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This document is a work in progress. See https://github.com/IDR/SubmissionWorkflow/pull/38 instead
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FileTagPossible ValuesOntology AccessionNotes
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StudyStudy Typehigh content screenEFO_0007550
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high content analysis of cellsEFO_0005397
(if HCA of cells in plates but no library of reagents)
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histology
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protein localization using 3D-SIM
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protein localization using dSTORM
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4D timelapse of in vivo cells
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3D-tracking of tagged chromatin loci
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in situ hybridizationOBI_0001686
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StudyScreen Technology Typegene deletion screenEFO_0007552
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RNAi screenEFO_0007551
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protein screenEFO_0005398
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compound screenEFO_0007553
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antibody screen
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ORF overexpression screen
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StudyScreen Typeprimary screenEFO_0007556
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secondary screenEFO_0007557
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validation screenEFO_0007558
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StudyLibrary TypesiRNA libraryEFO_0007564
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diploid homozygous deletion libraryEFO_0007562
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haploid deletion libraryEFO_0007561
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compound libraryEFO_0007569
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tag protein fusion libraryEFO_0007565
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GFP protein fusion libraryEFO_0007566
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YFP protein fusion libraryEFO_0007567
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HA­-Flag protein fusion libraryEFO_0007568
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ORF library
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antibody library
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none
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StudyCell Line or StrainValues from EFO
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StudyLibrary Experimental Conditions
Values from EFO e.g. compound, environmental stress, media
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StudyProtocol Typegrowth protocolEFO_0003789
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treatment protocolEFO_0003969
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HCS library protocolEFO_0007571
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HCS image acquistion and feature extraction protocolEFO_0007572
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HCS data analysis protocolEFO_0007573
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image acquisition and feature extraction protocol(not HCS)
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data analysis protocol(not HCS)
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StudyPhenotype Score Typeautomated
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manual
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automated then manuale.g. first automated to identify nuclear foci, then manual to identify subcompartment
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StudyProcessed Data Column Typelocatione.g. plate name, well name
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quality control
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reagent identifier
The siRNA, ORF, compound etc used to perturb the cells
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reagent description
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gene identifier
The target gene for siRNAs, the gene which has been knocked out or mutated, or the gene targeted for creating a tagged protein.
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gene symbol
The symbol of the targeted gene. Can have the name of the genome build in parentheses e.g Gene Symbol (Ensembl 81)
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gene description
More information about the target gene.
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experimental condition
The column containing information about any experimental variables e.g. media, environmental stress
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data
e.g. median GPF intensity for a GFP-tagged protein
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phenotypePhenotypes observed.
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other
E.g. "Replicate Number", or "Has Phenotype", or "Phenotype Annotation Level"
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Study
Processed Data Column Annotation Level
well
For results/phenotypes at the well level.
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(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).
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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).
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gene
A result/phenotype determined at the gene level (e.g. after taking into account the results from several siRNAs targetting the same genes)
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experimental condition
A result determined by grouping together results based on one or more experimental condition values.
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experimental condition and geneA result/phenotype determined from a combination of the gene and experimental condition
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experimental condition and reagentA result/phenotype determined from a combination of the reagent and experimental condition
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phenotype
A result determined from the analysis of the phenotypes e.g. grouping of phenotypes into groups like 'shape hits'
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multiple reagents
A result determined by grouping together of the results of multiple reagents e.g. classification of clusters of phenotypes
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image
Annotation is linked to an individual 5D image
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protein
A result/phenotype determined at the protein level (e.g. after taking into account the results from images of the same protein)
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LibraryControl Typeempty well
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positive control
e.g. transfection control, or gene knock down that gives a known phenotype
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negative control
e.g. scrambled siRNA, DMSO, cells but no treatment. Expected to have no effect on cells
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technical control
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unknown control
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Processed Data
Phenotypeuse CMPO terms where possible
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