavelength min, RNA channel"
float Metadata_Excitation_Low_AGP "Excitation wavelength min, AGP channel"
float Metadata_Excitation_Low_Mito "Excitation wavelength min, Mito channel"
float Metadata_Excitation_High_DNA "Excitation wavelength max, DNA channel"
float Metadata_Excitation_High_ER "Excitation wavelength max, ER channel"
float Metadata_Excitation_High_RNA "Excitation wavelength max, RNA channel"
float Metadata_Excitation_High_AGP "Excitation wavelength max, AGP channel"
float Metadata_Excitation_High_Mito "Excitation wavelength max, Mito channel"
float Metadata_Emission_Low_DNA "Emission wavelength min, DNA channel"
float Metadata_Emission_Low_ER "Emission wavelength min, ER channel"
float Metadata_Emission_Low_RNA "Emission wavelength min, RNA channel"
float Metadata_Emission_Low_AGP "Emission wavelength min, AGP channel"
float Metadata_Emission_Low_Mito "Emission wavelength min, Mito channel"
float Metadata_Emission_High_DNA "Emission wavelength max, DNA channel"
float Metadata_Emission_High_ER "Emission wavelength max, ER channel"
float Metadata_Emission_High_RNA "Emission wavelength max, RNA channel"
float Metadata_Emission_High_AGP "Emission wavelength max, AGP channel"
float Metadata_Emission_High_Mito "Emission wavelength max, Mito channel"
string Metadata_FPBase_Config "Fluorescence spectra config URL"
}
PLATE }|--|| CELLPROFILER-VERSION : ""
CELLPROFILER-VERSION {
string Metadata_Source "Data-generating center ID"
string Metadata_CellProfiler_Version "CellProfiler Version"
}