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keys.yaml
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project:
mandatory: True
list: False
display_name: 'Project'
desc: 'This part contains general information about the project.'
value:
id:
mandatory: True
list: False
display_name: 'ID'
desc: ''
value: null
whitelist: False
input_type: short_text
project_name:
mandatory: True
list: False
display_name: 'Project Name'
desc: ''
value: null
whitelist: False
input_type: short_text
date:
mandatory: True
list: False
display_name: 'Date'
desc: 'The date has the format dd.mm.yyyy'
value: null
whitelist: False
input_type: date
owner:
mandatory: True
list: False
display_name: 'Owner'
desc: 'The owner manages the project and acts as the first point of contact for questions.'
value:
name:
mandatory: True
list: False
display_name: 'Name'
desc: "The name should be entered in the format 'Last name, First name'. For public projects enter 'public'."
value: null
whitelist: False
input_type: short_text
ldap_name:
mandatory: True
list: False
display_name: 'LDAP Name'
desc: "For public projects enter '---'."
value: null
whitelist: False
input_type: short_text
department:
mandatory: True
list: False
display_name: 'Department'
desc: "For public projects enter 'alleAbt'."
value: null
whitelist: True
input_type: select
email:
mandatory: True
list: False
display_name: 'E-Mail'
desc: "For public projects enter '---'."
value: null
whitelist: False
input_type: short_text
address:
mandatory: False
list: False
display_name: 'Address'
desc: ''
value: null
whitelist: False
input_type: short_text
telephone:
mandatory: False
list: False
display_name: 'Telephone'
desc: ''
value: null
whitelist: False
input_type: short_text
nerd:
mandatory: False
list: True
display_name: 'Nerd'
desc: 'A nerd is a person assigned to the project to perform analysis.'
value:
name:
mandatory: True
list: False
display_name: 'Name'
desc: "The name should be entered in the format 'Last name, First name'. For public projects enter 'public'."
value: null
whitelist: False
input_type: short_text
ldap_name:
mandatory: True
list: False
display_name: 'LDAP Name'
desc: "For public projects enter '---'."
value: null
whitelist: False
input_type: short_text
department:
mandatory: True
list: False
display_name: 'Department'
desc: "For public projects enter 'alleAbt'."
value: null
whitelist: True
input_type: select
email:
mandatory: True
list: False
display_name: 'E-Mail'
desc: "For public projects enter '---'."
value: null
whitelist: False
input_type: short_text
address:
mandatory: False
list: False
display_name: 'Address'
desc: ''
value: null
whitelist: False
input_type: short_text
telephone:
mandatory: False
list: False
display_name: 'Telephone'
desc: ''
value: null
whitelist: False
input_type: short_text
description:
mandatory: True
list: False
display_name: 'Description'
desc: 'Here you need to enter a detailed description of the project.'
value: null
whitelist: False
input_type: long_text
further_description:
mandatory: False
list: True
display_name: 'Further Description / Additional Info'
desc: 'Here you can insert links to files or URLs that contain additional information. This can be a presentation or a paper, for example.'
value: null
whitelist: False
input_type: short_text
graphical_abstract:
mandatory: False
list: True
display_name: 'Graphical Abstract'
desc: 'Here you can insert links to files containing a graphical abstract.'
value: null
whitelist: False
input_type: short_text
experimental_setting:
mandatory: True
list: True
display_name: 'Experimental setting'
desc: 'This part contains the investigated experimental factors and conditions as well as information about the samples. You can specify multiple experimental settings for different organisms.'
value:
organism:
mandatory: True
list: False
display_name: 'Organism'
desc: 'The organism identifier is composed of the organism name and the Taxonomy ID.'
special_case:
merge: organism_name
value:
organism_name:
mandatory: True
list: False
display_name: 'Organism Name'
desc: ''
value: null
whitelist: True
input_type: select
taxonomy_id:
mandatory: True
list: False
display_name: 'Taxonomy ID'
desc: ''
value: null
whitelist: True
input_type: select
experimental_factors:
mandatory: True
list: True
display_name: 'Experimental Factors'
desc: 'This part contains the factors that were investigated in the experiment.'
value:
factor:
mandatory: True
list: False
display_name: 'Factor'
desc: ''
value: null
whitelist: True
input_type: select
values:
mandatory: True
list: False
display_name: 'Values'
desc: ''
value: null
whitelist: True
input_type: select
conditions:
mandatory: True
list: True
display_name: 'Conditions'
desc: ''
value:
condition_name:
mandatory: True
list: False
display_name: 'Condition Name'
desc: ''
value: null
whitelist: False
input_type: short_text
biological_replicates:
mandatory: False
list: False
display_name: 'Biological Replicates'
desc: 'A biological replicate is a biological distinct sample.'
value:
count:
mandatory: False
list: False
display_name: 'Count'
desc: ''
value: null
whitelist: False
input_type: number
samples:
mandatory: False
list: True
display_name: 'Samples'
desc: ''
value:
sample_name:
mandatory: True
list: False
display_name: 'Sample Name'
desc: ''
value: null
whitelist: False
input_type: long_text
pooled:
mandatory: True
list: False
display_name: 'Pooled'
desc: ''
value: False
whitelist: False
input_type: bool
number_of_measurements:
mandatory: False
list: False
display_name: 'Number of Measurements'
desc: ''
value: 1
whitelist: False
input_type: number
genotype:
mandatory: False
list: False
display_name: 'Genotype'
desc: ''
value: null
whitelist: True
input_type: select
gender:
mandatory: False
list: False
display_name: 'Gender'
desc: ''
value: null
whitelist: True
input_type: select
life_stage:
mandatory: False
list: False
display_name: 'Life stage'
desc: ''
value: null
whitelist: True
input_type: select
age:
mandatory: False
list: False
display_name: 'Age'
desc: ''
special_case:
value_unit: time
value:
value:
mandatory: True
list: False
display_name: 'Value'
desc: ''
value: null
whitelist: False
input_type: number
unit:
mandatory: True
list: False
display_name: 'Unit'
desc: ''
value: null
whitelist: True
input_type: select
ethnicity:
mandatory: False
list: False
display_name: 'Ethnicity'
desc: ''
value: null
whitelist: True
input_type: select
tissue:
mandatory: False
list: True
display_name: 'Tissue'
desc: ''
value: null
whitelist: True
input_type: select
cell_type:
mandatory: False
list: False
display_name: 'Cell type'
desc: ''
value: null
whitelist: True
input_type: select
cellular_compartment:
mandatory: False
list: True
display_name: 'Cellular Component'
desc: ''
value: null
whitelist: True
input_type: select
gene:
mandatory: False
list: False
display_name: 'Gene'
desc: ''
special_case:
merge: gene_name
value:
gene_name:
mandatory: True
list: False
display_name: 'Gene Name'
desc: ''
value: null
whitelist: True
input_type: select
ensembl_id:
mandatory: True
list: False
display_name: 'ENSEMBL-ID'
desc: ''
value: null
whitelist: True
input_type: select
disease:
mandatory: False
list: True
display_name: 'Disease'
desc: ''
special_case:
group: 'disease_type'
value:
disease_type:
mandatory: False
list: False
display_name: 'Type'
desc: ''
value: null
whitelist: True
input_type: select
disease_status:
mandatory: True
list: False
display_name: 'Status'
desc: ''
value: null
whitelist: True
input_type: select
disease_stage:
mandatory: False
list: False
display_name: 'Stage'
desc: ''
value: null
whitelist: True
input_type: select
injury:
mandatory: False
list: True
display_name: 'Injury'
desc: ''
special_case:
group: injury_type
value:
injury_status:
mandatory: True
list: False
display_name: 'Status'
desc: ''
value: null
whitelist: True
input_type: select
injury_type:
mandatory: False
list: False
display_name: 'Type'
desc: ''
value: null
whitelist: True
input_type: select
treatment:
mandatory: False
list: True
display_name: 'Treatment'
desc: ''
special_case:
group: 'treatment_type'
value:
treatment_type:
mandatory: False
list: False
display_name: 'Type'
desc: ''
value: null
whitelist: True
input_type: select
treatment_status:
mandatory: True
list: False
display_name: 'Status'
desc: ''
value: null
whitelist: True
input_type: select
treatment_duration:
mandatory: False
list: False
display_name: 'Duration'
desc: ''
special_case:
value_unit: time
value:
value:
mandatory: True
list: False
display_name: 'Value'
desc: ''
value: null
whitelist: False
input_type: number
unit:
mandatory: False
list: False
display_name: 'Unit'
desc: ''
value: null
whitelist: True
input_type: select
time_point:
mandatory: False
list: False
display_name: 'Time Point'
desc: ''
special_case:
value_unit: time
value:
value:
mandatory: False
list: False
display_name: 'Value'
desc: ''
value: null
whitelist: False
input_type: number
unit:
mandatory: False
list: False
display_name: 'Unit'
desc: ''
value: null
whitelist: True
input_type: select
body_mass_index:
mandatory: False
list: False
display_name: 'Body-Mass-Index'
desc: ''
special_case:
value_unit: bmi
value:
value:
mandatory: False
list: False
display_name: 'Value'
desc: ''
value: null
whitelist: False
input_type: number
unit:
mandatory: False
list: False
display_name: 'Unit'
desc: ''
value: 'kg/m2'
whitelist: True
input_type: select
flow:
mandatory: False
list: False
display_name: 'Flow'
desc: ''
value: null
whitelist: True
input_type: select
knockdown:
mandatory: False
list: False
display_name: 'Knockdown'
desc: ''
value: null
whitelist: True
input_type: select
enrichment:
mandatory: False
list: False
display_name: 'Enrichment / Histone-Mark / Pull-Down'
desc: 'Enrichment for bound protein/histone mark as a result of an antibody pulldown or similar procedure (e.g. ChIPSeq, Cut&Tag, RiboTag)'
value: null
whitelist: True
input_type: select
donor_count:
mandatory: True
list: False
display_name: 'Donor Count'
desc: ''
value: 1
whitelist: False
input_type: number
technical_replicates:
mandatory: True
list: False
display_name: 'Technical Replicates'
desc: 'Technical replicates are generated by performing a test on a biological replicate multiple times.'
value:
count:
mandatory: True
list: False
display_name: 'Count'
desc: ''
value: 1
whitelist: False
input_type: number
sample_name:
mandatory: True
list: True
display_name: 'Samples'
desc: ''
value: null
whitelist: False
input_type: short_text
technical_details:
mandatory: True
list: False
display_name: 'Technical Details'
desc: 'This part contains all technical details of the experiment including an analysis part that stores additional information e.g. about runs.'
value:
technique:
mandatory: True
list: True
display_name: 'Technique'
desc: ''
value: null
whitelist: True
input_type: select
analysis:
mandatory: False
list: False
display_name: 'Analysis'
desc: ''
value:
sample_preparation:
mandatory: False
list: True
display_name: 'Sample preparation'
desc: 'Here you can insert links to files or URLs that contain information regarding the sample preparation.'
value: null
whitelist: False
input_type: short_text
further_description:
mandatory: False
list: True
display_name: 'Further description'
desc: 'Here you can insert links to files or URLs that contain additional information. This can be a presentation or a paper, for example.'
value: null
whitelist: False
input_type: short_text
runs:
mandatory: False
list: True
display_name: 'Runs'
desc: ''
value:
date:
mandatory: True
list: False
display_name: 'Date'
desc: 'The date has the format dd.mm.yyyy'
value: null
whitelist: False
input_type: date
reference_genome:
mandatory: False
list: False
display_name: 'Reference Genome'
desc: ''
value: null
whitelist: True
input_type: select
parameters:
mandatory: False
list: True
display_name: 'Parameters'
desc: 'Here you can insert links to files that contain the parameters used for the run.'
value: null
whitelist: False
input_type: short_text
output:
mandatory: False
list: True
display_name: 'Output'
desc: 'Here you can insert links to the output files of the run.'
value: null
whitelist: False
input_type: short_text